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@article{DBLP:journals/bib/Amisaki24,
author = {Takashi Amisaki},
title = {Multilevel superposition for deciphering the conformational variability
of protein ensembles},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae137},
doi = {10.1093/BIB/BBAE137},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Amisaki24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ArulrajWIZFP24,
author = {Theinmozhi Arulraj and
Hanwen Wang and
Alberto Ippolito and
Shuming Zhang and
Elana J. Fertig and
Aleksander S. Popel},
title = {Leveraging multi-omics data to empower quantitative systems pharmacology
in immuno-oncology},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae131},
doi = {10.1093/BIB/BBAE131},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ArulrajWIZFP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BadaczewskaDawidWKK24,
author = {Aleksandra E. Badaczewska{-}Dawid and
Karol Wroblewski and
Mateusz Kurcinski and
Sebastian Kmiecik},
title = {Structure prediction of linear and cyclic peptides using CABS-flex},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae003},
doi = {10.1093/BIB/BBAE003},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BadaczewskaDawidWKK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BarbitoffULNGP24,
author = {Yury A Barbitoff and
Mikhail O. Ushakov and
Tatyana E. Lazareva and
Yulia A Nasykhova and
Andrey S. Glotov and
Alexander V. Predeus},
title = {Bioinformatics of germline variant discovery for rare disease diagnostics:
current approaches and remaining challenges},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad508},
doi = {10.1093/BIB/BBAD508},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BarbitoffULNGP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BrooksLMSNNSCG24,
author = {Thomas G. Brooks and
Nicholas F. Lahens and
Antonijo Mrcela and
Dimitra Sarantopoulou and
Soumyashant Nayak and
Amruta Naik and
Shaon Sengupta and
Peter S. Choi and
Gregory R. Grant},
title = {{BEERS2:} RNA-Seq simulation through high fidelity \emph{in silico}
modeling},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae164},
doi = {10.1093/BIB/BBAE164},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BrooksLMSNNSCG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BrouardMV24,
author = {C{\'{e}}line Brouard and
Rapha{\"{e}}l Mourad and
Nathalie Vialaneix},
title = {Should we really use graph neural networks for transcriptomic prediction?},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae027},
doi = {10.1093/BIB/BBAE027},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BrouardMV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaiLLHWBZ24,
author = {Yantong Cai and
Jia Lv and
Rui Li and
Xiaowen Huang and
Shi Wang and
Zhenmin Bao and
Qifan Zeng},
title = {Deqformer: high-definition and scalable deep learning probe design
method},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae007},
doi = {10.1093/BIB/BBAE007},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CaiLLHWBZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenAZZ24,
author = {Zhaojia Chen and
Noor ul Ain and
Qian Zhao and
Xingtan Zhang},
title = {From tradition to innovation: conventional and deep learning frameworks
in genome annotation},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae138},
doi = {10.1093/BIB/BBAE138},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenAZZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenH24,
author = {Xing Chen and
Li Huang},
title = {Computational model for drug research},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae158},
doi = {10.1093/BIB/BBAE158},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenSSTD24,
author = {Mingshuai Chen and
Mingai Sun and
Xi Su and
Prayag Tiwari and
Yijie Ding},
title = {Fuzzy kernel evidence Random Forest for identifying pseudouridine
sites},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae169},
doi = {10.1093/BIB/BBAE169},
timestamp = {Sun, 28 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenSSTD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZDWRY24,
author = {Ken Chen and
Yue Zhou and
Maolin Ding and
Yu Wang and
Zhixiang Ren and
Yuedong Yang},
title = {Self-supervised learning on millions of primary {RNA} sequences from
72 vertebrates improves sequence-based {RNA} splicing prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae163},
doi = {10.1093/BIB/BBAE163},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenZDWRY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZLQZ24,
author = {Qiuhao Chen and
Liyuan Zhang and
Yaojia Liu and
Zhonghao Qin and
Tianyi Zhao},
title = {PUTransGCN: identification of piRNA-disease associations based on
attention encoding graph convolutional network and positive unlabelled
learning},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae144},
doi = {10.1093/BIB/BBAE144},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenZLQZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChuwdhuryGCLKLD24,
author = {Gulam Sarwar Chuwdhury and
Yunshan Guo and
Chi{-}Leung Chiang and
Ka{-}On Lam and
Ngar{-}Woon Kam and
Zhonghua Liu and
Wei Dai},
title = {ImmuneMirror: {A} machine learning-based integrative pipeline and
web server for neoantigen prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae024},
doi = {10.1093/BIB/BBAE024},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChuwdhuryGCLKLD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Cinquin24,
author = {Olivier Cinquin},
title = {ChIP-GPT: a managed large language model for robust data extraction
from biomedical database records},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad535},
doi = {10.1093/BIB/BBAD535},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/Cinquin24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingXCLFSJ24,
author = {Xiao{-}Hong Ding and
Yi Xiao and
Fenfang Chen and
Cheng{-}Lin Liu and
Tong Fu and
Zhi{-}Ming Shao and
Yi{-}Zhou Jiang},
title = {The {HLA-I} landscape confers prognosis and antitumor immunity in
breast cancer},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae151},
doi = {10.1093/BIB/BBAE151},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingXCLFSJ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FangFLLYYZLSGQ24,
author = {Minghao Fang and
Jingwen Fang and
Songwen Luo and
Ke Liu and
Qiaoni Yu and
Jiaxuan Yang and
Youyang Zhou and
Zongkai Li and
Ruoming Sun and
Chuang Guo and
Kun Qu},
title = {eccDNA-pipe: an integrated pipeline for identification, analysis and
visualization of extrachromosomal circular {DNA} from high-throughput
sequencing data},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae034},
doi = {10.1093/BIB/BBAE034},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FangFLLYYZLSGQ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoSXCDZW24,
author = {Zhen Gao and
Yansen Su and
Junfeng Xia and
Rui{-}Fen Cao and
Yun Ding and
Chun{-}Hou Zheng and
Pi{-}Jing Wei},
title = {DeepFGRN: inference of gene regulatory network with regulation type
based on directed graph embedding},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae143},
doi = {10.1093/BIB/BBAE143},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaoSXCDZW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GeraultGCND24,
author = {Marc{-}Antoine Gerault and
Samuel Granjeaud and
Luc Camoin and
P{\"{a}}r Nordlund and
Lingyun Dai},
title = {{IMPRINTS.CETSA} and IMPRINTS.CETSA.app: an {R} package and a Shiny
application for the analysis and interpretation of {IMPRINTS-CETSA}
data},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae128},
doi = {10.1093/BIB/BBAE128},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GeraultGCND24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuWXHJLGLSY24,
author = {Shuang Gu and
Chaoliang Wen and
Zhen Xiao and
Qiang Huang and
Zheyi Jiang and
Honghong Liu and
Jia Gao and
Junying Li and
Congjiao Sun and
Ning Yang},
title = {MyoV: a deep learning-based tool for the automated quantification
of muscle fibers},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad528},
doi = {10.1093/BIB/BBAD528},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuWXHJLGLSY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoC24,
author = {Xinyu Guo and
Liang Chen},
title = {From {G1} to {M:} a comparative study of methods for identifying cell
cycle phases},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad517},
doi = {10.1093/BIB/BBAD517},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuoC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoHCYWHHC24,
author = {Yue Guo and
Haitao Hu and
Wenbo Chen and
Hao Yin and
Jian Wu and
Chang{-}Yu Hsieh and
Qiaojun He and
Ji Cao},
title = {SynergyX: a multi-modality mutual attention network for interpretable
drug synergy prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae015},
doi = {10.1093/BIB/BBAE015},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuoHCYWHHC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoWWZH24,
author = {Zhen{-}Hao Guo and
Yan{-}Bin Wang and
Siguo Wang and
Qinhu Zhang and
De{-}Shuang Huang},
title = {scCorrector: a robust method for integrating multi-study single-cell
data},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad525},
doi = {10.1093/BIB/BBAD525},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuoWWZH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoWYYHZL24,
author = {Lu{-}Xiang Guo and
Lei Wang and
Zhu{-}Hong You and
Chang{-}Qing Yu and
Meng{-}Lei Hu and
Bo{-}Wei Zhao and
Yang Li},
title = {Likelihood-based feature representation learning combined with neighborhood
information for predicting circRNA-miRNA associations},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae020},
doi = {10.1093/BIB/BBAE020},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuoWYYHZL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanLKSJLBJKL24,
author = {Seokjin Han and
Ji Eun Lee and
Seolhee Kang and
Minyoung So and
Hee Jin and
Jang Ho Lee and
Sunghyeob Baek and
Hyungjin Jun and
Tae Yong Kim and
Yun{-}Sil Lee},
title = {Standigm ASK{\texttrademark}: knowledge graph and artificial intelligence
platform applied to target discovery in idiopathic pulmonary fibrosis},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae035},
doi = {10.1093/BIB/BBAE035},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HanLKSJLBJKL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuXYLZS24,
author = {Yaofeng Hu and
Kai Xiao and
Hengyu Yang and
Xiaoping Liu and
Chuanchao Zhang and
Qianqian Shi},
title = {Spatially contrastive variational autoencoder for deciphering tissue
heterogeneity from spatially resolved transcriptomics},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae016},
doi = {10.1093/BIB/BBAE016},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuXYLZS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangFWZLWDS24,
author = {Fengjuan Huang and
Xinjie Fan and
Ying Wang and
Yu Zou and
Jiangfang Lian and
Chuang Wang and
Feng Ding and
Yunxiang Sun},
title = {Computational insights into the cross-talk between medin and A\emph{{\(\beta\)}}:
implications for age-related vascular risk factors in Alzheimer's
disease},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad526},
doi = {10.1093/BIB/BBAD526},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangFWZLWDS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangHLYTH24,
author = {Ming{-}Siang Huang and
Jen{-}Chieh Han and
Pei{-}Yen Lin and
Yu{-}Ting You and
Richard Tzong{-}Han Tsai and
Wen{-}Lian Hsu},
title = {Surveying biomedical relation extraction: a critical examination of
current datasets and the proposal of a new resource},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae132},
doi = {10.1093/BIB/BBAE132},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangHLYTH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangZMLWDFAD24,
author = {Jinze Huang and
Yang Zhao and
Bo Meng and
Ao Lu and
Yaoguang Wei and
Lianhua Dong and
Xiang Fang and
Dong An and
Xinhua Dai},
title = {{SEAOP:} a statistical ensemble approach for outlier detection in
quantitative proteomics data},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae129},
doi = {10.1093/BIB/BBAE129},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangZMLWDFAD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuynhC24,
author = {Tram Huynh and
Zixuan Cang},
title = {Topological and geometric analysis of cell states in single-cell transcriptomic
data},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae176},
doi = {10.1093/BIB/BBAE176},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuynhC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiZXXP24,
author = {Boya Ji and
Haitao Zou and
Liwen Xu and
Xiaolan Xie and
Shaoliang Peng},
title = {{MUSCLE:} multi-view and multi-scale attentional feature fusion for
microRNA-disease associations prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae167},
doi = {10.1093/BIB/BBAE167},
timestamp = {Sun, 28 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiZXXP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangPLLZL24,
author = {Jici Jiang and
Hongdi Pei and
Jiayu Li and
Mingxin Li and
Quan Zou and
Zhibin Lv},
title = {FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences
based on feature engineering and optimization},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae037},
doi = {10.1093/BIB/BBAE037},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JiangPLLZL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JoshiW24,
author = {Kandarp Joshi and
Dan O. Wang},
title = {epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic
regulation},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad521},
doi = {10.1093/BIB/BBAD521},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JoshiW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KangZG24,
author = {Yue Kang and
Hongyu Zhang and
Jinting Guan},
title = {scINRB: single-cell gene expression imputation with network regularization
and bulk RNA-seq data},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae148},
doi = {10.1093/BIB/BBAE148},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KangZG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KatchborianNetoABNFOBMLDSLC24,
author = {Albert Katchborian{-}Neto and
Matheus F. Alves and
Paula C. P. Bueno and
Karen de Jesus Nic{\'{a}}cio and
Miller S. Ferreira and
Tiago B. Oliveira and
Henrique Barbosa and
Michael Murgu and
Ana C. C. de Paula Ladvocat and
Danielle F. Dias and
Marisi G. Soares and
Jo{\~{a}}o Henrique Ghilardi Lago and
Daniela A Chagas{-}Paula},
title = {Integrative open workflow for confident annotation and molecular networking
of metabolomics {MSE/DIA} data},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae013},
doi = {10.1093/BIB/BBAE013},
timestamp = {Thu, 02 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KatchborianNetoABNFOBMLDSLC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KrishnanRG24,
author = {Sowmya Ramaswamy Krishnan and
Arijit Roy and
M. Michael Gromiha},
title = {Reliable method for predicting the binding affinity of RNA-small molecule
interactions using machine learning},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae002},
doi = {10.1093/BIB/BBAE002},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KrishnanRG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeiHWSWDZWG24,
author = {Lixin Lei and
Kaitai Han and
Zijun Wang and
Chaojing Shi and
Zhenghui Wang and
Ruoyan Dai and
Zhiwei Zhang and
Mengqiu Wang and
Qianjin Guo},
title = {Attention-guided variational graph autoencoders reveal heterogeneity
in spatial transcriptomics},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae173},
doi = {10.1093/BIB/BBAE173},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LeiHWSWDZWG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiJLLQY24,
author = {Pengyong Li and
Zhengxiang Jiang and
Tianxiao Liu and
Xinyu Liu and
Hui Qiao and
Xiaojun Yao},
title = {Improving drug response prediction via integrating gene relationships
with deep learning},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae153},
doi = {10.1093/BIB/BBAE153},
timestamp = {Sun, 28 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiJLLQY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiLSYSY24,
author = {Shuo Li and
Yan Liu and
Long{-}Chen Shen and
He Yan and
Jiangning Song and
Dong{-}Jun Yu},
title = {{GMFGRN:} a matrix factorization and graph neural network approach
for gene regulatory network inference},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad529},
doi = {10.1093/BIB/BBAD529},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiLSYSY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiLTW24,
author = {Kongming Li and
Jiahao Li and
Yuhao Tao and
Fei Wang},
title = {stDiff: a diffusion model for imputing spatial transcriptomics through
single-cell transcriptomics},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae171},
doi = {10.1093/BIB/BBAE171},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiLTW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuCGZYRZYHL24,
author = {Huanhuan Liu and
Qinwei Chen and
Jintao Guo and
Ying Zhou and
Zhiyu You and
Jun Ren and
Yuanyuan Zeng and
Jing Yang and
Jialiang Huang and
Qiyuan Li},
title = {Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional
programs in 36 human tissues},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae109},
doi = {10.1093/BIB/BBAE109},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuCGZYRZYHL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuLZ24,
author = {Jiaxuan Liu and
Yonggang Lu and
Li Zhu},
title = {A kinetic model for solving a combination optimization problem in
\emph{ab-initio} Cryo-EM 3D reconstruction},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad473},
doi = {10.1093/BIB/BBAD473},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuLZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuZ24,
author = {Haoquan Liu and
Yunjie Zhao},
title = {Integrated modeling of protein and {RNA}},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae139},
doi = {10.1093/BIB/BBAE139},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LlopPeiroPG24,
author = {Ariadna Llop{-}Peir{\'{o}} and
Gerard Pujadas and
Santiago Garcia{-}Vallv{\'{e}}},
title = {Challenges in distinguishing functional proteins from polyproteins
in databases: implications for drug discovery},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae012},
doi = {10.1093/BIB/BBAE012},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LlopPeiroPG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoWSLCZ24,
author = {Zeyu Luo and
Rui Wang and
Yawen Sun and
Junhao Liu and
Herman Z. Q. Chen and
Yu{-}Juan Zhang},
title = {Interpretable feature extraction and dimensionality reduction in {ESM2}
for protein localization prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad534},
doi = {10.1093/BIB/BBAD534},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuoWSLCZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaKY24,
author = {Guoxuan Ma and
Jian Kang and
Tianwei Yu},
title = {Bayesian functional analysis for untargeted metabolomics data with
matching uncertainty and small sample sizes},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae141},
doi = {10.1093/BIB/BBAE141},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaKY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaWCXJDWMCLSBSXRJD24,
author = {Wenyuan Ma and
Hui Wu and
Yiran Chen and
Hongxia Xu and
Junjie Jiang and
Bang Du and
Mingyu Wan and
Xiaolu Ma and
Xiaoyu Chen and
Lili Lin and
Xinhui Su and
Xuanwen Bao and
Yifei Shen and
Nong Xu and
Jian Ruan and
Haiping Jiang and
Yongfeng Ding},
title = {New techniques to identify the tissue of origin for cancer of unknown
primary in the era of precision medicine: progress and challenges},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae028},
doi = {10.1093/BIB/BBAE028},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MaWCXJDWMCLSBSXRJD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaestriFMTUPLBNP24,
author = {Simone Maestri and
Mattia Furlan and
Logan Mulroney and
Lucia Coscujuela Tarrero and
Camilla Ugolini and
Fabio Dalla Pozza and
Tommaso Leonardi and
Ewan Birney and
Francesco Nicassio and
Mattia Pelizzola},
title = {Benchmarking of computational methods for m6A profiling with Nanopore
direct {RNA} sequencing},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae001},
doi = {10.1093/BIB/BBAE001},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MaestriFMTUPLBNP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MelloTBV24,
author = {Fabio N. de Mello and
Ana C. Tahira and
Maria Gabriela Berzoti{-}Coelho and
Sergio Verjovski{-}Almeida},
title = {The CUT{\&}RUN greenlist: genomic regions of consistent noise
are effective normalizing factors for quantitative epigenome mapping},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad538},
doi = {10.1093/BIB/BBAD538},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MelloTBV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MengLSLWZPWJ24,
author = {Jing Meng and
Jingze Liu and
Wenkai Song and
Honglei Li and
Jiangyuan Wang and
Le Zhang and
Yousong Peng and
Aiping Wu and
Taijiao Jiang},
title = {{PREDAC-CNN:} predicting antigenic clusters of seasonal influenza
{A} viruses with convolutional neural network},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae033},
doi = {10.1093/BIB/BBAE033},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MengLSLWZPWJ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MengWMSLHLZ24,
author = {Qiuchen Meng and
Lei Wei and
Kun Ma and
Ming Shi and
Xinyi Lin and
Joshua W. K. Ho and
Yinqing Li and
Xuegong Zhang},
title = {scDecouple: decoupling cellular response from infected proportion
bias in scCRISPR-seq},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae011},
doi = {10.1093/BIB/BBAE011},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MengWMSLHLZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MiaoSMLWY24,
author = {Yan Miao and
Zhenyuan Sun and
Chenjing Ma and
Chen Lin and
Guohua Wang and
Chunxue Yang},
title = {VirGrapher: a graph-based viral identifier for long sequences from
metagenomes},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae036},
doi = {10.1093/BIB/BBAE036},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MiaoSMLWY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MuLZZIWWFC24,
author = {Junxi Mu and
Zhengxin Li and
Bo Zhang and
Qi Zhang and
Jamshed Iqbal and
Abdul Wadood and
Ting Wei and
Yan Feng and
Hai{-}Feng Chen},
title = {Graphormer supervised \emph{de novo} protein design method and function
validation},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae135},
doi = {10.1093/BIB/BBAE135},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MuLZZIWWFC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NiuWCZX24,
author = {Mengting Niu and
Chunyu Wang and
Yaojia Chen and
Quan Zou and
Lei Xu},
title = {Identification, characterization and expression analysis of circRNA
encoded by SARS-CoV-1 and SARS-CoV-2},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad537},
doi = {10.1093/BIB/BBAD537},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/NiuWCZX24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NourbakhshDSTP24,
author = {Mona Nourbakhsh and
Kristine Degn and
Astrid Saksager and
Matteo Tiberti and
Elena Papaleo},
title = {Prediction of cancer driver genes and mutations: the potential of
integrative computational frameworks},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad519},
doi = {10.1093/BIB/BBAD519},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/NourbakhshDSTP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/OlaverriMendizabalVBRP24,
author = {Danel Olaverri{-}Mendizabal and
Luis Vitores Valcarcel and
Naroa Barrena and
Carlos J. Rodr{\'{\i}}guez and
Francisco J. Planes},
title = {Review and meta-analysis of the genetic Minimal Cut Set approach for
gene essentiality prediction in cancer metabolism},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae115},
doi = {10.1093/BIB/BBAE115},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/OlaverriMendizabalVBRP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ParkMH24,
author = {Youngjune Park and
Nils P. Muttray and
Anne{-}Christin Hauschild},
title = {Species-agnostic transfer learning for cross-species transcriptomics
data integration without gene orthology},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae004},
doi = {10.1093/BIB/BBAE004},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ParkMH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PathakK24,
author = {Rajesh Kumar Pathak and
Jun{-}Mo Kim},
title = {Veterinary systems biology for bridging the phenotype-genotype gap
via computational modeling for disease epidemiology and animal welfare},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae025},
doi = {10.1093/BIB/BBAE025},
timestamp = {Wed, 01 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PathakK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PengCTSJ24,
author = {Chen Peng and
Qiong Chen and
Shangjin Tan and
Xiaotao Shen and
Chao Jiang},
title = {Generalized reporter score-based enrichment analysis for omics data},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae116},
doi = {10.1093/BIB/BBAE116},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PengCTSJ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PengLJW24,
author = {Zhao Peng and
Jiaqiang Li and
Xingpeng Jiang and
Cuihong Wan},
title = {sOCP: a framework predicting smORF coding potential based on {TIS}
and in-frame features and effectively applied in the human genome},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae147},
doi = {10.1093/BIB/BBAE147},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PengLJW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/QiuNDDWLZXTWQ24,
author = {Jingxuan Qiu and
Wanchun Nie and
Hao Ding and
Jia Dai and
Yiwen Wei and
Dezhi Li and
Yuxi Zhang and
Junting Xie and
Xinxin Tian and
Nannan Wu and
Tianyi Qiu},
title = {{PB-LKS:} a python package for predicting phage-bacteria interaction
through local K-mer strategy},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae010},
doi = {10.1093/BIB/BBAE010},
timestamp = {Wed, 20 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/QiuNDDWLZXTWQ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SilSKMS24,
author = {Priyotosh Sil and
Ajay Subbaroyan and
Saumitra Kulkarni and
Olivier C. Martin and
Areejit Samal},
title = {Biologically meaningful regulatory logic enhances the convergence
rate in Boolean networks and bushiness of their state transition graph},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae150},
doi = {10.1093/BIB/BBAE150},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SilSKMS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SunCZZLZZG24,
author = {Min Sun and
Jing Chen and
Chang Zhao and
Lihua Zhang and
Maili Liu and
Yukui Zhang and
Qun Zhao and
Zhou Gong},
title = {Enhancing protein dynamics analysis with hydrophilic polyethylene
glycol cross-linkers},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae026},
doi = {10.1093/BIB/BBAE026},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/SunCZZLZZG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianHXTS24,
author = {Zhen Tian and
Chenguang Han and
Lewen Xu and
Zhixia Teng and
Wei Song},
title = {{MGCNSS:} miRNA-disease association prediction with multi-layer graph
convolution and distance-based negative sample selection strategy},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae168},
doi = {10.1093/BIB/BBAE168},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TianHXTS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/VasighizakerHZR24,
author = {Akram Vasighizaker and
Sheena Hora and
Raymond Zeng and
Luis Rueda},
title = {{SEGCECO:} Subgraph Embedding of Gene expression matrix for prediction
of CEll-cell COmmunication},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae160},
doi = {10.1093/BIB/BBAE160},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/VasighizakerHZR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/VisonaBDS24,
author = {Giovanni Vison{\`{a}} and
Emmanuelle Bouzigon and
Florence Demenais and
Gabriele Beate Schweikert},
title = {Network propagation for {GWAS} analysis: a practical guide to leveraging
molecular networks for disease gene discovery},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae014},
doi = {10.1093/BIB/BBAE014},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/VisonaBDS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/VuralOzdenizCAYODK24,
author = {Merve Vural{-}Ozdeniz and
Kubra Calisir and
Rana Acar and
Aysenur Yavuz and
Mustafa M. Ozgur and
Ertugrul Dalgic and
Ozlen Konu},
title = {CAP-RNAseq: an integrated pipeline for functional annotation and prioritization
of co-expression clusters},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad536},
doi = {10.1093/BIB/BBAD536},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/VuralOzdenizCAYODK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangL24,
author = {Seunghyun Wang and
Doheon Lee},
title = {Community cohesion looseness in gene networks reveals individualized
drug targets and resistance},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae175},
doi = {10.1093/BIB/BBAE175},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLLZYECLT24,
author = {Lijuan Wang and
Ying Lu and
Doudou Li and
Yajing Zhou and
Lili Yu and
Ines Mesa Eguiagaray and
Harry Campbell and
Xue Li and
Evropi Theodoratou},
title = {The landscape of the methodology in drug repurposing using human genomic
data: a systematic review},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad527},
doi = {10.1093/BIB/BBAD527},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangLLZYECLT24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLWLL24,
author = {Meng Wang and
Chuqi Lei and
Jianxin Wang and
Yaohang Li and
Min Li},
title = {TripHLApan: predicting {HLA} molecules binding peptides based on triple
coding matrix and transfer learning},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae154},
doi = {10.1093/BIB/BBAE154},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangLWLL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLZWZ24,
author = {Hui Wang and
Dong Liu and
Kailong Zhao and
Yajun Wang and
Guijun Zhang},
title = {SPDesign: protein sequence designer based on structural sequence profile
using ultrafast shape recognition},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae146},
doi = {10.1093/BIB/BBAE146},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangLZWZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangOCR24,
author = {Conghao Wang and
Hiok Hian Ong and
Shunsuke Chiba and
Jagath C. Rajapakse},
title = {{GLDM:} hit molecule generation with constrained graph latent diffusion
model},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae142},
doi = {10.1093/BIB/BBAE142},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangOCR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangWLGWMZL24,
author = {Zechen Wang and
Sheng Wang and
Yangyang Li and
Jingjing Guo and
Yanjie Wei and
Yuguang Mu and
Liangzhen Zheng and
Weifeng Li},
title = {A new paradigm for applying deep learning to protein-ligand interaction
prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae145},
doi = {10.1093/BIB/BBAE145},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangWLGWMZL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangYJGWXSXZZ24,
author = {Xinyan Wang and
Kuo Yang and
Ting Jia and
Fanghui Gu and
Chongyu Wang and
Kuan Xu and
Zixin Shu and
Jianan Xia and
Qiang Zhu and
Xuezhong Zhou},
title = {KDGene: knowledge graph completion for disease gene prediction using
interactional tensor decomposition},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae161},
doi = {10.1093/BIB/BBAE161},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangYJGWXSXZZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZWLZCWSW24,
author = {Shenjie Wang and
Xiaoyan Zhu and
Xuwen Wang and
Yuqian Liu and
Minchao Zhao and
Zhili Chang and
Xiaonan Wang and
Yang Shao and
Jiayin Wang},
title = {TMBstable: a variant caller controls performance variation across
heterogeneous sequencing samples},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae159},
doi = {10.1093/BIB/BBAE159},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangZWLZCWSW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WeiIZX24,
author = {Qingyue Wei and
Md Tauhidul Islam and
Yuyin Zhou and
Lei Xing},
title = {Self-supervised deep learning of gene-gene interactions for improved
gene expression recovery},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae031},
doi = {10.1093/BIB/BBAE031},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WeiIZX24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WeiZZXXWXYF24,
author = {Zhenyu Wei and
Chengkui Zhao and
Min Zhang and
Jiayu Xu and
Nan Xu and
Shiwei Wu and
Xiaohui Xin and
Lei Yu and
Weixing Feng},
title = {Meta-DHGNN: method for CRS-related cytokines analysis in {CAR-T} therapy
based on meta-learning directed heterogeneous graph neural network},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae104},
doi = {10.1093/BIB/BBAE104},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WeiZZXXWXYF24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WrightWMCRSPJGRYSM24,
author = {Adam Wright and
Mark D. Wilkinson and
Christopher J. Mungall and
Scott Cain and
Stephen Richards and
Paul W. Sternberg and
Ellen Provin and
Jonathan L. Jacobs and
Scott Geib and
Daniela Raciti and
Karen Yook and
Lincoln Stein and
David C. Molik},
title = {{FAIR} Header Reference genome: a TRUSTworthy standard},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae122},
doi = {10.1093/BIB/BBAE122},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WrightWMCRSPJGRYSM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X24,
title = {Correction to: Introducing {\(\pi\)}-HelixNovo for practical large-scale
de novo peptide sequencing},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae134},
doi = {10.1093/BIB/BBAE134},
timestamp = {Sun, 28 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X24a,
title = {Correction to: Adjustment of scRNA-seq data to improve cell-type decomposition
of spatial transcriptomics},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae155},
doi = {10.1093/BIB/BBAE155},
timestamp = {Sun, 28 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X24a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X24b,
title = {Correction to: Inflated false discovery rate due to volcano plots:
problem and solutions},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae149},
doi = {10.1093/BIB/BBAE149},
timestamp = {Sun, 28 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X24b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X24c,
title = {Correction to: DeepFormer: a hybrid network based on convolutional
neural network and flow-attention mechanism for identifying the function
of {DNA} sequences},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae181},
doi = {10.1093/BIB/BBAE181},
timestamp = {Sun, 28 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X24c.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuCH24,
author = {Sheng{-}Yong Xu and
Shanshan Cai and
Zhi{-}Qiang Han},
title = {Evaluating the efficacy of {MEANGS} for mitochondrial genome assembly
of cartilaginous and ray-finned fish species},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae041},
doi = {10.1093/BIB/BBAE041},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XuCH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuLHCLL24,
author = {Zhanyu Xu and
Haibo Liao and
Liuliu Huang and
Qingfeng Chen and
Wei Lan and
Shikang Li},
title = {{IBPGNET:} lung adenocarcinoma recurrence prediction based on neural
network interpretability},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae080},
doi = {10.1093/BIB/BBAE080},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XuLHCLL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuZGJZP24,
author = {Wang Xu and
Houfang Zhang and
Wenhan Guo and
Lijun Jiang and
Yunjie Zhao and
Yunhui Peng},
title = {Deciphering principles of nucleosome interactions and impact of cancer-associated
mutations from comprehensive interaction network analysis},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad532},
doi = {10.1093/BIB/BBAD532},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XuZGJZP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangLSLXHXHLHWC24,
author = {Tingpeng Yang and
Tianze Ling and
Boyan Sun and
Zhendong Liang and
Fan Xu and
Xiansong Huang and
Linhai Xie and
Yonghong He and
Leyuan Li and
Fuchu He and
Yu Wang and
Cheng Chang},
title = {Introducing {\(\pi\)}-HelixNovo for practical large-scale de novo
peptide sequencing},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae021},
doi = {10.1093/BIB/BBAE021},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangLSLXHXHLHWC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangWLJWZZD24,
author = {Xiaodi Yang and
Stefan Wuchty and
Zeyin Liang and
Li Ji and
Bingjie Wang and
Jialin Zhu and
Ziding Zhang and
Yujun Dong},
title = {Multi-modal features-based human-herpesvirus protein-protein interaction
prediction by using LightGBM},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae005},
doi = {10.1093/BIB/BBAE005},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangWLJWZZD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YinWZ24,
author = {Wang Yin and
You Wan and
Yuan Zhou},
title = {SpatialcoGCN: deconvolution and spatial information-aware simulation
of spatial transcriptomics data via deep graph co-embedding},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae130},
doi = {10.1093/BIB/BBAE130},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YinWZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuZCZLLLZMS24,
author = {Chunjiang Yu and
Hui Zong and
Yalan Chen and
Yibin Zhou and
Xingyun Liu and
Yuxin Lin and
Jiakun Li and
Xiaonan Zheng and
Hua Min and
Bairong Shen},
title = {{PCAO2:} an ontology for integration of prostate cancer associated
genotypic, phenotypic and lifestyle data},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae136},
doi = {10.1093/BIB/BBAE136},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YuZCZLLLZMS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuanWWGD24,
author = {Musu Yuan and
Hui Wan and
Zihao Wang and
Qirui Guo and
Minghua Deng},
title = {{SPANN:} annotating single-cell resolution spatial transcriptome data
with scRNA-seq data},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad533},
doi = {10.1093/BIB/BBAD533},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YuanWWGD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZangRYWWLTS24,
author = {Yue Zang and
Xia Ran and
Jie Yuan and
Hao Wu and
Youya Wang and
He Li and
Huajing Teng and
Zhongsheng Sun},
title = {Genomic hallmarks and therapeutic targets of ribosome biogenesis in
cancer},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae023},
doi = {10.1093/BIB/BBAE023},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZangRYWWLTS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZengGGYSP24,
author = {Junxiang Zeng and
Xiupan Gao and
Limei Gao and
Youyou Yu and
Lisong Shen and
Xiujun Pan},
title = {Recognition of rare antinuclear antibody patterns based on a novel
attention-based enhancement framework},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad531},
doi = {10.1093/BIB/BBAD531},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZengGGYSP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaiCD24,
author = {Yuyao Zhai and
Liang Chen and
Minghua Deng},
title = {scEVOLVE: cell-type incremental annotation without forgetting for
single-cell RNA-seq data},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae039},
doi = {10.1093/BIB/BBAE039},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaiCD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangCLLPN24,
author = {Weihang Zhang and
Yang Cui and
Bowen Liu and
Martin Loza and
Sung{-}Joon Park and
Kenta Nakai},
title = {HyGAnno: hybrid graph neural network-based cell type annotation for
single-cell {ATAC} sequencing data},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae152},
doi = {10.1093/BIB/BBAE152},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangCLLPN24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangJZWGH24,
author = {Tinghe Zhang and
Sumin Jo and
Michelle Zhang and
Kai Wang and
Shou{-}Jiang Gao and
Yufei Huang},
title = {Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae170},
doi = {10.1093/BIB/BBAE170},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangJZWGH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLD24,
author = {Yibo Zhang and
Wenyu Liu and
Junbo Duan},
title = {On the core segmentation algorithms of copy number variation detection
tools},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae022},
doi = {10.1093/BIB/BBAE022},
timestamp = {Fri, 05 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangLD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangMYGD24,
author = {Jin Zhang and
Zikang Ma and
Yan Yang and
Lei Guo and
Lei Du},
title = {Modeling genotype-protein interaction and correlation for Alzheimer's
disease: a multi-omics imaging genetics study},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae038},
doi = {10.1093/BIB/BBAE038},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangMYGD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangSZLCC24,
author = {Le Zhang and
Wenkai Song and
Tinghao Zhu and
Yang Liu and
Wei Chen and
Yang Cao},
title = {ConvNeXt-MHC: improving MHC-peptide affinity prediction by structure-derived
degenerate coding and the ConvNeXt model},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae133},
doi = {10.1093/BIB/BBAE133},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangSZLCC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangZYYLLNX24,
author = {Shi Zhang and
Rui Zhang and
Kai Yuan and
Lu Yang and
Chang Liu and
Yuting Liu and
Xumin Ni and
Shuhua Xu},
title = {Reconstructing complex admixture history using a hierarchical model},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad540},
doi = {10.1093/BIB/BBAD540},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangZYYLLNX24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangZZ24,
author = {Chengcheng Zhang and
Tianyi Zang and
Tianyi Zhao},
title = {{KGE-UNIT:} toward the unification of molecular interactions prediction
based on knowledge graph and multi-task learning on drug discovery},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae043},
doi = {10.1093/BIB/BBAE043},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangZZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoB24,
author = {Hangjia Zhao and
Michael Baudis},
title = {labelSeg: segment annotation for tumor copy number alteration profiles},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad541},
doi = {10.1093/BIB/BBAD541},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoZQLMHML24,
author = {Hongyuan Zhao and
Suyi Zhang and
Hui Qin and
Xiaogang Liu and
Dongna Ma and
Xiao Han and
Jian Mao and
Shuangping Liu},
title = {DSNetax: a deep learning species annotation method based on a deep-shallow
parallel framework},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae157},
doi = {10.1093/BIB/BBAE157},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoZQLMHML24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhengSSLLZZPFZLLXZ24,
author = {Lingyan Zheng and
Shuiyang Shi and
Xiuna Sun and
Mingkun Lu and
Yang Liao and
Sisi Zhu and
Hongning Zhang and
Ziqi Pan and
Pan Fang and
Zhenyu Zeng and
Honglin Li and
Zhaorong Li and
Weiwei Xue and
Feng Zhu},
title = {MoDAFold: a strategy for predicting the structure of missense mutant
protein based on AlphaFold2 and molecular dynamics},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae006},
doi = {10.1093/BIB/BBAE006},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhengSSLLZZPFZLLXZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhouLWL24,
author = {Songqi Zhou and
Yang Li and
Wenyuan Wu and
Li Li},
title = {scMMT: a multi-use deep learning approach for cell annotation, protein
prediction and embedding in single-cell RNA-seq data},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad523},
doi = {10.1093/BIB/BBAD523},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhouLWL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhuLLJY24,
author = {Yi{-}Heng Zhu and
Zi Liu and
Yan Liu and
Zhiwei Ji and
Dong{-}Jun Yu},
title = {{ULDNA:} integrating unsupervised multi-source language models with
LSTM-attention network for high-accuracy protein-DNA binding site
prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae040},
doi = {10.1093/BIB/BBAE040},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhuLLJY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AbdellahGGFCCAZKHMMS23,
author = {Marwan Abdellah and
Juan Jose Garcia{-}Cantero and
Nadir Rom{\'{a}}n Guerrero and
Alessandro Foni and
Jay S. Coggan and
Corrado Cal{\`{\i}} and
Marco Agus and
Eleftherios Zisis and
Daniel Keller and
Markus Hadwiger and
Pierre J. Magistretti and
Henry Markram and
Felix Sch{\"{u}}rmann},
title = {Ultraliser: a framework for creating multiscale, high-fidelity and
geometrically realistic 3D models for \emph{in silico} neuroscience},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac491},
doi = {10.1093/BIB/BBAC491},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AbdellahGGFCCAZKHMMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AbeS23,
author = {Ko Abe and
Teppei Shimamura},
title = {{UNMF:} a unified nonnegative matrix factorization for multi-dimensional
omics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad253},
doi = {10.1093/BIB/BBAD253},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AbeS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AdamsKGBYO23,
author = {Alison K. Adams and
Brandon D. Kristy and
Myranda Gorman and
Peter Balint{-}Kurti and
G. Craig Yencho and
Bode A. Olukolu},
title = {Qmatey: an automated pipeline for fast exact matching-based alignment
and strain-level taxonomic binning and profiling of metagenomes},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad351},
doi = {10.1093/BIB/BBAD351},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AdamsKGBYO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AhmedCLYZ23,
author = {Khandakar Tanvir Ahmed and
Sze Cheng and
Qian Li and
Jeongsik Yong and
Wei Zhang},
title = {Incomplete time-series gene expression in integrative study for islet
autoimmunity prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac537},
doi = {10.1093/BIB/BBAC537},
timestamp = {Wed, 15 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AhmedCLYZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AhmedRRR23,
author = {Shehab Sarar Ahmed and
Zaara Tasnim Rifat and
M. Saifur Rahman and
M. Sohel Rahman},
title = {Succinylated lysine residue prediction revisited},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac510},
doi = {10.1093/BIB/BBAC510},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AhmedRRR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AkhtyamovSRSM23,
author = {Pavel Akhtyamov and
Layal Shaheen and
Mikhail Raevskiy and
Alexey Stupnikov and
Yulia A. Medvedeva},
title = {scATAC-seq preprocessing and imputation evaluation system for visualization,
clustering and digital footprinting},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad447},
doi = {10.1093/BIB/BBAD447},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AkhtyamovSRSM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AlamSAYLJJC23,
author = {Mohammad Rizwan Alam and
Kyung Jin Seo and
Jamshid Abdul{-}Ghafar and
Kwangil Yim and
Sung Hak Lee and
Hyun{-}Jong Jang and
Chan Kwon Jung and
Yosep Chong},
title = {Recent application of artificial intelligence on histopathologic image-based
prediction of gene mutation in solid cancers},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad151},
doi = {10.1093/BIB/BBAD151},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AlamSAYLJJC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AlcorizaBalaguerGBJL23,
author = {Mar{\'{\i}}a Isabel Alcoriza{-}Balaguer and
Juan Carlos Garc{\'{\i}}a{-}Ca{\~{n}}averas and
Marta Benet and
Oscar Juan{-}Vidal and
Agust{\'{\i}}n Lahoz},
title = {FAMetA: a mass isotopologue-based tool for the comprehensive analysis
of fatty acid metabolism},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad064},
doi = {10.1093/BIB/BBAD064},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AlcorizaBalaguerGBJL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AsimIFDA23,
author = {Muhammad Nabeel Asim and
Muhammad Ali Ibrahim and
Ahtisham Fazeel and
Andreas Dengel and
Sheraz Ahmed},
title = {{DNA-MP:} a generalized {DNA} modifications predictor for multiple
species based on powerful sequence encoding method},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac546},
doi = {10.1093/BIB/BBAC546},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AsimIFDA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AthayaRLH23,
author = {Tasbiraha Athaya and
Rony Chowdhury Ripan and
Xiaoman Li and
Haiyan Hu},
title = {Multimodal deep learning approaches for single-cell multi-omics data
integration},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad313},
doi = {10.1093/BIB/BBAD313},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AthayaRLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BaiYL23,
author = {Tao Bai and
Ke Yan and
Bin Liu},
title = {DAmiRLocGNet: miRNA subcellular localization prediction by combining
miRNA-disease associations and graph convolutional networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad212},
doi = {10.1093/BIB/BBAD212},
timestamp = {Thu, 28 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BaiYL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BajiyaDAR23,
author = {Nisha Bajiya and
Anjali Dhall and
Suchet Aggarwal and
Gajendra P. S. Raghava},
title = {Advances in the field of phage-based therapy with special emphasis
on computational resources},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac574},
doi = {10.1093/BIB/BBAC574},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BajiyaDAR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BangLPPNGPK23,
author = {Ina Bang and
Sang{-}Mok Lee and
Seojoung Park and
Joon Young Park and
Linh Khanh Nong and
Ye Gao and
Bernhard O. Palsson and
Donghyuk Kim},
title = {Deep-learning optimized {DEOCSU} suite provides an iterable pipeline
for accurate ChIP-exo peak calling},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad024},
doi = {10.1093/BIB/BBAD024},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BangLPPNGPK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BaoCZSSL23,
author = {Jingxuan Bao and
Changgee Chang and
Qiyiwen Zhang and
Andrew J. Saykin and
Li Shen and
Qi Long},
title = {Integrative analysis of multi-omics and imaging data with incorporation
of biological information via structural Bayesian factor analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad073},
doi = {10.1093/BIB/BBAD073},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BaoCZSSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BeltranBFZLMC23,
author = {Jorge Beltr{\'{a}}n and
Lisandra Herrera Bel{\'{e}}n and
Jorge G. Farias and
Mauricio Zamorano and
Nicol{\'{a}}s Lefin and
Javiera Miranda and
Fernanda Parraguez Contreras},
title = {VirusHound-I: prediction of viral proteins involved in the evasion
of host adaptive immune response using the random forest algorithm
and generative adversarial network for data augmentation},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad434},
doi = {10.1093/BIB/BBAD434},
timestamp = {Fri, 26 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BeltranBFZLMC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BeslicTRWM23,
author = {Denis Beslic and
Georg Tscheuschner and
Bernhard Y. Renard and
Michael G. Weller and
Thilo Muth},
title = {Comprehensive evaluation of peptide \emph{de novo} sequencing tools
for monoclonal antibody assembly},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac542},
doi = {10.1093/BIB/BBAC542},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BeslicTRWM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BhartiNJSB23,
author = {Vandana Bharti and
Shabari S. Nair and
Akshat Jain and
Kaushal Kumar Shukla and
Bhaskar Biswas},
title = {Concept drift detection in toxicology datasets using discriminative
subgraph-based drift detector},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac506},
doi = {10.1093/BIB/BBAC506},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BhartiNJSB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BianZZXW23,
author = {Jilong Bian and
Xi Zhang and
Xiying Zhang and
Dali Xu and
Guohua Wang},
title = {MCANet: shared-weight-based MultiheadCrossAttention network for drug-target
interaction prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad082},
doi = {10.1093/BIB/BBAD082},
timestamp = {Wed, 19 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BianZZXW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Bishop23,
author = {Martin Bishop},
title = {Editorial},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad176},
doi = {10.1093/BIB/BBAD176},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Bishop23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BistTC23,
author = {Prem Singh Bist and
Hilal Tayara and
Kil To Chong},
title = {Sars-escape network for escape prediction of {SARS-COV-2}},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad140},
doi = {10.1093/BIB/BBAD140},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BistTC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BlampeyBDPRAC23,
author = {Quentin Blampey and
Nad{\`{e}}ge Bercovici and
Charles{-}Antoine Dutertre and
Isabelle Pic and
Joana Mourato Ribeiro and
Fabrice Andr{\'{e}} and
Paul{-}Henry Courn{\`{e}}de},
title = {A biology-driven deep generative model for cell-type annotation in
cytometry},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad260},
doi = {10.1093/BIB/BBAD260},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BlampeyBDPRAC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BuratinBG23,
author = {Alessia Buratin and
Stefania Bortoluzzi and
Enrico Gaffo},
title = {Systematic benchmarking of statistical methods to assess differential
expression of circular RNAs},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac612},
doi = {10.1093/BIB/BBAC612},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BuratinBG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaiZZG23,
author = {Guoxing Cai and
Wenyi Zhao and
Zhan Zhou and
Xun Gu},
title = {{MATTE:} a pipeline of transcriptome module alignment for anti-noise
phenotype-gene-related analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad207},
doi = {10.1093/BIB/BBAD207},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/CaiZZG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaoGWHZMWJMCJYWWCY23,
author = {Qiushi Cao and
Cheng Ge and
Xuejie Wang and
Peta J. Harvey and
Zixuan Zhang and
Yuan Ma and
Xianghong Wang and
Xinying Jia and
Mehdi Mobli and
David J. Craik and
Tao Jiang and
Jinbo Yang and
Zhiqiang Wei and
Yan Wang and
Shan Chang and
Rilei Yu},
title = {Designing antimicrobial peptides using deep learning and molecular
dynamic simulations},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad058},
doi = {10.1093/BIB/BBAD058},
timestamp = {Tue, 30 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CaoGWHZMWJMCJYWWCY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaoGYY23,
author = {Yue Cao and
Shila Ghazanfar and
Pengyi Yang and
Jean Y. H. Yang},
title = {Benchmarking of analytical combinations for {COVID-19} outcome prediction
using single-cell {RNA} sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad159},
doi = {10.1093/BIB/BBAD159},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CaoGYY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CarterCA23,
author = {Elena Lucy Carter and
Chrystala Constantinidou and
Mohammad Tauqeer Alam},
title = {Applications of genome-scale metabolic models to investigate microbial
metabolic adaptations in response to genetic or environmental perturbations},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad439},
doi = {10.1093/BIB/BBAD439},
timestamp = {Mon, 01 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CarterCA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChangCLLKWT23,
author = {Kai{-}Li Chang and
Jia{-}Hong Chen and
Tzu{-}Chieh Lin and
Jun{-}Yi Leu and
Cheng{-}Fu Kao and
Jin Yung Wong and
Huai{-}Kuang Tsai},
title = {Short human eccDNAs are predictable from sequences},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad147},
doi = {10.1093/BIB/BBAD147},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChangCLLKWT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenBL23,
author = {Feng Chen and
Yubo Bai and
Chunhe Li},
title = {Estimation of non-equilibrium transition rate from gene expression
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad113},
doi = {10.1093/BIB/BBAD113},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenBL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenC23,
author = {Lei Chen and
Yuwei Chen},
title = {RMTLysPTM: recognizing multiple types of lysine {PTM} sites by deep
analysis on sequences},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad450},
doi = {10.1093/BIB/BBAD450},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenCJSWW23,
author = {Hongwei Chen and
Yunpeng Cai and
Chaojie Ji and
Gurudeeban Selvaraj and
Dongqing Wei and
Hongyan Wu},
title = {AdaPPI: identification of novel protein functional modules via adaptive
graph convolution networks in a protein-protein interaction network},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac523},
doi = {10.1093/BIB/BBAC523},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenCJSWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenCLYZT23,
author = {Juntao Chen and
Jiannan Chao and
Huan Liu and
Fenglong Yang and
Quan Zou and
Furong Tang},
title = {{WMSA} 2: a multiple {DNA/RNA} sequence alignment tool implemented
with accurate progressive mode and a fast win-win mode combining the
center star and progressive strategies},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad190},
doi = {10.1093/BIB/BBAD190},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenCLYZT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenCWLLT23,
author = {Yu{-}Hsin Chen and
Kuan{-}Hao Chao and
Jin Yung Wong and
Chien{-}Fu Liu and
Jun{-}Yi Leu and
Huai{-}Kuang Tsai},
title = {A feature extraction free approach for protein interactome inference
from co-elution data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad229},
doi = {10.1093/BIB/BBAD229},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenCWLLT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenGCXSXCWD23,
author = {Sikang Chen and
Jian Gao and
Jiexuan Chen and
Yufeng Xie and
Zheyuan Shen and
Lei Xu and
Jinxin Che and
Jian Wu and
Xiaowu Dong},
title = {ClusterX: a novel representation learning-based deep clustering framework
for accurate visual inspection in virtual screening},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad126},
doi = {10.1093/BIB/BBAD126},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenGCXSXCWD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenH23,
author = {Xing Chen and
Li Huang},
title = {Computational model for disease research},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac615},
doi = {10.1093/BIB/BBAC615},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenHLHTCLL23,
author = {Hsin{-}Hua Chen and
Chun{-}Wei Hsueh and
Chia{-}Hwa Lee and
Ting{-}Yi Hao and
Tzu{-}Ying Tu and
Lan{-}Yun Chang and
Jih{-}Chin Lee and
Chun{-}Yu Lin},
title = {{SWEET:} a single-sample network inference method for deciphering
individual features in disease},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad032},
doi = {10.1093/BIB/BBAD032},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenHLHTCLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenLGBLPCS23,
author = {Ruyi Chen and
Fuyi Li and
Xudong Guo and
Yue Bi and
Chen Li and
Shirui Pan and
Lachlan J. M. Coin and
Jiangning Song},
title = {{ATTIC} is an integrated approach for predicting A-to-I {RNA} editing
sites in three species},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad170},
doi = {10.1093/BIB/BBAD170},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenLGBLPCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenLLCQCWHH23,
author = {Yi{-}Gang Chen and
Yang{-}Chi{-}Dung Lin and
Yijun Luo and
Xiao{-}Xuan Cai and
Peng Qiu and
Shi{-}Dong Cui and
Zhe Wang and
Hsi{-}Yuan Huang and
Hsien{-}Da Huang},
title = {Quantitative model for genome-wide cyclic {AMP} receptor protein binding
site identification and characteristic analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad138},
doi = {10.1093/BIB/BBAD138},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenLLCQCWHH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenSGLM23,
author = {Jiung{-}Wen Chen and
Lisa Shrestha and
George Green and
Andr{\'{e}} Leier and
Tatiana T. Marquez{-}Lago},
title = {The hitchhikers' guide to {RNA} sequencing and functional analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac529},
doi = {10.1093/BIB/BBAC529},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenSGLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenWL23,
author = {Wenlan Chen and
Hong Wang and
Cheng Liang},
title = {Deep multi-view contrastive learning for cancer subtype identification},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad282},
doi = {10.1093/BIB/BBAD282},
timestamp = {Thu, 26 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenXQYXT23,
author = {Bo Chen and
Ziwei Xie and
Jiezhong Qiu and
Zhaofeng Ye and
Jinbo Xu and
Jie Tang},
title = {Improved the heterodimer protein complex prediction with protein language
models},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad221},
doi = {10.1093/BIB/BBAD221},
timestamp = {Wed, 06 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenXQYXT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenYZL23,
author = {Siqi Chen and
Xuhua Yan and
Ruiqing Zheng and
Min Li},
title = {Bubble: a fast single-cell RNA-seq imputation using an autoencoder
constrained by bulk RNA-seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac580},
doi = {10.1093/BIB/BBAC580},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenYZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZLZC23,
author = {Hongjun Chen and
Yekai Zhou and
Yongjing Liu and
Peijing Zhang and
Ming Chen},
title = {Network integration and protein structural binding analysis of neurodegeneration-related
interactome},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad237},
doi = {10.1093/BIB/BBAD237},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenZLZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZLZQ23,
author = {Yamao Chen and
Shengyu Zhou and
Ming Li and
Fangqing Zhao and
Ji Qi},
title = {{STEEL} enables high-resolution delineation of spatiotemporal transcriptomic
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad068},
doi = {10.1093/BIB/BBAD068},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenZLZQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZS23,
author = {Yuanyuan Chen and
Hao Zhang and
Xiao Sun},
title = {Improving the performance of single-cell RNA-seq data mining based
on relative expression orderings},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac556},
doi = {10.1093/BIB/BBAC556},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZWZHGL23,
author = {Kai Chen and
Xiaodong Zhu and
Jiahao Wang and
Ziqi Zhao and
Lei Hao and
Xinsheng Guo and
Yuanning Liu},
title = {MFPred: prediction of ncRNA families based on multi-feature fusion},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad303},
doi = {10.1093/BIB/BBAD303},
timestamp = {Mon, 23 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenZWZHGL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChengHL23,
author = {Andrew Cheng and
Guanyu Hu and
Wei Vivian Li},
title = {Benchmarking cell-type clustering methods for spatially resolved transcriptomics
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac475},
doi = {10.1093/BIB/BBAC475},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChengHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChengLZRGWZL23,
author = {Zhiwei Cheng and
Leijie Li and
Yuening Zhang and
Yongyong Ren and
Jianlei Gu and
Xinbo Wang and
Hongyu Zhao and
Hui Lu},
title = {HBV-infected hepatocellular carcinoma can be robustly classified into
three clinically relevant subgroups by a novel analytical protocol},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac601},
doi = {10.1093/BIB/BBAC601},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChengLZRGWZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChoQLTLLRARLDW23,
author = {Hunyong Cho and
Yixiang Qu and
Chuwen Liu and
Boyang Tang and
Ruiqi Lyu and
Bridget M. Lin and
Jeffrey Roach and
M. Andrea Azcarate{-}Peril and
Apoena Aguiar Ribeiro and
Michael I. Love and
Kimon Divaris and
Di Wu},
title = {Comprehensive evaluation of methods for differential expression analysis
of metatranscriptomics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad279},
doi = {10.1093/BIB/BBAD279},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChoQLTLLRARLDW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChristensenLTHMNDBPRS23,
author = {Erik Christensen and
Ping Luo and
Andrei L. Turinsky and
Mia Husic and
Alaina Mahalanabis and
Alaine Naidas and
Juan Javier D{\'{\i}}az{-}Mej{\'{\i}}a and
Michael Brudno and
Trevor J. Pugh and
Arun K. Ramani and
Parisa Shooshtari},
title = {Evaluation of single-cell RNAseq labelling algorithms using cancer
datasets},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac561},
doi = {10.1093/BIB/BBAC561},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChristensenLTHMNDBPRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CiaPR23,
author = {Gabriel Cia and
Fabrizio Pucci and
Marianne Rooman},
title = {Critical review of conformational B-cell epitope prediction methods},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac567},
doi = {10.1093/BIB/BBAC567},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/CiaPR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ConevRDFKFCZAK23,
author = {Anja Conev and
Maur{\'{\i}}cio Menegatti Rigo and
Didier Devaurs and
Andr{\'{e}} Faustino Fonseca and
Hussain Kalavadwala and
Martiela Vaz de Freitas and
Cecilia Clementi and
Geancarlo Zanatta and
Dinler Amaral Antunes and
Lydia E. Kavraki},
title = {EnGens: a computational framework for generation and analysis of representative
protein conformational ensembles},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad242},
doi = {10.1093/BIB/BBAD242},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ConevRDFKFCZAK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CuiLBWL23,
author = {Lingyu Cui and
Hongfei Li and
Jilong Bian and
Guohua Wang and
Yingjian Liang},
title = {Unsupervised construction of gene regulatory network based on single-cell
multi-omics data of colorectal cancer},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad011},
doi = {10.1093/BIB/BBAD011},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/CuiLBWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CuiW23,
author = {Tao Cui and
Tingting Wang},
title = {A comprehensive assessment of hurdle and zero-inflated models for
single cell RNA-sequencing analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad272},
doi = {10.1093/BIB/BBAD272},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/CuiW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DarmawanLAR23,
author = {Jeremie Theddy Darmawan and
Jenq{-}Shiou Leu and
Cries Avian and
Nanda Rizqia Pradana Ratnasari},
title = {MITNet: a fusion transformer and convolutional neural network architecture
approach for T-cell epitope prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad202},
doi = {10.1093/BIB/BBAD202},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DarmawanLAR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DavydovBPC23,
author = {Alexey N. Davydov and
Dmitry Bolotin and
Stanislav V. Poslavsky and
Dmitry M. Chudakov},
title = {Comment on 'rigorous benchmarking of {T} cell receptor repertoire
profiling methods for cancer {RNA} sequencing'},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad354},
doi = {10.1093/BIB/BBAD354},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DavydovBPC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DefoAR23,
author = {Joel Defo and
Denis Awany and
Raj Ramesar},
title = {From {SNP} to pathway-based {GWAS} meta-analysis: do current meta-analysis
approaches resolve power and replication in genetic association studies?},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac600},
doi = {10.1093/BIB/BBAC600},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DefoAR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DengCZXFWS23,
author = {Tao Deng and
Siyu Chen and
Ying Zhang and
Yuanbin Xu and
Da Feng and
Hao Wu and
Xiaobo Sun},
title = {A cofunctional grouping-based approach for non-redundant feature gene
selection in unannotated single-cell RNA-seq analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad042},
doi = {10.1093/BIB/BBAD042},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DengCZXFWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DengLWJYLVKWZ23,
author = {Wenxuan Deng and
Bolun Li and
Jiawei Wang and
Wei Jiang and
Xiting Yan and
Ningshan Li and
Milica Vukmirovic and
Naftali Kaminski and
Jing Wang and
Hongyu Zhao},
title = {A novel Bayesian framework for harmonizing information across tissues
and studies to increase cell type deconvolution accuracy},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac616},
doi = {10.1093/BIB/BBAC616},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DengLWJYLVKWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DengZZCLT23,
author = {Juntao Deng and
Xiao Zhou and
Pengyan Zhang and
Weibin Cheng and
Min Liu and
Junzhang Tian},
title = {{IEPAPI:} a method for immune epitope prediction by incorporating
antigen presentation and immunogenicity},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad171},
doi = {10.1093/BIB/BBAD171},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DengZZCLT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingKHZ23,
author = {Wubin Ding and
Diljeet Kaur and
Steve Horvath and
Wanding Zhou},
title = {Comparative epigenome analysis using Infinium {DNA} methylation BeadChips},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac617},
doi = {10.1093/BIB/BBAC617},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingKHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingWZGLY23,
author = {Pengju Ding and
Yifei Wang and
Xinyu Zhang and
Xin Gao and
Guozhu Liu and
Bin Yu},
title = {DeepSTF: predicting transcription factor binding sites by interpretable
deep neural networks combining sequence and shape},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad231},
doi = {10.1093/BIB/BBAD231},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingWZGLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingZQGCMGYWL23,
author = {Ruofan Ding and
Xudong Zou and
Yangmei Qin and
Lihai Gong and
Hui Chen and
Xuelian Ma and
Shouhong Guang and
Chen Yu and
Gao Wang and
Lei Li},
title = {xQTLbiolinks: a comprehensive and scalable tool for integrative analysis
of molecular QTLs},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad440},
doi = {10.1093/BIB/BBAD440},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingZQGCMGYWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DongWXO23,
author = {Jie Dong and
Zheng Wu and
Huanle Xu and
Defang Ouyang},
title = {FormulationAI: a novel web-based platform for drug formulation design
driven by artificial intelligence},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad419},
doi = {10.1093/BIB/BBAD419},
timestamp = {Fri, 08 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DongWXO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DongYWXLLG23,
author = {Weihe Dong and
Qiang Yang and
Jian Wang and
Long Xu and
Xiaokun Li and
Gongning Luo and
Xin Gao},
title = {Multi-modality attribute learning-based method for drug-protein interaction
prediction based on deep neural network},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad161},
doi = {10.1093/BIB/BBAD161},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DongYWXLLG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DorneyDRHS23,
author = {Ryley Dorney and
Bijay P. Dhungel and
John E. J. Rasko and
Lionel Hebbard and
Ulf Schmitz},
title = {Recent advances in cancer fusion transcript detection},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac519},
doi = {10.1093/BIB/BBAC519},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DorneyDRHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DouDCDGT23,
author = {Mingliang Dou and
Jiaqi Ding and
Genlang Chen and
Junwen Duan and
Fei Guo and
Jijun Tang},
title = {{IK-DDI:} a novel framework based on instance position embedding and
key external text for {DDI} extraction},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad099},
doi = {10.1093/BIB/BBAD099},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DouDCDGT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DuDXL23,
author = {Zhenjiao Du and
Xingjian Ding and
Yixiang Xu and
Yonghui Li},
title = {UniDL4BioPep: a universal deep learning architecture for binary classification
in peptide bioactivity},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad135},
doi = {10.1093/BIB/BBAD135},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DuDXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DuGZHTCZ23,
author = {Lianming Du and
Chaoyue Geng and
Qiang{-}Lin Zeng and
Ting Huang and
Jie Tang and
Yiwen Chu and
Kelei Zhao},
title = {Dockey: a modern integrated tool for large-scale molecular docking
and virtual screening},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad047},
doi = {10.1093/BIB/BBAD047},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DuGZHTCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DuYWMZBHJCW23,
author = {Wenjie Du and
Xiaoting Yang and
Di Wu and
Fenfen Ma and
Baicheng Zhang and
Chaochao Bao and
Yaoyuan Huo and
Jun Jiang and
Xin Chen and
Yang Wang},
title = {Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors
for conformational and chiral stereoisomers},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac560},
doi = {10.1093/BIB/BBAC560},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DuYWMZBHJCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DuanTWGF23,
author = {Daoyu Duan and
Wen Tang and
Runshu Wang and
Zhenxing Guo and
Hao Feng},
title = {Evaluation of epitranscriptome-wide N6-methyladenosine differential
analysis methods},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad139},
doi = {10.1093/BIB/BBAD139},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DuanTWGF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DuanWZLZLZHZZ23,
author = {Meiyu Duan and
Yueying Wang and
Dong Zhao and
Hongmei Liu and
Gongyou Zhang and
Kewei Li and
Haotian Zhang and
Lan Huang and
Ruochi Zhang and
Fengfeng Zhou},
title = {Orchestrating information across tissues via a novel multitask {GAT}
framework to improve quantitative gene regulation relation modeling
for survival analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad238},
doi = {10.1093/BIB/BBAD238},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DuanWZLZLZHZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DurouxS23,
author = {Diane Duroux and
Kristel Van Steen},
title = {netANOVA: novel graph clustering technique with significance assessment
via hierarchical {ANOVA}},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad029},
doi = {10.1093/BIB/BBAD029},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DurouxS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ElimelechZoharO23,
author = {Karin Elimelech{-}Zohar and
Yaron Orenstein},
title = {An overview on nucleic-acid G-quadruplex prediction: from rule-based
methods to deep neural networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad252},
doi = {10.1093/BIB/BBAD252},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ElimelechZoharO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FalgaroneVROK23,
author = {Th{\'{e}}o Falgarone and
Etienne Villain and
Fran{\c{c}}ois D. Richard and
Zarifa Osmanli and
Andrey V. Kajava},
title = {Census of exposed aggregation-prone regions in proteomes},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad183},
doi = {10.1093/BIB/BBAD183},
timestamp = {Mon, 25 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FalgaroneVROK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FanCZLF23,
author = {Yetian Fan and
April S. Chan and
Jun Zhu and
Suet Yi Leung and
Xiaodan Fan},
title = {A Bayesian model for identifying cancer subtypes from paired methylation
profiles},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac568},
doi = {10.1093/BIB/BBAC568},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FanCZLF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FanJLCC23,
author = {Rui Fan and
Xiangwen Ji and
Jianwei Li and
Qinghua Cui and
Chunmei Cui},
title = {Defining the single base importance of human mRNAs and lncRNAs},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad321},
doi = {10.1093/BIB/BBAD321},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FanJLCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FanPTCS23,
author = {Xiao Fan and
Hongbing Pan and
Alan Tian and
Wendy K. Chung and
Yufeng Shen},
title = {{SHINE:} protein language model-based pathogenicity prediction for
short inframe insertion and deletion variants},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac584},
doi = {10.1093/BIB/BBAC584},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FanPTCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FangLW23,
author = {Kechi Fang and
Chuan Li and
Jing Wang},
title = {An automatic immunofluorescence pattern classification framework for
HEp-2 image based on supervised learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad144},
doi = {10.1093/BIB/BBAD144},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FangLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FangXWJCWW23,
author = {Yitian Fang and
Fan Xu and
Lesong Wei and
Yi Jiang and
Jie Chen and
Leyi Wei and
Dong{-}Qing Wei},
title = {{AFP-MFL:} accurate identification of antifungal peptides using multi-view
feature learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac606},
doi = {10.1093/BIB/BBAC606},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FangXWJCWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FarhadiAMAA23,
author = {Fatemeh Farhadi and
Mohammad Allahbakhsh and
Ali Maghsoudi and
Nadieh Armin and
Haleh Amintoosi},
title = {DiMo: discovery of microRNA motifs using deep learning and motif embedding},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad182},
doi = {10.1093/BIB/BBAD182},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FarhadiAMAA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FengJLLZL23,
author = {Hailin Feng and
Dongdong Jin and
Jian Li and
Yane Li and
Quan Zou and
Tongcun Liu},
title = {Matrix reconstruction with reliable neighbors for predicting potential
MiRNA-disease associations},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac571},
doi = {10.1093/BIB/BBAC571},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FengJLLZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FengWMLHCY23,
author = {Ze{-}Ying Feng and
Xue{-}Hong Wu and
Jun{-}Long Ma and
Min Li and
Ge{-}Fei He and
Dong{-}Sheng Cao and
Guo{-}Ping Yang},
title = {{DKADE:} a novel framework based on deep learning and knowledge graph
for identifying adverse drug events and related medications},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad228},
doi = {10.1093/BIB/BBAD228},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FengWMLHCY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FengZFZSS23,
author = {Yue{-}Hua Feng and
Shao{-}Wu Zhang and
Yi{-}Yang Feng and
Qing{-}Qing Zhang and
Ming{-}Hui Shi and
Jian{-}Yu Shi},
title = {A social theory-enhanced graph representation learning framework for
multitask prediction of drug-drug interactions},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac602},
doi = {10.1093/BIB/BBAC602},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FengZFZSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FiannacaRPGU23,
author = {Antonino Fiannaca and
Massimo La Rosa and
Laura La Paglia and
Salvatore Gaglio and
Alfonso Urso},
title = {{GOWDL:} gene ontology-driven wide and deep learning model for cell
typing of scRNA-seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad332},
doi = {10.1093/BIB/BBAD332},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FiannacaRPGU23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FuWZQWP23,
author = {Ping Fu and
Yifan Wu and
Zhiyuan Zhang and
Ye Qiu and
Yirong Wang and
Yousong Peng},
title = {{VIGA:} a one-stop tool for eukaryotic virus identification and genome
assembly from next-generation-sequencing data},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad444},
doi = {10.1093/BIB/BBAD444},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FuWZQWP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FuYLZTZZXZ23,
author = {Jianbo Fu and
Qingxia Yang and
Yongchao Luo and
Song Zhang and
Jing Tang and
Ying Zhang and
Hongning Zhang and
Hanxiang Xu and
Feng Zhu},
title = {Label-free proteome quantification and evaluation},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac477},
doi = {10.1093/BIB/BBAC477},
timestamp = {Fri, 03 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FuYLZTZZXZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GanCXGZ23,
author = {Yanglan Gan and
Yuhan Chen and
Guangwei Xu and
Wenjing Guo and
Guobing Zou},
title = {Deep enhanced constraint clustering based on contrastive learning
for scRNA-seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad222},
doi = {10.1093/BIB/BBAD222},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GanCXGZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoSWLLZS23,
author = {Hongyan Gao and
Jianqiang Sun and
Yukun Wang and
Yuer Lu and
Liyu Liu and
Qi Zhao and
Jianwei Shuai},
title = {Predicting metabolite-disease associations based on auto-encoder and
non-negative matrix factorization},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad259},
doi = {10.1093/BIB/BBAD259},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaoSWLLZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoSXLLCBGSWZHHCD23,
author = {Jian Gao and
Zheyuan Shen and
Yufeng Xie and
Jialiang Lu and
Yang Lu and
Sikang Chen and
Qingyu Bian and
Yue Guo and
Liteng Shen and
Jian Wu and
Binbin Zhou and
Tingjun Hou and
Qiaojun He and
Jinxin Che and
Xiaowu Dong},
title = {TransFoxMol: predicting molecular property with focused attention},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad306},
doi = {10.1093/BIB/BBAD306},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GaoSXLLCBGSWZHHCD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoZCLZDXZS23,
author = {Siqi Gao and
Hanwen Zhu and
Kangwen Cai and
Leiqin Liu and
Zhiqiang Zhang and
Yi Ding and
Yaochen Xu and
Xiaoqi Zheng and
Jiantao Shi},
title = {TRAmHap: accurate prediction of transcriptional activity from {DNA}
methylation haplotypes in bisulfite-sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad214},
doi = {10.1093/BIB/BBAD214},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaoZCLZDXZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoZLLFLKLFW23,
author = {Pengfei Gao and
Haonan Zhao and
Zheng Luo and
Yifan Lin and
Wanjie Feng and
Yaling Li and
Fanjiang Kong and
Xia Li and
Chao Fang and
Xutong Wang},
title = {SoyDNGP: a web-accessible deep learning framework for genomic prediction
in soybean breeding},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad349},
doi = {10.1093/BIB/BBAD349},
timestamp = {Mon, 23 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaoZLLFLKLFW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoZLLGY23,
author = {Hongli Gao and
Bin Zhang and
Long Liu and
Shan Li and
Xin Gao and
Bin Yu},
title = {A universal framework for single-cell multi-omics data integration
with graph convolutional networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad081},
doi = {10.1093/BIB/BBAD081},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaoZLLGY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GautamBBZLHP23,
author = {Anupam Gautam and
Debaleena Bhowmik and
Sayantani Basu and
Wenhuan Zeng and
Abhishake Lahiri and
Daniel H. Huson and
Sandip Paul},
title = {Microbiome Metabolome Integration Platform {(MMIP):} a web-based platform
for microbiome and metabolome data integration and feature identification},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad325},
doi = {10.1093/BIB/BBAD325},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GautamBBZLHP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GeLCMW23,
author = {Shu{-}Guang Ge and
Jian Liu and
Yuhu Cheng and
Xiaojing Meng and
Xuesong Wang},
title = {Multi-view spectral clustering with latent representation learning
for applications on multi-omics cancer subtyping},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac500},
doi = {10.1093/BIB/BBAC500},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GeLCMW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GeLIALTYWXSY23,
author = {Fang Ge and
Chen Li and
Shahid Iqbal and
Muhammad Arif and
Fuyi Li and
Maha A. Thafar and
Zihao Yan and
Apilak Worachartcheewan and
Xiaofeng Xu and
Jiangning Song and
Dong{-}Jun Yu},
title = {VPatho: a deep learning-based two-stage approach for accurate prediction
of gain-of-function and loss-of-function variants},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac535},
doi = {10.1093/BIB/BBAC535},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GeLIALTYWXSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GePCXZ23,
author = {Fengqi Ge and
Chunxiang Peng and
Xinyue Cui and
Yuhao Xia and
Guijun Zhang},
title = {Inter-domain distance prediction based on deep learning for domain
assembly},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad100},
doi = {10.1093/BIB/BBAD100},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GePCXZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GimenoRR23,
author = {Marian Gimeno and
Katyna Sada del Real and
Angel Rubio},
title = {Precision oncology: a review to assess interpretability in several
explainable methods},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad200},
doi = {10.1093/BIB/BBAD200},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GimenoRR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GinerIHP23,
author = {G{\"{o}}knur Giner and
Saima Ikram and
Marco J. Herold and
Anthony T. Papenfuss},
title = {A systematic review of computational methods for designing efficient
guides for {CRISPR} {DNA} base editor systems},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad205},
doi = {10.1093/BIB/BBAD205},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GinerIHP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GongWLFGFZ23,
author = {Haoran Gong and
Jianguo Wen and
Ruihan Luo and
Yuzhou Feng and
Jingjing Guo and
Hongguang Fu and
Xiaobo Zhou},
title = {Integrated mRNA sequence optimization using deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad001},
doi = {10.1093/BIB/BBAD001},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GongWLFGFZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GossiPCMJR23,
author = {Federico Gossi and
Pushpak Pati and
Panagiotis Chouvardas and
Adriano Luca Martinelli and
Marianna Kruithof{-}de Julio and
Maria Anna Rapsomaniki},
title = {Matching single cells across modalities with contrastive learning
and optimal transport},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad130},
doi = {10.1093/BIB/BBAD130},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GossiPCMJR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuBYLKK23,
author = {Jeonghyeon Gu and
Dongmin Bang and
Jungseob Yi and
Sangseon Lee and
Dong Kyu Kim and
Sun Kim},
title = {A model-agnostic framework to enhance knowledge graph-based drug combination
prediction with drug-drug interaction data and supervised contrastive
learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad285},
doi = {10.1093/BIB/BBAD285},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuBYLKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuSYZLLSXWHK23,
author = {Shukai Gu and
Chao Shen and
Jiahui Yu and
Hong Zhao and
Huanxiang Liu and
Liwei Liu and
Rong Sheng and
Lei Xu and
Zhe Wang and
Tingjun Hou and
Yu Kang},
title = {Can molecular dynamics simulations improve predictions of protein-ligand
binding affinity with machine learning?},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad008},
doi = {10.1093/BIB/BBAD008},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuSYZLLSXWHK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuanJ23,
author = {Zengrui Guan and
Zhenran Jiang},
title = {Transformer-based anti-noise models for CRISPR-Cas9 off-target activities
prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad127},
doi = {10.1093/BIB/BBAD127},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuanJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoZJLGZZYW23,
author = {Binjie Guo and
Hanyu Zheng and
Haohan Jiang and
Xiaodan Li and
Naiyu Guan and
Yanming Zuo and
Yicheng Zhang and
Hengfu Yang and
Xuhua Wang},
title = {Enhanced compound-protein binding affinity prediction by representing
protein multimodal information via a coevolutionary strategy},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac628},
doi = {10.1093/BIB/BBAC628},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuoZJLGZZYW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuptaS23,
author = {Sagar Gupta and
Ravi Shankar},
title = {miWords: transformer-based composite deep learning for highly accurate
discovery of pre-miRNA regions across plant genomes},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad088},
doi = {10.1093/BIB/BBAD088},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuptaS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HamamotoTSMKAKK23,
author = {Ryuji Hamamoto and
Ken Takasawa and
Norio Shinkai and
Hidenori Machino and
Nobuji Kouno and
Ken Asada and
Masaaki Komatsu and
Syuzo Kaneko},
title = {Analysis of super-enhancer using machine learning and its application
to medical biology},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad107},
doi = {10.1093/BIB/BBAD107},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HamamotoTSMKAKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanFWZSHZLZ23,
author = {Shen Han and
Haitao Fu and
Yuyang Wu and
Ganglan Zhao and
Zhenyu Song and
Feng Huang and
Zhongfei Zhang and
Shichao Liu and
Wen Zhang},
title = {HimGNN: a novel hierarchical molecular graph representation learning
framework for property prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad305},
doi = {10.1093/BIB/BBAD305},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HanFWZSHZLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanPKLLLOK23,
author = {So{-}Ra Han and
Mingyu Park and
Sai Kosaraju and
Jeungmin Lee and
Hyun Lee and
Jun Hyuck Lee and
Tae{-}Jin Oh and
Mingon Kang},
title = {Evidential deep learning for trustworthy prediction of enzyme commission
number},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad401},
doi = {10.1093/BIB/BBAD401},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HanPKLLLOK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanWCACYWL23,
author = {Yanqiang Han and
Zhilong Wang and
An Chen and
Imran Ali and
Junfei Cai and
Simin Ye and
Zhiyun Wei and
Jin{-}Jin Li},
title = {A deep transfer learning-based protocol accelerates full quantum mechanics
calculation of protein},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac532},
doi = {10.1093/BIB/BBAC532},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HanWCACYWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanWHC23,
author = {Chen{-}Di Han and
Chun{-}Chun Wang and
Li Huang and
Xing Chen},
title = {{MCFF-MTDDI:} multi-channel feature fusion for multi-typed drug-drug
interaction prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad215},
doi = {10.1093/BIB/BBAD215},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HanWHC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanWWZYXZXDW23,
author = {Ke Han and
Jianchun Wang and
Yu Wang and
Lei Zhang and
Mengyao Yu and
Fang Xie and
Dequan Zheng and
Yaoqun Xu and
Yijie Ding and
Jie Wan},
title = {A review of methods for predicting {DNA} N6-methyladenine sites},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac514},
doi = {10.1093/BIB/BBAC514},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HanWWZYXZXDW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HaoZZCWCSYWSZWCZ23,
author = {Jie Hao and
Jiawei Zou and
Jiaqiang Zhang and
Ke Chen and
Duojiao Wu and
Wei Cao and
Guoguo Shang and
Jean Yee Hwa Yang and
KongFatt Wong{-}Lin and
Hourong Sun and
Zhen Zhang and
Xiangdong Wang and
Wantao Chen and
Xin Zou},
title = {scSTAR reveals hidden heterogeneity with a real-virtual cell pair
structure across conditions in single-cell {RNA} sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad062},
doi = {10.1093/BIB/BBAD062},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HaoZZCWCSYWSZWCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeGSS23,
author = {Shujun He and
Baizhen Gao and
Rushant Sabnis and
Qing Sun},
title = {RNAdegformer: accurate prediction of mRNA degradation at nucleotide
resolution with deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac581},
doi = {10.1093/BIB/BBAC581},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HeGSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeLLZ23,
author = {Guang{-}Xing He and
Jun Liu and
Dong Liu and
Guijun Zhang},
title = {GraphGPSM: a global scoring model for protein structure using graph
neural networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad219},
doi = {10.1093/BIB/BBAD219},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HeLLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeQFB23,
author = {Qiang He and
Wei Qiao and
Hui Fang and
Yang Bao},
title = {Improving the identification of miRNA-disease associations with multi-task
learning on gene-disease networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad203},
doi = {10.1093/BIB/BBAD203},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HeQFB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeXCWW23,
author = {Wenchuang He and
Kunli Xiang and
Caijin Chen and
Jie Wang and
Zhiqiang Wu},
title = {Master graph: an essential integrated assembly model for the plant
mitogenome based on a graph-based framework},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac522},
doi = {10.1093/BIB/BBAC522},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HeXCWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeYSZXH23,
author = {Yi{-}Zhou He and
Yue Yang and
Xiao{-}Rui Su and
Bo{-}Wei Zhao and
Shengwu Xiong and
Lun Hu},
title = {Incorporating higher order network structures to improve miRNA-disease
association prediction based on functional modularity},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac562},
doi = {10.1093/BIB/BBAC562},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HeYSZXH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeYYHSZCFWWY23,
author = {Chun He and
Xinhai Ye and
Yi Yang and
Liya Hu and
Yuxuan Si and
Xianxin Zhao and
Longfei Chen and
Qi Fang and
Ying Wei and
Fei Wu and
Gongyin Ye},
title = {DeepAlgPro: an interpretable deep neural network model for predicting
allergenic proteins},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad246},
doi = {10.1093/BIB/BBAD246},
timestamp = {Tue, 16 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HeYYHSZCFWWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HenaoLAGTLOS23,
author = {Juan D. Henao and
Michael Lauber and
Manuel Azevedo and
Anastasiia Grekova and
Fabian J. Theis and
Markus List and
Christoph Ogris and
Benjamin Schubert},
title = {Multi-omics regulatory network inference in the presence of missing
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad309},
doi = {10.1093/BIB/BBAD309},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HenaoLAGTLOS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HongLLSDLTH23,
author = {Danni Hong and
Hongli Lin and
Lifang Liu and
Muya Shu and
Jianwu Dai and
Falong Lu and
Mengsha Tong and
Jialiang Huang},
title = {Complexity of enhancer networks predicts cell identity and disease
genes revealed by single-cell multi-omics analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac508},
doi = {10.1093/BIB/BBAC508},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HongLLSDLTH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HorlacherCHSGLMM23,
author = {Marc Horlacher and
Giulia Cantini and
Julian Hesse and
Patrick Schinke and
Nicolas Goedert and
Shubhankar Londhe and
Lambert Moyon and
Annalisa Marsico},
title = {A systematic benchmark of machine learning methods for protein-RNA
interaction prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad307},
doi = {10.1093/BIB/BBAD307},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HorlacherCHSGLMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HosseiniZ23,
author = {Sayed{-}Rzgar Hosseini and
Xiaobo Zhou},
title = {CCSynergy: an integrative deep-learning framework enabling context-aware
prediction of anti-cancer drug synergy},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac588},
doi = {10.1093/BIB/BBAC588},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HosseiniZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuFCCQS23,
author = {Ruyun Hu and
Lihao Fu and
Yongcan Chen and
Junyu Chen and
Yu Qiao and
Tong Si},
title = {Protein engineering via Bayesian optimization-guided evolutionary
algorithm and robotic experiments},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac570},
doi = {10.1093/BIB/BBAC570},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuFCCQS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuFLZZXCCMSZS23,
author = {Huan Hu and
Zhen Feng and
Hai Lin and
Junjie Zhao and
Yaru Zhang and
Fei Xu and
Lingling Chen and
Feng Chen and
Yunlong Ma and
Jianzhong Su and
Qi Zhao and
Jianwei Shuai},
title = {Modeling and analyzing single-cell multimodal data with deep parametric
inference},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad005},
doi = {10.1093/BIB/BBAD005},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuFLZZXCCMSZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuLZHZYXLKH23,
author = {Zhiqiang Hu and
Wenfeng Liu and
Chenbin Zhang and
Jiawen Huang and
Shaoting Zhang and
Huiqun Yu and
Yi Xiong and
Hao Liu and
Song Ke and
Liang Hong},
title = {{SAM-DTA:} a sequence-agnostic model for drug-target binding affinity
prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac533},
doi = {10.1093/BIB/BBAC533},
timestamp = {Mon, 02 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuLZHZYXLKH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuLZTLL23,
author = {Dayu Hu and
Ke Liang and
Sihang Zhou and
Wenxuan Tu and
Meng Liu and
Xinwang Liu},
title = {scDFC: {A} deep fusion clustering method for single-cell RNA-seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad216},
doi = {10.1093/BIB/BBAD216},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuLZTLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuS23,
author = {Jianchang Hu and
Silke Szymczak},
title = {A review on longitudinal data analysis with random forest},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad002},
doi = {10.1093/BIB/BBAD002},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangSCLHS23,
author = {Yuan{-}Qin Huang and
Ping Sun and
Yi Chen and
Huanxiang Liu and
Ge{-}Fei Hao and
Bao{-}An Song},
title = {Bioinformatics toolbox for exploring target mutation-induced drug
resistance},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad033},
doi = {10.1093/BIB/BBAD033},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangSCLHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangVPAM23,
author = {Yu{-}Ning Huang and
Mohammad Vahed and
Kerui Peng and
Houda Alachkar and
Serghei Mangul},
title = {Response to 'comment on rigorous benchmarking of {T} cell receptor
repertoire profiling methods for cancer {RNA} sequencing' by Davydov
A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov {D.M}},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad355},
doi = {10.1093/BIB/BBAD355},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangVPAM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangWLZY23,
author = {Zimo Huang and
Jun Wang and
Xudong Lu and
Azlan Mohd Zain and
Guoxian Yu},
title = {scGGAN: single-cell RNA-seq imputation by graph-based generative adversarial
network},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad040},
doi = {10.1093/BIB/BBAD040},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangWLZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangWZZ23,
author = {Yan Huang and
Stefan Wuchty and
Yuan Zhou and
Ziding Zhang},
title = {{SGPPI:} structure-aware prediction of protein-protein interactions
in rigorous conditions with graph convolutional network},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad020},
doi = {10.1093/BIB/BBAD020},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangWZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangZCYLZXYXHZ23,
author = {Weibin Huang and
Yuhui Zhang and
Songyao Chen and
Haofan Yin and
Guangyao Liu and
Huaqi Zhang and
Jiannan Xu and
Jishang Yu and
Yujian Xia and
Yulong He and
Changhua Zhang},
title = {Personalized immune subtypes based on machine learning predict response
to checkpoint blockade in gastric cancer},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac554},
doi = {10.1093/BIB/BBAC554},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangZCYLZXYXHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangZLZYHCCWJ23,
author = {Yu'e Huang and
Shunheng Zhou and
Haizhou Liu and
Xu Zhou and
Mengqin Yuan and
Fei Hou and
Sina Chen and
Jiahao Chen and
Lihong Wang and
Wei Jiang},
title = {DRdriver: identifying drug resistance driver genes using individual-specific
gene regulatory network},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad066},
doi = {10.1093/BIB/BBAD066},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangZLZYHCCWJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangZYZXCX23,
author = {Xiaoqiang Huang and
Jun Zhou and
Dongshan Yang and
Jifeng Zhang and
Xiaofeng Xia and
Yuqing Eugene Chen and
Jie Xu},
title = {Decoding CRISPR-Cas {PAM} recognition with UniDesign},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad133},
doi = {10.1093/BIB/BBAD133},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangZYZXCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/IbeneLPAT23,
author = {Mandy Ib{\'{e}}n{\'{e}} and
Audrey Legendre and
Guillaume Postic and
Eric Angel and
Fariza Tahi},
title = {C-RCPred: a multi-objective algorithm for interactive secondary structure
prediction of {RNA} complexes integrating user knowledge and {SHAPE}
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad225},
doi = {10.1093/BIB/BBAD225},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/IbeneLPAT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiLLDHC23,
author = {Kai{-}Yue Ji and
Chong Liu and
Zhao{-}Qian Liu and
Yafeng Deng and
Tingjun Hou and
Dong{-}Sheng Cao},
title = {Comprehensive assessment of nine target prediction web services: which
should we choose for target fishing?},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad014},
doi = {10.1093/BIB/BBAD014},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiLLDHC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiWC23,
author = {Xiangwen Ji and
Edwin Wang and
Qinghua Cui},
title = {Deciphering gene contributions and etiologies of somatic mutational
signatures of cancer},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad017},
doi = {10.1093/BIB/BBAD017},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiaHZ23,
author = {Peilin Jia and
Ruifeng Hu and
Zhongming Zhao},
title = {Benchmark of embedding-based methods for accurate and transferable
prediction of drug response},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad098},
doi = {10.1093/BIB/BBAD098},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiaHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiaLBST23,
author = {Shangru Jia and
Artem Lysenko and
Keith A. Boroevich and
Alok Sharma and
Tatsuhiko Tsunoda},
title = {scDeepInsight: a supervised cell-type identification method for scRNA-seq
data with deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad266},
doi = {10.1093/BIB/BBAD266},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JiaLBST23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiaWDCCZ23,
author = {Long{-}Hao Jia and
Yingjian Wu and
Yanqi Dong and
Jingchao Chen and
Wei{-}Hua Chen and
Xing{-}Ming Zhao},
title = {A survey on computational strategies for genome-resolved gut metagenomics},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad162},
doi = {10.1093/BIB/BBAD162},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiaWDCCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiaZLQRLMZADCS23,
author = {Xiaoti Jia and
Pei Zhao and
Fuyi Li and
Zhaohui Qin and
Haoran Ren and
Junzhou Li and
Chunbo Miao and
Quanzhi Zhao and
Tatsuya Akutsu and
Gensheng Dou and
Zhen Chen and
Jiangning Song},
title = {ResNetKhib: a novel cell type-specific tool for predicting lysine
2-hydroxyisobutylation sites via transfer learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad063},
doi = {10.1093/BIB/BBAD063},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiaZLQRLMZADCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangCLG23,
author = {Peiran Jiang and
Ruoxi Cai and
Jose Lugo{-}Martinez and
Yaping Guo},
title = {A hybrid positive unlabeled learning framework for uncovering scaffolds
across human proteome by measuring the propensity to drive phase separation},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad009},
doi = {10.1093/BIB/BBAD009},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangCLG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangHL23,
author = {Yuepeng Jiang and
Miaozhe Huo and
Shuai Cheng Li},
title = {TEINet: a deep learning framework for prediction of TCR-epitope binding
specificity},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad086},
doi = {10.1093/BIB/BBAD086},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangL23,
author = {Yuepeng Jiang and
Shuai Cheng Li},
title = {Deep autoregressive generative models capture the intrinsics embedded
in T-cell receptor repertoires},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad038},
doi = {10.1093/BIB/BBAD038},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangXLSGZZ23,
author = {Jing Jiang and
Junlin Xu and
Yuansheng Liu and
Bosheng Song and
Xiulan Guo and
Xiangxiang Zeng and
Quan Zou},
title = {Dimensionality reduction and visualization of single-cell RNA-seq
data with an improved deep variational autoencoder},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad152},
doi = {10.1093/BIB/BBAD152},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangXLSGZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangYSSYLZJSY23,
author = {Jing{-}Zhe Jiang and
Wen{-}Guang Yuan and
Jiayu Shang and
Ying{-}Hui Shi and
Li{-}Ling Yang and
Min Liu and
Peng Zhu and
Tao Jin and
Yanni Sun and
Li{-}Hong Yuan},
title = {Virus classification for viral genomic fragments using PhaGCN2},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac505},
doi = {10.1093/BIB/BBAC505},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JiangYSSYLZJSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangZYZM23,
author = {Minghao Jiang and
Shiyan Zhang and
Hongxin Yin and
Zhiyi Zhuo and
Guoyu Meng},
title = {A comprehensive benchmarking of differential splicing tools for RNA-seq
analysis at the event level},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad121},
doi = {10.1093/BIB/BBAD121},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangZYZM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangZZYLWCZWXSX23,
author = {Gaofei Jiang and
Jiaxuan Zhang and
Yaozhong Zhang and
Xinrun Yang and
Tingting Li and
Ningqi Wang and
Xingjian Chen and
Fang{-}Jie Zhao and
Zhong Wei and
Yangchun Xu and
Qirong Shen and
Wei Xue},
title = {DCiPatho: deep cross-fusion networks for genome scale identification
of pathogens},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad194},
doi = {10.1093/BIB/BBAD194},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangZZYLWCZWXSX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JingXYYNHDCLTZ23,
author = {Kai Jing and
Yewen Xu and
Yang Yang and
Pengfei Yin and
Duo Ning and
Guangyu Huang and
Yuqing Deng and
Gengzhan Chen and
Guoliang Li and
Simon Zhongyuan Tian and
Meizhen Zheng},
title = {ScSmOP: a universal computational pipeline for single-cell single-molecule
multiomics data analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad343},
doi = {10.1093/BIB/BBAD343},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JingXYYNHDCLTZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JustynaAS23,
author = {Marek Justyna and
Maciej Antczak and
Marta Szachniuk},
title = {Machine learning for {RNA} 2D structure prediction benchmarked on
experimental data},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad153},
doi = {10.1093/BIB/BBAD153},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JustynaAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KangXWPYRC23,
author = {Yan Kang and
Yulong Xu and
Xinchao Wang and
Bin Pu and
Xuekun Yang and
Yulong Rao and
Jianguo Chen},
title = {{HN-PPISP:} a hybrid network based on MLP-Mixer for protein-protein
interaction site prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac480},
doi = {10.1093/BIB/BBAC480},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KangXWPYRC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KarimISBLCRD23,
author = {Md. Rezaul Karim and
Tanhim Islam and
Md Shajalal and
Oya Beyan and
Christoph Lange and
Michael Cochez and
Dietrich Rebholz{-}Schuhmann and
Stefan Decker},
title = {Explainable {AI} for Bioinformatics: Methods, Tools and Applications},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad236},
doi = {10.1093/BIB/BBAD236},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KarimISBLCRD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KattanAW23,
author = {Rebecca Elizabeth Kattan and
Deena Ayesh and
Wenqi Wang},
title = {Analysis of affinity purification-related proteomic data for studying
protein-protein interaction networks in cells},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad010},
doi = {10.1093/BIB/BBAD010},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KattanAW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KawaguchiTFRTKG23,
author = {Risa Karakida Kawaguchi and
Ziqi Tang and
Stephan Fischer and
Chandana Rajesh and
Rohit Tripathy and
Peter K. Koo and
Jesse A. Gillis},
title = {Learning single-cell chromatin accessibility profiles using meta-analytic
marker genes},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac541},
doi = {10.1093/BIB/BBAC541},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KawaguchiTFRTKG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KhandujaKM23,
author = {Akshay Khanduja and
Manish Kumar and
Debasisa Mohanty},
title = {ProsmORF-pred: a machine learning-based method for the identification
of small ORFs in prokaryotic genomes},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad101},
doi = {10.1093/BIB/BBAD101},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KhandujaKM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KimHLLKK23,
author = {Donghyo Kim and
Doyeon Ha and
Kwanghwan Lee and
Heetak Lee and
Inhae Kim and
Sanguk Kim},
title = {An evolution-based machine learning to identify cancer type-specific
driver mutations},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac593},
doi = {10.1093/BIB/BBAC593},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KimHLLKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KimKYLLZ23,
author = {Pora Kim and
Himansu Kumar and
Chengyuan Yang and
Ruihan Luo and
Jiajia Liu and
Xiaobo Zhou},
title = {Systematic investigation of the homology sequences around the human
fusion gene breakpoints in pan-cancer - bioinformatics study for a
potential link to {MMEJ}},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad314},
doi = {10.1093/BIB/BBAD314},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KimKYLLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KnightKPGOW23,
author = {Connor H. Knight and
Faraz Khan and
Ankit Patel and
Upkar S. Gill and
Jessica Okosun and
Jun Wang},
title = {{IBRAP:} integrated benchmarking single-cell RNA-sequencing analytical
pipeline},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad061},
doi = {10.1093/BIB/BBAD061},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KnightKPGOW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KobetsUGDMGSRK23,
author = {Victoria A Kobets and
Sergey V. Ulianov and
Aleksandra A. Galitsyna and
Semen A. Doronin and
Elena A. Mikhaleva and
Mikhail S. Gelfand and
Yuri Y. Shevelyov and
Sergey V. Razin and
Ekaterina E. Khrameeva},
title = {HiConfidence: a novel approach uncovering the biological signal in
Hi-C data affected by technical biases},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad044},
doi = {10.1093/BIB/BBAD044},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KobetsUGDMGSRK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KongWHLWWG23,
author = {Weijia Kong and
Bertrand Jern Han Wong and
Harvard Wai Hann Hui and
Kai Peng Lim and
Yulan Wang and
Limsoon Wong and
Wilson Wen Bin Goh},
title = {ProJect: a powerful mixed-model missing value imputation method},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad233},
doi = {10.1093/BIB/BBAD233},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KongWHLWWG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KoudijsBG23,
author = {Karel K. M. Koudijs and
Stefan B{\"{o}}hringer and
Henk{-}Jan Guchelaar},
title = {Validation of transcriptome signature reversion for drug repurposing
in oncology},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac490},
doi = {10.1093/BIB/BBAC490},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KoudijsBG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KumarPCTDR23,
author = {Nishant Kumar and
Sumeet Patiyal and
Shubham Choudhury and
Ritu Tomer and
Anjali Dhall and
Gajendra P. S. Raghava},
title = {DMPPred: a tool for identification of antigenic regions responsible
for inducing type 1 diabetes mellitus},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac525},
doi = {10.1093/BIB/BBAC525},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KumarPCTDR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LaiG23,
author = {Fei{-}Liao Lai and
Feng Gao},
title = {Auto-Kla: a novel web server to discriminate lysine lactylation sites
using automated machine learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad070},
doi = {10.1093/BIB/BBAD070},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LaiG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LainscsekT23,
author = {Xenia Lainscsek and
Leila Taher},
title = {Predicting chromosomal compartments directly from the nucleotide sequence
with {DNA-DDA}},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad198},
doi = {10.1093/BIB/BBAD198},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LainscsekT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LanDZLCLWC23,
author = {Wei Lan and
Yi Dong and
Hongyu Zhang and
Chunling Li and
Qingfeng Chen and
Jin Liu and
Jianxin Wang and
Yi{-}Ping Phoebe Chen},
title = {Benchmarking of computational methods for predicting circRNA-disease
associations},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac613},
doi = {10.1093/BIB/BBAC613},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LanDZLCLWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeLC23,
author = {Nguyen{-}Quoc{-}Khanh Le and
Wanru Li and
Yanshuang Cao},
title = {Sequence-based prediction model of protein crystallization propensity
using machine learning and two-level feature selection},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad319},
doi = {10.1093/BIB/BBAD319},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LeLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeeCJCJSJL23,
author = {Kanggeun Lee and
Dongbin Cho and
Jinho Jang and
Kang Choi and
Hyoung{-}oh Jeong and
Jiwon Seo and
Won{-}Ki Jeong and
Semin Lee},
title = {{RAMP:} response-aware multi-task learning with contrastive regularization
for cancer drug response prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac504},
doi = {10.1093/BIB/BBAC504},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LeeCJCJSJL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeeHHLMHBDTLP23,
author = {Sanghun Lee and
Georg Hahn and
Julian Hecker and
Sharon Marie Lutz and
Kristina Mullin and
Winston Hide and
Lars Bertram and
Dawn L. Demeo and
Rudolph E. Tanzi and
Christoph Lange and
Dmitry Prokopenko},
title = {A comparison between similarity matrices for principal component analysis
to assess population stratification in sequenced genetic data sets},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac611},
doi = {10.1093/BIB/BBAC611},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LeeHHLMHBDTLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeeKKYY23,
author = {Joongho Lee and
Minsoo Kim and
Keunsoo Kang and
Chul{-}Su Yang and
Seokhyun Yoon},
title = {Hierarchical cell-type identifier accurately distinguishes immune-cell
subtypes enabling precise profiling of tissue microenvironment with
single-cell RNA-sequencing},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad006},
doi = {10.1093/BIB/BBAD006},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LeeKKYY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeeYLZZYCMRLH23,
author = {Lindsay Lee and
Miao Yu and
Xiaoqi Li and
Chenxu Zhu and
Yanxiao Zhang and
Hongyu Yu and
Ziyin Chen and
Shreya Mishra and
Bing Ren and
Yun Li and
Ming Hu},
title = {SnapHiC-D: a computational pipeline to identify differential chromatin
contacts from single-cell Hi-C data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad315},
doi = {10.1093/BIB/BBAD315},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LeeYLZZYCMRLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeiCZC23,
author = {Tianyuan Lei and
Ruoyu Chen and
Shaoqiang Zhang and
Yong Chen},
title = {Self-supervised deep clustering of single-cell RNA-seq data to hierarchically
detect rare cell populations},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad335},
doi = {10.1093/BIB/BBAD335},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LeiCZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeventhalDL23,
author = {Emily L. Leventhal and
Andrea R. Daamen and
Peter E. Lipsky},
title = {Letter to the editor: testing the effectiveness of MyPROSLE in classifying
patients with lupus nephritis},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad322},
doi = {10.1093/BIB/BBAD322},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LeventhalDL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiARLHTCLHZL23,
author = {Ruoxing Li and
Mehmet Altan and
Alexandre Reuben and
Ruitao Lin and
John V. Heymach and
Hai Tran and
Runzhe Chen and
Latasha Little and
Shawna Hubert and
Jianjun Zhang and
Ziyi Li},
title = {A novel statistical method for decontaminating T-cell receptor sequencing
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad230},
doi = {10.1093/BIB/BBAD230},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiARLHTCLHZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiCW23,
author = {Xiayang Li and
Moxuan Chen and
Huaming Wu},
title = {Multiple errors correction for position-limited {DNA} sequences with
{GC} balance and no homopolymer for DNA-based data storage},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac484},
doi = {10.1093/BIB/BBAC484},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiCXJ23,
author = {Mei Li and
Xiangrui Cai and
Sihan Xu and
Hua Ji},
title = {Metapath-aggregated heterogeneous graph neural network for drug-target
interaction prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac578},
doi = {10.1093/BIB/BBAC578},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiCXJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiGWGW23,
author = {Yang Li and
Zihou Guo and
Keqi Wang and
Xin Gao and
Guohua Wang},
title = {End-to-end interpretable disease-gene association prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad118},
doi = {10.1093/BIB/BBAD118},
timestamp = {Wed, 12 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiGWGW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiHCGWSNR23,
author = {Xue Li and
Peifu Han and
Wenqi Chen and
Changnan Gao and
Shuang Wang and
Tao Song and
Muyuan Niu and
Alfonso Rodr{\'{\i}}guez{-}Pat{\'{o}}n},
title = {{MARPPI:} boosting prediction of protein-protein interactions with
multi-scale architecture residual network},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac524},
doi = {10.1093/BIB/BBAC524},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiHCGWSNR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiHKZZZ23,
author = {Han Li and
Xuan He and
Lawrence Kurowski and
Ruotian Zhang and
Dan Zhao and
Jianyang Zeng},
title = {Improving comparative analyses of Hi-C data via contrastive self-supervised
learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad193},
doi = {10.1093/BIB/BBAD193},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiHKZZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiLSLL23,
author = {Pingjing Li and
Hong Liu and
Jialiang Sun and
Jianguo Lu and
Jian Liu},
title = {HiBrowser: an interactive and dynamic browser for synchronous Hi-C
data visualization},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad283},
doi = {10.1093/BIB/BBAD283},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiLSLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiMHGGZW23,
author = {Haochen Li and
Tianxing Ma and
Minsheng Hao and
Wenbo Guo and
Jin Gu and
Xuegong Zhang and
Lei Wei},
title = {Decoding functional cell-cell communication events by multi-view graph
learning on spatial transcriptomics},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad359},
doi = {10.1093/BIB/BBAD359},
timestamp = {Thu, 02 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiMHGGZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiNAA23,
author = {Yijia Li and
Jonathan Nguyen and
David C. Anastasiu and
Edgar A. Arriaga},
title = {CosTaL: an accurate and scalable graph-based clustering algorithm
for high-dimensional single-cell data analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad157},
doi = {10.1093/BIB/BBAD157},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiNAA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiRC23,
author = {Baiqing Li and
Ting Ran and
Hongming Chen},
title = {3D based generative {PROTAC} linker design with reinforcement learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad323},
doi = {10.1093/BIB/BBAD323},
timestamp = {Wed, 27 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiRC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiSWSYLLCWWWL23,
author = {Huiyu Li and
Chen Shen and
Gongji Wang and
Qinru Sun and
Kai Yu and
Zefeng Li and
Xinggong Liang and
Run Chen and
Hao Wu and
Fan Wang and
Zhenyuan Wang and
Chunfeng Lian},
title = {BloodNet: An attention-based deep network for accurate, efficient,
and costless bloodstain time since deposition inference},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac557},
doi = {10.1093/BIB/BBAC557},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiSWSYLLCWWWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiWQW23,
author = {Bing Li and
Tian Wang and
Min Qian and
Shuang Wang},
title = {{MKMR:} a multi-kernel machine regression model to predict health
outcomes using human microbiome data},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad158},
doi = {10.1093/BIB/BBAD158},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiWQW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiWZ23,
author = {Peilong Li and
Junfeng Wei and
Ying Zhu},
title = {CellGO: a novel deep learning-based framework and webserver for cell-type-specific
gene function interpretation},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad417},
doi = {10.1093/BIB/BBAD417},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiWZC23,
author = {Tian{-}Hao Li and
Chun{-}Chun Wang and
Li Zhang and
Xing Chen},
title = {{SNRMPACDC:} computational model focused on Siamese network and random
matrix projection for anticancer synergistic drug combination prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac503},
doi = {10.1093/BIB/BBAC503},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiWZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiXCZTC23,
author = {Lin Li and
Rui Xia and
Wei Chen and
Qi Zhao and
Peng Tao and
Luonan Chen},
title = {Single-cell causal network inferred by cross-mapping entropy},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad281},
doi = {10.1093/BIB/BBAD281},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiXCZTC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiXTWZLLZSXZBZS23,
author = {Lun Li and
Bo Xu and
Dongmei Tian and
Anke Wang and
Junwei Zhu and
Cuiping Li and
Na Li and
Wei Zhao and
Leisheng Shi and
Yongbiao Xue and
Zhang Zhang and
Yiming Bao and
Wenming Zhao and
Shuhui Song},
title = {McAN: a novel computational algorithm and platform for constructing
and visualizing haplotype networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad174},
doi = {10.1093/BIB/BBAD174},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiXTWZLLZSXZBZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZMZZ23,
author = {Juntao Li and
Hongmei Zhang and
Bingyu Mu and
Hongliang Zuo and
Kanglei Zhou},
title = {Identifying phenotype-associated subpopulations through LP{\_}SGL},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad424},
doi = {10.1093/BIB/BBAD424},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiZMZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZSZWL23,
author = {Zimeng Li and
Shichao Zhu and
Bin Shao and
Xiangxiang Zeng and
Tong Wang and
Tie{-}Yan Liu},
title = {{DSN-DDI:} an accurate and generalized framework for drug-drug interaction
prediction by dual-view representation learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac597},
doi = {10.1093/BIB/BBAC597},
timestamp = {Tue, 04 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiZSZWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZWSSXWL23,
author = {Kai Li and
Ping Zhang and
Zilin Wang and
Wei Shen and
Weicheng Sun and
Jinsheng Xu and
Zi Wen and
Li Li},
title = {iEnhance: a multi-scale spatial projection encoding network for enhancing
chromatin interaction data resolution},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad245},
doi = {10.1093/BIB/BBAD245},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiZWSSXWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZXZ23,
author = {Yan Li and
Shao{-}Wu Zhang and
Ming{-}Yu Xie and
Tong Zhang},
title = {PhenoDriver: interpretable framework for studying personalized phenotype-associated
driver genes in breast cancer},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad291},
doi = {10.1093/BIB/BBAD291},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiZXZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZYLGZ23,
author = {Min Li and
Baoying Zhao and
Rui Yin and
Chengqian Lu and
Fei Guo and
Min Zeng},
title = {GraphLncLoc: long non-coding {RNA} subcellular localization prediction
using graph convolutional networks based on sequence to graph transformation},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac565},
doi = {10.1093/BIB/BBAC565},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiZYLGZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiangCDDLADXZGLGG23,
author = {Mang Liang and
Sheng Cao and
Tianyu Deng and
Lili Du and
Keanning Li and
Bingxing An and
Yueying Du and
Lingyang Xu and
Lupei Zhang and
Xue Gao and
Junya Li and
Peng Guo and
Huijiang Gao},
title = {{MAK:} a machine learning framework improved genomic prediction via
multi-target ensemble regressor chains and automatic selection of
assistant traits},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad043},
doi = {10.1093/BIB/BBAD043},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiangCDDLADXZGLGG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiangZWL23,
author = {Qi Liang and
Wenxiang Zhang and
Hao Wu and
Bin Liu},
title = {LncRNA-disease association identification using graph auto-encoder
and learning to rank},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac539},
doi = {10.1093/BIB/BBAC539},
timestamp = {Fri, 30 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiangZWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiaoXZW23,
author = {Ying Liao and
Yisha Xiang and
Mingjie Zheng and
Jun Wang},
title = {DeepMiceTL: a deep transfer learning based prediction of mice cardiac
conduction diseases using early electrocardiograms},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad109},
doi = {10.1093/BIB/BBAD109},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiaoXZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiaoZQZ23,
author = {Shaofeng Liao and
Yujun Zhang and
Yifei Qi and
Zhuqing Zhang},
title = {Evaluation of sequence-based predictors for phase-separating protein},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad213},
doi = {10.1093/BIB/BBAD213},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiaoZQZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LimFL23,
author = {Hendrick Gao{-}Min Lim and
Yang C. Fann and
Yuan{-}Chii Gladys Lee},
title = {{COWID:} an efficient cloud-based genomics workflow for scalable identification
of {SARS-COV-2}},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad280},
doi = {10.1093/BIB/BBAD280},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LimFL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinDZYZSCZCSYZ23,
author = {Xuan Lin and
Lichang Dai and
Yafang Zhou and
Zu{-}Guo Yu and
Wen Zhang and
Jian{-}Yu Shi and
Dong{-}Sheng Cao and
Li Zeng and
Haowen Chen and
Bosheng Song and
Philip S. Yu and
Xiangxiang Zeng},
title = {Comprehensive evaluation of deep and graph learning on drug-drug interactions
prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad235},
doi = {10.1093/BIB/BBAD235},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LinDZYZSCZCSYZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinJWKY23,
author = {Jiadong Lin and
Peng Jia and
Songbo Wang and
Walter A. Kosters and
Kai Ye},
title = {Comparison and benchmark of structural variants detected from long
read and long-read assembly},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad188},
doi = {10.1093/BIB/BBAD188},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LinJWKY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinO23,
author = {Zerun Lin and
Le Ou{-}Yang},
title = {Inferring gene regulatory networks from single-cell gene expression
data via deep multi-view contrastive learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac586},
doi = {10.1093/BIB/BBAC586},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LinO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinQCSZACWLLJ23,
author = {Zhe Lin and
Yangmei Qin and
Hao Chen and
Dan Shi and
Mindong Zhong and
Te An and
Linshan Chen and
Yiquan Wang and
Fan Lin and
Guang Li and
Zhi{-}Liang Ji},
title = {TransIntegrator: capture nearly full protein-coding transcript variants
via integrating Illumina and PacBio transcriptomes},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad334},
doi = {10.1093/BIB/BBAD334},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LinQCSZACWLLJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinWZLXXQL23,
author = {Jiacheng Lin and
Lijun Wu and
Jinhua Zhu and
Xiaobo Liang and
Yingce Xia and
Shufang Xie and
Tao Qin and
Tie{-}Yan Liu},
title = {{R2-DDI:} relation-aware feature refinement for drug-drug interaction
prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac576},
doi = {10.1093/BIB/BBAC576},
timestamp = {Mon, 29 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LinWZLXXQL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinYH23,
author = {Peicong Lin and
Yumeng Yan and
Sheng{-}You Huang},
title = {DeepHomo2.0: improved protein-protein contact prediction of homodimers
by transformer-enhanced deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac499},
doi = {10.1093/BIB/BBAC499},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LinYH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuFLX23,
author = {Xiang Liu and
Huitao Feng and
Zhi L{\"{u}} and
Kelin Xia},
title = {Persistent Tor-algebra for protein-protein interaction analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad046},
doi = {10.1093/BIB/BBAD046},
timestamp = {Wed, 19 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuFLX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuFLZCY23,
author = {Teng Liu and
Zhao{-}Yu Fang and
Xin Li and
Li{-}Ning Zhang and
Dong{-}Sheng Cao and
Ming{-}Zhu Yin},
title = {Graph deep learning enabled spatial domains identification for spatial
transcriptomics},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad146},
doi = {10.1093/BIB/BBAD146},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuFLZCY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuHHF23,
author = {Ran Liu and
Ye{-}Fan Hu and
Jian{-}Dong Huang and
Xiaodan Fan},
title = {A Bayesian approach to estimate MHC-peptide binding threshold},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad208},
doi = {10.1093/BIB/BBAD208},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuHHF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuHSHGXZL23,
author = {Li Liu and
Kaiyuan Han and
Huimin Sun and
Lu Han and
Dong Gao and
Qilemuge Xi and
Lirong Zhang and
Hao Lin},
title = {A comprehensive review of bioinformatics tools for chromatin loop
calling},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad072},
doi = {10.1093/BIB/BBAD072},
timestamp = {Wed, 04 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuHSHGXZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuHXMLZG23,
author = {Chun{-}Jie Liu and
Fei{-}Fei Hu and
Gui{-}Yan Xie and
Ya{-}Ru Miao and
Xin{-}Wen Li and
Yan Zeng and
An{-}Yuan Guo},
title = {{GSCA:} an integrated platform for gene set cancer analysis at genomic,
pharmacogenomic and immunogenomic levels},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac558},
doi = {10.1093/BIB/BBAC558},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuHXMLZG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuJD23,
author = {Hui Liu and
Ye Jin and
Hanjing Ding},
title = {MDBuilder: a PyMOL plugin for the preparation of molecular dynamics
simulations},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad057},
doi = {10.1093/BIB/BBAD057},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuJD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuKL23,
author = {Jiayi Liu and
Anat Kreimer and
Wei Vivian Li},
title = {Differential variability analysis of single-cell gene expression data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad294},
doi = {10.1093/BIB/BBAD294},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuKL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuLSG23,
author = {Jian Liu and
Pingjing Li and
Jialiang Sun and
Jun Guo},
title = {{LPAD:} using network construction and label propagation to detect
topologically associating domains from Hi-C data},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad165},
doi = {10.1093/BIB/BBAD165},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuLSG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuLSHPGLSL23,
author = {Hongjia Liu and
Huamei Li and
Amit Sharma and
Wenjuan Huang and
Duo Pan and
Yu Gu and
Lu Lin and
Xiao Sun and
Hongde Liu},
title = {scAnno: a deconvolution strategy-based automatic cell type annotation
tool for single-cell RNA-sequencing data sets},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad179},
doi = {10.1093/BIB/BBAD179},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuLSHPGLSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuLZLHLGL23,
author = {Jiashu Liu and
Cui{-}Xiang Lin and
Xiaoqi Zhang and
Zongxuan Li and
Wenkui Huang and
Jin Liu and
Yuanfang Guan and
Hong{-}Dong Li},
title = {Computational approaches for detecting disease-associated alternative
splicing events},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad106},
doi = {10.1093/BIB/BBAD106},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuLZLHLGL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuS23,
author = {Qingchun Liu and
Kai Song},
title = {ProgCAE: a deep learning-based method that integrates multi-omics
data to predict cancer subtypes},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad196},
doi = {10.1093/BIB/BBAD196},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuSGLSZ23,
author = {Yuansheng Liu and
Xiangzhen Shen and
Yongshun Gong and
Yiping Liu and
Bosheng Song and
Xiangxiang Zeng},
title = {Sequence Alignment/Map format: a comprehensive review of approaches
and applications},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad320},
doi = {10.1093/BIB/BBAD320},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuSGLSZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuTG23,
author = {Jing Liu and
Xinghua Tang and
Xiao Guan},
title = {Grain protein function prediction based on self-attention mechanism
and bidirectional {LSTM}},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac493},
doi = {10.1093/BIB/BBAC493},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuTG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuTLFYP23,
author = {Wei Liu and
Ting Tang and
Xu Lu and
Xiangzheng Fu and
Yu Yang and
Li Peng},
title = {{MPCLCDA:} predicting circRNA-disease associations by using automatically
selected meta-path and contrastive learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad227},
doi = {10.1093/BIB/BBAD227},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuTLFYP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuW23,
author = {Tong Liu and
Zheng Wang},
title = {HiC4D: forecasting spatiotemporal Hi-C data with residual ConvLSTM},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad263},
doi = {10.1093/BIB/BBAD263},
timestamp = {Mon, 23 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuWLSGSCY23,
author = {Yan Liu and
Guo Wei and
Chen Li and
Long{-}Chen Shen and
Robin B. Gasser and
Jiangning Song and
Dijun Chen and
Dong{-}Jun Yu},
title = {TripletCell: a deep metric learning framework for accurate annotation
of cell types at the single-cell level},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad132},
doi = {10.1093/BIB/BBAD132},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuWLSGSCY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuWST23,
author = {Bin Liu and
Jin Wang and
Kaiwei Sun and
Grigorios Tsoumakas},
title = {Fine-grained selective similarity integration for drug-target interaction
prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad085},
doi = {10.1093/BIB/BBAD085},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuWST23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuWYZZ23,
author = {Yuhang Liu and
Zixuan Wang and
Hao Yuan and
Guiquan Zhu and
Yongqing Zhang},
title = {{HEAP:} a task adaptive-based explainable deep learning framework
for enhancer activity prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad286},
doi = {10.1093/BIB/BBAD286},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuWYZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuYLFSYP23,
author = {Wei Liu and
Yu Yang and
Xu Lu and
Xiangzheng Fu and
Ruiqing Sun and
Li Yang and
Li Peng},
title = {{NSRGRN:} a network structure refinement method for gene regulatory
network inference},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad129},
doi = {10.1093/BIB/BBAD129},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuYLFSYP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuZHHDCTLRHLCW23,
author = {Tianyuan Liu and
Bohao Zou and
Manman He and
Yongfei Hu and
Yiying Dou and
Tianyu Cui and
Puwen Tan and
Shaobin Li and
Shuan Rao and
Yan Huang and
Sixi Liu and
Kaican Cai and
Dong Wang},
title = {LncReader: identification of dual functional long noncoding RNAs using
a multi-head self-attention mechanism},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac579},
doi = {10.1093/BIB/BBAC579},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuZHHDCTLRHLCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuZLLSZ23,
author = {Dong Liu and
Biao Zhang and
Jun Liu and
Hui Li and
Le Song and
Guijun Zhang},
title = {Assessing protein model quality based on deep graph coupled networks
using protein language model},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad420},
doi = {10.1093/BIB/BBAD420},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuZLLSZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuZXLLLGLTYZ23,
author = {Mingzhu Liu and
Jian Zhou and
Qilemuge Xi and
Yuchao Liang and
Haicheng Li and
Pengfei Liang and
Yuting Guo and
Ming Liu and
Temuqile Temuqile and
Lei Yang and
Yongchun Zuo},
title = {A computational framework of routine test data for the cost-effective
chronic disease prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad054},
doi = {10.1093/BIB/BBAD054},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuZXLLLGLTYZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuZZ23,
author = {Jun Liu and
Kai{-}Long Zhao and
Guijun Zhang},
title = {Improved model quality assessment using sequence and structural information
by enhanced deep neural networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac507},
doi = {10.1093/BIB/BBAC507},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuZZWCJZZ23,
author = {Qiao Liu and
Wanwen Zeng and
Wei Zhang and
Sicheng Wang and
Hongyang Chen and
Rui Jiang and
Mu Zhou and
Shaoting Zhang},
title = {Deep generative modeling and clustering of single cell Hi-C data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac494},
doi = {10.1093/BIB/BBAC494},
timestamp = {Mon, 02 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuZZWCJZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuPX23,
author = {Yao Lu and
Zhiqiang Pang and
Jianguo Xia},
title = {Comprehensive investigation of pathway enrichment methods for functional
interpretation of {LC-MS} global metabolomics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac553},
doi = {10.1093/BIB/BBAC553},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuPX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuQALBLLT23,
author = {Na Lu and
Yi Qiao and
Pengfei An and
Jiajian Luo and
Changwei Bi and
Musheng Li and
Zuhong Lu and
Jing Tu},
title = {Exploration of whole genome amplification generated chimeric sequences
in long-read sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad275},
doi = {10.1093/BIB/BBAD275},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuQALBLLT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuWLLTPLGXY23,
author = {Ruiqiang Lu and
Jun Wang and
Pengyong Li and
Yuquan Li and
Shuoyan Tan and
Yiting Pan and
Huanxiang Liu and
Peng Gao and
Guotong Xie and
Xiaojun Yao},
title = {Improving drug-target affinity prediction via feature fusion and knowledge
distillation},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad145},
doi = {10.1093/BIB/BBAD145},
timestamp = {Tue, 22 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuWLLTPLGXY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuZJZ23,
author = {Haojie Lu and
Shuo Zhang and
Zhou Jiang and
Ping Zeng},
title = {Leveraging trans-ethnic genetic risk scores to improve association
power for complex traits in underrepresented populations},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad232},
doi = {10.1093/BIB/BBAD232},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuZJZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuZZLDW23,
author = {Chengqian Lu and
Lishen Zhang and
Min Zeng and
Wei Lan and
Guihua Duan and
Jianxin Wang},
title = {Inferring disease-associated circRNAs by multi-source aggregation
based on heterogeneous graph neural network},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac549},
doi = {10.1093/BIB/BBAC549},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuZZLDW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuZZNXL23,
author = {Qi Lu and
Ruihan Zhang and
Hongyuan Zhou and
Dongxuan Ni and
Weilie Xiao and
Jin Li},
title = {MetaHMEI: meta-learning for prediction of few-shot histone modifying
enzyme inhibitors},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad115},
doi = {10.1093/BIB/BBAD115},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuZZNXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoGCYZYL23,
author = {Junwei Luo and
Ting Guan and
Guolin Chen and
Zhonghua Yu and
Haixia Zhai and
Chaokun Yan and
Huimin Luo},
title = {{SLHSD:} hybrid scaffolding method based on short and long reads},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad169},
doi = {10.1093/BIB/BBAD169},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuoGCYZYL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoLPYMHHL23,
author = {Mengqi Luo and
Shangfu Li and
Yuxuan Pang and
Lantian Yao and
Renfei Ma and
Hsi{-}Yuan Huang and
Hsien{-}Da Huang and
Tzong{-}Yi Lee},
title = {Extraction of microRNA-target interaction sentences from biomedical
literature by deep learning approach},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac497},
doi = {10.1093/BIB/BBAC497},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuoLPYMHHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoWMZHTZ23,
author = {Yongchao Luo and
Panpan Wang and
Minjie Mou and
Hanqi Zheng and
Jiajun Hong and
Lin Tao and
Feng Zhu},
title = {A novel strategy for designing the magic shotguns for distantly related
target pairs},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac621},
doi = {10.1093/BIB/BBAC621},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuoWMZHTZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoWZCLZL23,
author = {Jiaqi Luo and
Xueying Wang and
Yiping Zou and
Lingxi Chen and
Wei Liu and
Wei Zhang and
Shuai Cheng Li},
title = {Quantitative annotations of T-Cell repertoire specificity},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad175},
doi = {10.1093/BIB/BBAD175},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuoWZCLZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Ma23,
author = {Shuangge Ma},
title = {Editorial},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad258},
doi = {10.1093/BIB/BBAD258},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Ma23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaLPLHL23,
author = {Renfei Ma and
Shangfu Li and
Luca Parisi and
Wenshuo Li and
Hsien{-}Da Huang and
Tzong{-}Yi Lee},
title = {Holistic similarity-based prediction of phosphorylation sites for
understudied kinases},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac624},
doi = {10.1093/BIB/BBAC624},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaLPLHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaSL23,
author = {Wentai Ma and
Leisheng Shi and
Mingkun Li},
title = {A fast and accurate method for SARS-CoV-2 genomic tracing},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad339},
doi = {10.1093/BIB/BBAD339},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MaSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaZ23,
author = {Yingjun Ma and
Junjiang Zhong},
title = {Logistic tensor decomposition with sparse subspace learning for prediction
of multiple disease types of human-virus protein-protein interactions},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac604},
doi = {10.1093/BIB/BBAC604},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MakrodimitrisPAR23,
author = {Stavros Makrodimitris and
Bram Pronk and
Tamim Abdelaal and
Marcel J. T. Reinders},
title = {An in-depth comparison of linear and non-linear joint embedding methods
for bulk and single-cell multi-omics},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad416},
doi = {10.1093/BIB/BBAD416},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MakrodimitrisPAR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MallickCMB23,
author = {Koushik Mallick and
Sikim Chakraborty and
Saurav Mallik and
Sanghamitra Bandyopadhyay},
title = {A scalable unsupervised learning of scRNAseq data detects rare cells
through integration of structure-preserving embedding, clustering
and outlier detection},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad125},
doi = {10.1093/BIB/BBAD125},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MallickCMB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MartinezEnguitaDJG23,
author = {David Mart{\'{\i}}nez{-}Enguita and
Sanjiv K. Dwivedi and
Rebecka J{\"{o}}rnsten and
Mika Gustafsson},
title = {{NCAE:} data-driven representations using a deep network-coherent
{DNA} methylation autoencoder identify robust disease and risk factor
signatures},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad293},
doi = {10.1093/BIB/BBAD293},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MartinezEnguitaDJG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MateosZZE23,
author = {Pablo Acera Mateos and
You Zhou and
Kathi Zarnack and
Eduardo Eyras},
title = {Concepts and methods for transcriptome-wide prediction of chemical
messenger {RNA} modifications with machine learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad163},
doi = {10.1093/BIB/BBAD163},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MateosZZE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/McGibbonSDGHXYSB23,
author = {Miles McGibbon and
Steven R. Shave and
Jie Dong and
Yumiao Gao and
Douglas R. Houston and
Jiancong Xie and
Yuedong Yang and
Philippe Schwaller and
Vincent Blay},
title = {From intuition to {AI:} evolution of small molecule representations
in drug discovery},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad422},
doi = {10.1093/BIB/BBAD422},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/McGibbonSDGHXYSB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MengGT23,
author = {Qiaozhen Meng and
Fei Guo and
Jijun Tang},
title = {Improved structure-related prediction for insufficient homologous
proteins using {MSA} enhancement and pre-trained language model},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad217},
doi = {10.1093/BIB/BBAD217},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MengGT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MengTHLF23,
author = {Guanqun Meng and
Wen Tang and
Emina Huang and
Ziyi Li and
Hao Feng},
title = {A comprehensive assessment of cell type-specific differential expression
methods in bulk data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac516},
doi = {10.1093/BIB/BBAC516},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MengTHLF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MengWXLTPZTY23,
author = {Yajie Meng and
Yi Wang and
Junlin Xu and
Changcheng Lu and
Xianfang Tang and
Tao Peng and
Ben{-}gong Zhang and
Geng Tian and
Jialiang Yang},
title = {Drug repositioning based on weighted local information augmented graph
neural network},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad431},
doi = {10.1093/BIB/BBAD431},
timestamp = {Wed, 14 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MengWXLTPZTY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MilanoC23,
author = {Marianna Milano and
Mario Cannataro},
title = {Network models in bioinformatics: modeling and analysis for complex
diseases},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad016},
doi = {10.1093/BIB/BBAD016},
timestamp = {Wed, 19 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MilanoC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MinadakisTDS23,
author = {George Minadakis and
Marios Tomazou and
Nikolas Dietis and
George M. Spyrou},
title = {Vir2Drug: a drug repurposing framework based on protein similarities
between pathogens},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac536},
doi = {10.1093/BIB/BBAC536},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MinadakisTDS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MingWYZTTL23,
author = {Yongfan Ming and
Wenkang Wang and
Rui Yin and
Min Zeng and
Li Tang and
Shizhe Tang and
Min Li},
title = {A review of enzyme design in catalytic stability by artificial intelligence},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad065},
doi = {10.1093/BIB/BBAD065},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MingWYZTTL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MochizukiSTNTKN23,
author = {Takako Mochizuki and
Mika Sakamoto and
Yasuhiro Tanizawa and
Takuro Nakayama and
Goro Tanifuji and
Ryoma Kamikawa and
Yasukazu Nakamura},
title = {A practical assembly guideline for genomes with various levels of
heterozygosity},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad337},
doi = {10.1093/BIB/BBAD337},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MochizukiSTNTKN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MolinPGBBMKBB23,
author = {Anna Dal Molin and
Caterina Tretti Parenzan and
Enrico Gaffo and
Cristina Borin and
Elena Boldrin and
Lueder H. Meyer and
Geertruij te Kronnie and
Silvia Bresolin and
Stefania Bortoluzzi},
title = {Discovery of fusion circular RNAs in leukemia with \emph{KMT2A::AFF1}
rearrangements by the new software CircFusion},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac589},
doi = {10.1093/BIB/BBAC589},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MolinPGBBMKBB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MoutsopoulosWM23,
author = {Ilias Moutsopoulos and
Eleanor C. Williams and
Irina Mohorianu},
title = {bulkAnalyseR: an accessible, interactive pipeline for analysing and
sharing bulk multi-modal sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac591},
doi = {10.1093/BIB/BBAC591},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MoutsopoulosWM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MukherjeeRHMB23,
author = {Sumit Mukherjee and
Matan Drory Retwitzer and
Sara M. Hubbell and
Michelle M. Meyer and
Danny Barash},
title = {A computational approach for the identification of distant homologs
of bacterial riboswitches based on inverse {RNA} folding},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad110},
doi = {10.1093/BIB/BBAD110},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MukherjeeRHMB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MusilJHBKDB23,
author = {Milos Musil and
Andrej Jezik and
Jana Horackova and
Simeon Borko and
Petr Kabourek and
Jir{\'{\i}} Damborsk{\'{y}} and
David Bednar},
title = {FireProt 2.0: web-based platform for the fully automated design of
thermostable proteins},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad425},
doi = {10.1093/BIB/BBAD425},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MusilJHBKDB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NakamuraMZWHCS23,
author = {Andrew Nakamura and
Hanze Meng and
Minglei Zhao and
Fengbin Wang and
Jie Hou and
Renzhi Cao and
Dong Si},
title = {Fast and automated protein-DNA/RNA macromolecular complex modeling
from cryo-EM maps},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac632},
doi = {10.1093/BIB/BBAC632},
timestamp = {Tue, 27 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NakamuraMZWHCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NazzariHHRCKC23,
author = {Marta Nazzari and
Duncan Hauser and
Marcel van Herwijnen and
M{\'{\i}}rian Romitti and
Daniel J. Carvalho and
Anna M. Kip and
Florian Caiment},
title = {{CODA:} a combo-Seq data analysis workflow},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac582},
doi = {10.1093/BIB/BBAC582},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NazzariHHRCKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NguyenVM23,
author = {An{-}phi Nguyen and
Stefania Vasilaki and
Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez},
title = {{FLAN:} feature-wise latent additive neural models for biological
applications},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad056},
doi = {10.1093/BIB/BBAD056},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NguyenVM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NingZGCLLY23,
author = {Qiao Ning and
Yaomiao Zhao and
Jun Gao and
Chen Chen and
Xiang Li and
Tingting Li and
Minghao Yin},
title = {{AMHMDA:} attention aware multi-view similarity networks and hypergraph
learning for miRNA-disease associations identification},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad094},
doi = {10.1093/BIB/BBAD094},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NingZGCLLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NiuLTLZZTWLLWZ23,
author = {Qikai Niu and
Hongtao Li and
Lin Tong and
Sihong Liu and
Wenjing Zong and
Siqi Zhang and
Siwei Tian and
Jingai Wang and
Jun Liu and
Bing Li and
Zhong Wang and
Huamin Zhang},
title = {{TCMFP:} a novel herbal formula prediction method based on network
target's score integrated with semi-supervised learning genetic algorithms},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad102},
doi = {10.1093/BIB/BBAD102},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NiuLTLZZTWLLWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NoorAAQQ23,
author = {Fatima Noor and
Muhammad Asif and
Usman Ali Ashfaq and
Muhammad Qasim and
Muhammad Tahir Ul Qamar},
title = {Machine learning for synergistic network pharmacology: a comprehensive
overview},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad120},
doi = {10.1093/BIB/BBAD120},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NoorAAQQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NourbakhshSTCCOTP23,
author = {Mona Nourbakhsh and
Astrid Saksager and
Nikola Tom and
Xi Steven Chen and
Antonio Colaprico and
Catharina Olsen and
Matteo Tiberti and
Elena Papaleo},
title = {A workflow to study mechanistic indicators for driver gene prediction
with Moonlight},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad274},
doi = {10.1093/BIB/BBAD274},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NourbakhshSTCCOTP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/OellerKBASV23,
author = {Marc Oeller and
Ryan Kang and
Rosie Bell and
Hannes Ausserw{\"{o}}ger and
Pietro Sormanni and
Michele Vendruscolo},
title = {Sequence-based prediction of pH-dependent protein solubility using
CamSol},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad004},
doi = {10.1093/BIB/BBAD004},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/OellerKBASV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/OrozcoAriasLCAJPTIG23,
author = {Simon Orozco{-}Arias and
Luis Humberto L{\'{o}}pez{-}Murillo and
Mariana S. Candamil{-}Cortes and
Maradey Arias and
Paula A. Jaimes and
Alexandre Rossi Paschoal and
Reinel Tabares{-}Soto and
Gustavo A. Isaza and
Romain Guyot},
title = {Inpactor2: a software based on deep learning to identify and classify
LTR-retrotransposons in plant genomes},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac511},
doi = {10.1093/BIB/BBAC511},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/OrozcoAriasLCAJPTIG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/OzdilekAOAADR23,
author = {A Samet {\"{O}}zdilek and
Ahmet Atakan and
G{\"{o}}khan {\"{O}}zsari and
Aybar C. Acar and
M. Volkan Atalay and
Tunca Dogan and
Ahmet S{\"{u}}reyya Rifaioglu},
title = {ProFAB - open protein functional annotation benchmark},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac627},
doi = {10.1093/BIB/BBAC627},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/OzdilekAOAADR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PaisSCBABGMC23,
author = {Giulia Pais and
Giulio Spinozzi and
Daniela Cesana and
Fabrizio Benedicenti and
Alessandra Albertini and
Maria Ester Bernardo and
Bernhard Gentner and
Eugenio Montini and
Andrea Calabria},
title = {ISAnalytics enables longitudinal and high-throughput clonal tracking
studies in hematopoietic stem cell gene therapy applications},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac551},
doi = {10.1093/BIB/BBAC551},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PaisSCBABGMC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PakLSKK23,
author = {Minwoo Pak and
Sangseon Lee and
Inyoung Sung and
Bonil Koo and
Sun Kim},
title = {Improved drug response prediction by drug target data integration
via network-based profiling},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad034},
doi = {10.1093/BIB/BBAD034},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PakLSKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PanAGJSWHSY23,
author = {Xingxin Pan and
Zeynep H. Coban Akdemir and
Ruixuan Gao and
Xiaoqian Jiang and
Gloria M. Sheynkman and
Erxi Wu and
Jason H. Huang and
Nidhi Sahni and
S. Stephen Yi},
title = {AD-Syn-Net: systematic identification of Alzheimer's disease-associated
mutation and co-mutation vulnerabilities via deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad030},
doi = {10.1093/BIB/BBAD030},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PanAGJSWHSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PanJZ23,
author = {Shuheng Pan and
Xinyi Jiang and
Kai Zhang},
title = {{WSGMB:} weight signed graph neural network for microbial biomarker
identification},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad448},
doi = {10.1093/BIB/BBAD448},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/PanJZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PanPNA23,
author = {Qisheng Pan and
Stephanie Portelli and
Thanh{-}Binh Nguyen and
David B. Ascher},
title = {Characterization on the oncogenic effect of the missense mutations
of p53 via machine learning},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad428},
doi = {10.1093/BIB/BBAD428},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/PanPNA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PanRHR23,
author = {Chenxu Pan and
Ren{\'{e}} Rahn and
David Heller and
Knut Reinert},
title = {Linear: a framework to enable existing software to resolve structural
variants in long reads with flexible and efficient alignment-free
statistical models},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad071},
doi = {10.1093/BIB/BBAD071},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/PanRHR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PanYYZFZRMWWS23,
author = {Jie Pan and
Zhuhong You and
Wencai You and
Tian Zhao and
Chenlu Feng and
Xuexia Zhang and
Fengzhi Ren and
Sanxing Ma and
Fan Wu and
Shiwei Wang and
Yanmei Sun},
title = {{PTBGRP:} predicting phage-bacteria interactions with graph representation
learning on microbial heterogeneous information network},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad328},
doi = {10.1093/BIB/BBAD328},
timestamp = {Thu, 11 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PanYYZFZRMWWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PangLDYCX23,
author = {Jiali Pang and
Bilin Liang and
Ruifeng Ding and
Qiujuan Yan and
Ruiyao Chen and
Jie Xu},
title = {A denoised multi-omics integration framework for cancer subtype classification
and survival prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad304},
doi = {10.1093/BIB/BBAD304},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PangLDYCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ParkBPYC23,
author = {Musun Park and
Su{-}Jin Baek and
Sang{-}Min Park and
Jin{-}Mu Yi and
Seongwon Cha},
title = {Comparative study of the mechanism of natural compounds with similar
structures using docking and transcriptome data for improving \emph{in
silico} herbal medicine experimentations},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad344},
doi = {10.1093/BIB/BBAD344},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ParkBPYC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ParsaniaCSMDW23,
author = {Chirag Parsania and
Ruiwen Chen and
Pooja Sethiya and
Zhengqiang Miao and
Liguo Dong and
Koon Ho Wong},
title = {FungiExpresZ: an intuitive package for fungal gene expression data
analysis, visualization and discovery},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad051},
doi = {10.1093/BIB/BBAD051},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ParsaniaCSMDW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PatiyalDBSR23,
author = {Sumeet Patiyal and
Anjali Dhall and
Khushboo Bajaj and
Harshita Sahu and
Gajendra P. S. Raghava},
title = {Prediction of RNA-interacting residues in a protein using {CNN} and
evolutionary profile},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac538},
doi = {10.1093/BIB/BBAC538},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PatiyalDBSR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PengLMZK23,
author = {Zhenling Peng and
Zixia Li and
Qiaozhen Meng and
Bi Zhao and
Lukasz A. Kurgan},
title = {{CLIP:} accurate prediction of disordered linear interacting peptides
from protein sequences using co-evolutionary information},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac502},
doi = {10.1093/BIB/BBAC502},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/PengLMZK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PengLZKS23,
author = {Xiaoqing Peng and
Yiming Li and
Mengxi Zou and
Xiangyan Kong and
Yu Sheng},
title = {{CATAD:} exploring topologically associating domains from an insight
of core-attachment structure},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad204},
doi = {10.1093/BIB/BBAD204},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PengLZKS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PengNCVPMNHKMBNPABARM23,
author = {Kerui Peng and
Theodore S. Nowicki and
Katie Campbell and
Mohammad Vahed and
Dandan Peng and
Yiting Meng and
Anish Nagareddy and
Yu{-}Ning Huang and
Aaron Karlsberg and
Zachary Miller and
Jaqueline J. Brito and
Brian B. Nadel and
Victoria M. Pak and
Malak S. Abedalthagafi and
Amanda M. Burkhardt and
Houda Alachkar and
Antoni Ribas and
Serghei Mangul},
title = {Rigorous benchmarking of T-cell receptor repertoire profiling methods
for cancer {RNA} sequencing},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad220},
doi = {10.1093/BIB/BBAD220},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PengNCVPMNHKMBNPABARM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PhamPSKSLJM23,
author = {Nhat Truong Pham and
Le Thi Phan and
Jimin Seo and
Yeonwoo Kim and
Minkyung Song and
Sukchan Lee and
Young{-}Jun Jeon and
Balachandran Manavalan},
title = {Advancing the accuracy of SARS-CoV-2 phosphorylation site detection
via meta-learning approach},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad433},
doi = {10.1093/BIB/BBAD433},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/PhamPSKSLJM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PradhanMNPGP23,
author = {Upendra Kumar Pradhan and
Prabina Kumar Meher and
Sanchita Naha and
Soumen Pal and
Ajit Gupta and
Rajender Parsad},
title = {P\emph{l}DBPred: a novel computational model for discovery of {DNA}
binding proteins in plants},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac483},
doi = {10.1093/BIB/BBAC483},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PradhanMNPGP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PrakashB23,
author = {Anil Prakash and
Moinak Banerjee},
title = {An interpretable block-attention network for identifying regulatory
feature interactions},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad250},
doi = {10.1093/BIB/BBAD250},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PrakashB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PuWLCL23,
author = {Juhua Pu and
Bingchen Wang and
Xingwu Liu and
Lingxi Chen and
Shuai Cheng Li},
title = {{SMURF:} embedding single-cell RNA-seq data with matrix factorization
preserving self-consistency},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad026},
doi = {10.1093/BIB/BBAD026},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PuWLCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/QianHTX23,
author = {Hao Qian and
Wenjing Huang and
Shikui Tu and
Lei Xu},
title = {KGDiff: towards explainable target-aware molecule generation with
knowledge guidance},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad435},
doi = {10.1093/BIB/BBAD435},
timestamp = {Mon, 01 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/QianHTX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/QianSWFCTLZZYOC23,
author = {Sheng Hu Qian and
Meng{-}Wei Shi and
Dan{-}Yang Wang and
Justin M. Fear and
Lu Chen and
Yi{-}Xuan Tu and
Hong{-}Shan Liu and
Yuan Zhang and
Shuai{-}Jie Zhang and
Shan{-}Shan Yu and
Brian Oliver and
Zhen{-}Xia Chen},
title = {Integrating massive RNA-seq data to elucidate transcriptome dynamics
in \emph{Drosophila melanogaster}},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad177},
doi = {10.1093/BIB/BBAD177},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/QianSWFCTLZZYOC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/QiuW23,
author = {Yuchi Qiu and
Guo{-}Wei Wei},
title = {Artificial intelligence-aided protein engineering: from topological
data analysis to deep protein language models},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad289},
doi = {10.1093/BIB/BBAD289},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/QiuW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/QiuYZZ23,
author = {Yushan Qiu and
Chang Yan and
Pu Zhao and
Quan Zou},
title = {{SSNMDI:} a novel joint learning model of semi-supervised non-negative
matrix factorization and data imputation for clustering of single-cell
RNA-seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad149},
doi = {10.1093/BIB/BBAD149},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/QiuYZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RaffoP23,
author = {Andrea Raffo and
Jonas Paulsen},
title = {The shape of chromatin: insights from computational recognition of
geometric patterns in Hi-C data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad302},
doi = {10.1093/BIB/BBAD302},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/RaffoP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RebolledoSSM23,
author = {Camilo Rebolledo and
Juan Pablo Silva and
Nicol{\'{a}}s Saavedra and
Vinicius Maracaja{-}Coutinho},
title = {Computational approaches for circRNAs prediction and \emph{in silico}
characterization},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad154},
doi = {10.1093/BIB/BBAD154},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/RebolledoSSM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RhrissorrakraiULP23,
author = {Kahn Rhrissorrakrai and
Filippo Utro and
Chaya Levovitz and
Laxmi Parida},
title = {Lesion Shedding Model: unraveling site-specific contributions to ctDNA},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad059},
doi = {10.1093/BIB/BBAD059},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/RhrissorrakraiULP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RomagnoliNGPLBFPSMDMBMB23,
author = {Dario Romagnoli and
Agostina Nardone and
Francesca Galardi and
Marta Paoli and
Francesca De Luca and
Chiara Biagioni and
Gian Marco Franceschini and
Marta Pestrin and
Giuseppina Sanna and
Erica Moretti and
Francesca Demichelis and
Ilenia Migliaccio and
Laura Biganzoli and
Luca Malorni and
Matteo Benelli},
title = {{MIMESIS:} minimal DNA-methylation signatures to quantify and classify
tumor signals in tissue and cell-free {DNA} samples},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad015},
doi = {10.1093/BIB/BBAD015},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/RomagnoliNGPLBFPSMDMBMB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RoseKFKLP23,
author = {Tim D. Rose and
Nikolai K{\"{o}}hler and
Lisa Falk and
Lucie Klischat and
Olga Lazareva and
Josch Konstantin Pauling},
title = {Lipid network and moiety analysis for revealing enzymatic dysregulation
and mechanistic alterations from lipidomics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac572},
doi = {10.1093/BIB/BBAC572},
timestamp = {Tue, 09 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/RoseKFKLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RuWSYQM23,
author = {Zhongying Ru and
Yangyang Wu and
Jinning Shao and
Jianwei Yin and
Linghui Qian and
Xiaoye Miao},
title = {A dual-modal graph learning framework for identifying interaction
events among chemical and biotech drugs},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad271},
doi = {10.1093/BIB/BBAD271},
timestamp = {Fri, 10 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/RuWSYQM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RuanJLLLHL23,
author = {Xinru Ruan and
Changzhi Jiang and
Peixuan Lin and
Yuan Lin and
Juan Liu and
Shaohui Huang and
Xiangrong Liu},
title = {{MSGCL:} inferring miRNA-disease associations based on multi-view
self-supervised graph structure contrastive learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac623},
doi = {10.1093/BIB/BBAC623},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/RuanJLLLHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RuizREBEAMGO23,
author = {Jos{\'{e}} Luis Ruiz and
Susanne Reimering and
Juan David Escobar{-}Prieto and
Nicolas M. B. Brancucci and
Diego F. Echeverry and
Abdirahman I Abdi and
Matthias Marti and
Elena G{\'{o}}mez{-}D{\'{\i}}az and
Thomas D. Otto},
title = {From contigs towards chromosomes: automatic improvement of long read
assemblies {(ILRA)}},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad248},
doi = {10.1093/BIB/BBAD248},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/RuizREBEAMGO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SatoH23,
author = {Kengo Sato and
Michiaki Hamada},
title = {Recent trends in {RNA} informatics: a review of machine learning and
deep learning for {RNA} secondary structure prediction and {RNA} drug
discovery},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad186},
doi = {10.1093/BIB/BBAD186},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SatoH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ScottBoyerDBOPPD23,
author = {Marie{-}Pier Scott{-}Boyer and
Pascal Dufour and
Fran{\c{c}}ois Belleau and
R{\'{e}}gis Ongaro{-}Carcy and
Cl{\'{e}}ment Plessis and
Olivier P{\'{e}}rin and
Arnaud Droit},
title = {Use of Elasticsearch-based business intelligence tools for integration
and visualization of biological data},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad348},
doi = {10.1093/BIB/BBAD348},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ScottBoyerDBOPPD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SebastianRK23,
author = {Softya Sebastian and
Swarup Roy and
Jugal Kalita},
title = {A generic parallel framework for inferring large-scale gene regulatory
networks from expression profiles: application to Alzheimer's disease
network},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac482},
doi = {10.1093/BIB/BBAC482},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SebastianRK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ShangTS23,
author = {Jiayu Shang and
Xubo Tang and
Yanni Sun},
title = {PhaTYP: predicting the lifestyle for bacteriophages using {BERT}},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac487},
doi = {10.1093/BIB/BBAC487},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ShangTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ShaoYLMLYCLH23,
author = {Mengjie Shao and
Nanjiao Ying and
Qian Liang and
Nan Ma and
Sebastian Leptihn and
Yunsong Yu and
Huan Chen and
Chengzhi Liu and
Xiaoting Hua},
title = {P\emph{dif}-mediated antibiotic resistance genes transfer in bacteria
identified by pdifFinder},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac521},
doi = {10.1093/BIB/BBAC521},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ShaoYLMLYCLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SharmaPDBS23,
author = {Harsh Sharma and
Trishna Pani and
Ujjaini Dasgupta and
Jyotsna Batra and
Ravi Datta Sharma},
title = {Prediction of transcript structure and concentration using RNA-Seq
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad022},
doi = {10.1093/BIB/BBAD022},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SharmaPDBS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ShenDSZQS23,
author = {Ke Shen and
Ahmad Ud Din and
Baivab Sinha and
Yi Zhou and
Fuliang Qian and
Bairong Shen},
title = {Translational informatics for human microbiota: data resources, models
and applications},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad168},
doi = {10.1093/BIB/BBAD168},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ShenDSZQS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ShenFLLML23,
author = {Bihan Shen and
Fangyoumin Feng and
Kunshi Li and
Ping Lin and
Liangxiao Ma and
Hong Li},
title = {A systematic assessment of deep learning methods for drug response
prediction: from in vitro to clinical applications},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac605},
doi = {10.1093/BIB/BBAC605},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ShenFLLML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ShengWHGCXF23,
author = {Nan Sheng and
Yan Wang and
Lan Huang and
Ling Gao and
Yangkun Cao and
Xuping Xie and
Yuan Fu},
title = {Multi-task prediction-based graph contrastive learning for inferring
the relationship among lncRNAs, miRNAs and diseases},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad276},
doi = {10.1093/BIB/BBAD276},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ShengWHGCXF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ShengWLQLGCH23,
author = {Yuqi Sheng and
Jiashuo Wu and
Xiangmei Li and
Jiayue Qiu and
Ji Li and
Qinyu Ge and
Liang Cheng and
Junwei Han},
title = {iATMEcell: identification of abnormal tumor microenvironment cells
to predict the clinical outcomes in cancer based on cell-cell crosstalk
network},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad074},
doi = {10.1093/BIB/BBAD074},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ShengWLQLGCH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SherkatghanadACM23,
author = {Zeinab Sherkatghanad and
Moloud Abdar and
J{\'{e}}r{\'{e}}my Charlier and
Vladimir Makarenkov},
title = {Using traditional machine learning and deep learning methods for on-
and off-target prediction in CRISPR/Cas9: a review},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad131},
doi = {10.1093/BIB/BBAD131},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SherkatghanadACM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ShiLLS23,
author = {Mingguang Shi and
Xuefeng Li and
Mingna Li and
Yichong Si},
title = {Attention-based generative adversarial networks improve prognostic
outcome prediction of cancer from multimodal data},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad329},
doi = {10.1093/BIB/BBAD329},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ShiLLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ShiZLL23,
author = {Xuejing Shi and
Juntong Zhu and
Yahui Long and
Cheng Liang},
title = {Identifying spatial domains of spatially resolved transcriptomics
via multi-view graph convolutional networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad278},
doi = {10.1093/BIB/BBAD278},
timestamp = {Mon, 23 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ShiZLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SiY23,
author = {Yunda Si and
Chengfei Yan},
title = {Improved inter-protein contact prediction using dimensional hybrid
residual networks and protein language models},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad039},
doi = {10.1093/BIB/BBAD039},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SiY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SilvaAP23,
author = {Bruna Moreira da Silva and
David B. Ascher and
Douglas E. V. Pires},
title = {epitope1D: accurate taxonomy-aware B-cell linear epitope prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad114},
doi = {10.1093/BIB/BBAD114},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SilvaAP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SongLJGWGCL23,
author = {Bo Song and
Hao Li and
Mengyun Jiang and
Zhongtian Gao and
Suikang Wang and
Lei Gao and
Yunsheng Chen and
Wujiao Li},
title = {slORFfinder: a tool to detect open reading frames resulting from \emph{trans}-splicing
of spliced leader sequences},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac610},
doi = {10.1093/BIB/BBAC610},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/SongLJGWGCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SongWWHNM23,
author = {Yiyou Song and
Yue Wang and
Xuan Wang and
Daiyun Huang and
Anh Nguyen and
Jia Meng},
title = {Multi-task adaptive pooling enabled synergetic learning of {RNA} modification
across tissue, type and species from low-resolution epitranscriptomes},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad105},
doi = {10.1093/BIB/BBAD105},
timestamp = {Mon, 27 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SongWWHNM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SongYCCZY23,
author = {Yidong Song and
Qianmu Yuan and
Sheng Chen and
Ken Chen and
Yaoqi Zhou and
Yuedong Yang},
title = {Fast and accurate protein intrinsic disorder prediction by using a
pretrained language model},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad173},
doi = {10.1093/BIB/BBAD173},
timestamp = {Wed, 21 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/SongYCCZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SongYZY23,
author = {Yidong Song and
Qianmu Yuan and
Huiying Zhao and
Yuedong Yang},
title = {Accurately identifying nucleic-acid-binding sites through geometric
graph learning on language model predicted structures},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad360},
doi = {10.1093/BIB/BBAD360},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SongYZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/StouracBKPDPMPSSSDB23,
author = {Jan Stourac and
Simeon Borko and
Rayyan T. Khan and
Petra Pokorna and
Adam Dobias and
Joan Planas{-}Iglesias and
Stanislav Mazurenko and
Gaspar R. P. Pinto and
Veronika Szotkowska and
Jaroslav Sterba and
Ondrej Slaby and
Jir{\'{\i}} Damborsk{\'{y}} and
David Bednar},
title = {PredictONCO: a web tool supporting decision-making in precision oncology
by extending the bioinformatics predictions with advanced computing
and machine learning},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad441},
doi = {10.1093/BIB/BBAD441},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/StouracBKPDPMPSSSDB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SuLWTZ23,
author = {Yansen Su and
Rongxin Lin and
Jing Wang and
Dayu Tan and
Chun{-}Hou Zheng},
title = {Denoising adaptive deep clustering with self-attention mechanism on
single-cell sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad021},
doi = {10.1093/BIB/BBAD021},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SuLWTZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SuWLLH23,
author = {Benzhe Su and
Weiwei Wang and
Xiaohui Lin and
Shenglan Liu and
Xin Huang},
title = {Identifying the potential miRNA biomarkers based on multi-view networks
and reinforcement learning for diseases},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad427},
doi = {10.1093/BIB/BBAD427},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/SuWLLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SubbaroyanSMS23,
author = {Ajay Subbaroyan and
Priyotosh Sil and
Olivier C. Martin and
Areejit Samal},
title = {Leveraging developmental landscapes for model selection in Boolean
gene regulatory networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad160},
doi = {10.1093/BIB/BBAD160},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SubbaroyanSMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SunKRGC23,
author = {Jianfeng Sun and
Arulsamy Kulandaisamy and
Jinlong Ru and
M. Michael Gromiha and
Adam P. Cribbs},
title = {TMKit: a Python interface for computational analysis of transmembrane
proteins},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad288},
doi = {10.1093/BIB/BBAD288},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SunKRGC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SunSCWTDZY23,
author = {Haoran Sun and
Zhaoqi Song and
Qiuming Chen and
Meiling Wang and
Furong Tang and
Lijun Dou and
Quan Zou and
Fenglong Yang},
title = {MMiKG: a knowledge graph-based platform for path mining of microbiota-mental
diseases interactions},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad340},
doi = {10.1093/BIB/BBAD340},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SunSCWTDZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SunWXHWHJ23,
author = {Han Sun and
Yue Wang and
Zhen Xiao and
Xiaoyun Huang and
Haodong Wang and
Tingting He and
Xingpeng Jiang},
title = {multiMiAT: an optimal microbiome-based association test for multicategory
phenotypes},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad012},
doi = {10.1093/BIB/BBAD012},
timestamp = {Thu, 28 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/SunWXHWHJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SunWZ23,
author = {Lei Sun and
Gongming Wang and
Zhihua Zhang},
title = {SimCH: simulation of single-cell {RNA} sequencing data by modeling
cellular heterogeneity at gene expression level},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac590},
doi = {10.1093/BIB/BBAC590},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/SunWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SusmeljRMGG23,
author = {Anna Klimovskaia Susmelj and
Yani Ren and
Yann Vander Meersche and
Jean{-}Christophe Gelly and
Tatiana Galochkina},
title = {Poincar{\'{e}} maps for visualization of large protein families},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad103},
doi = {10.1093/BIB/BBAD103},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SusmeljRMGG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SzulcMBS23,
author = {Natalia A Szulc and
Zuzanna Mackiewicz and
Janusz M. Bujnicki and
Filip Stefaniak},
title = {Structural interaction fingerprints and machine learning for predicting
and explaining binding of small molecule ligands to {RNA}},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad187},
doi = {10.1093/BIB/BBAD187},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SzulcMBS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TangLLZYSS23,
author = {Ziyang Tang and
Xiang Liu and
Zuotian Li and
Tonglin Zhang and
Baijian Yang and
Jing Su and
Qianqian Song},
title = {SpaRx: elucidate single-cell spatial heterogeneity of drug responses
for personalized treatment},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad338},
doi = {10.1093/BIB/BBAD338},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TangLLZYSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TangYYZFZZWLLZ23,
author = {Zhenshuang Tang and
Lilin Yin and
Dong Yin and
Haohao Zhang and
Yuhua Fu and
Guangliang Zhou and
Yunxiang Zhao and
Zhiquan Wang and
Xiaolei Liu and
Xinyun Li and
Shuhong Zhao},
title = {Development and application of an efficient genomic mating method
to maximize the production performances of three-way crossbred pigs},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac587},
doi = {10.1093/BIB/BBAC587},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/TangYYZFZZWLLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TangZLPZYZ23,
author = {Tao Tang and
Xiaocai Zhang and
Yuansheng Liu and
Hui Peng and
Binshuang Zheng and
Yanlin Yin and
Xiangxiang Zeng},
title = {Machine learning on protein-protein interaction prediction: models,
challenges and trends},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad076},
doi = {10.1093/BIB/BBAD076},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/TangZLPZYZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TangZYSS23,
author = {Ziyang Tang and
Tonglin Zhang and
Baijian Yang and
Jing Su and
Qianqian Song},
title = {spaCI: deciphering spatial cellular communications through adaptive
graph model},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac563},
doi = {10.1093/BIB/BBAC563},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TangZYSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TaoWWWZNWWCDCL23,
author = {Ziyu Tao and
Shixiang Wang and
Chenxu Wu and
Tao Wu and
Xiangyu Zhao and
Wei Ning and
Guangshuai Wang and
Jinyu Wang and
Jing Chen and
Kaixuan Diao and
Fuxiang Chen and
Xue{-}Song Liu},
title = {The repertoire of copy number alteration signatures in human cancer},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad053},
doi = {10.1093/BIB/BBAD053},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TaoWWWZNWWCDCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TeitzSSF23,
author = {Joshua Teitz and
J{\"{o}}rg Sander and
Hassan Sarker and
Carlos Fernandez{-}Patron},
title = {Potential of dissimilarity measure-based computation of protein thermal
stability data for determining protein interactions},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad143},
doi = {10.1093/BIB/BBAD143},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TeitzSSF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianLXZZLXLZZ23,
author = {Saisai Tian and
Yanan Li and
Jia Xu and
Lijun Zhang and
Jinbo Zhang and
Jinyuan Lu and
Xike Xu and
Xin Luan and
Jing Zhao and
Weidong Zhang},
title = {{COIMMR:} a computational framework to reveal the contribution of
herbal ingredients against human cancer via immune microenvironment
and metabolic reprogramming},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad346},
doi = {10.1093/BIB/BBAD346},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/TianLXZZLXLZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianWYLY23,
author = {Yanan Tian and
Xiaorui Wang and
Xiaojun Yao and
Huanxiang Liu and
Ying Yang},
title = {Predicting molecular properties based on the interpretable graph neural
network with multistep focus mechanism},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac534},
doi = {10.1093/BIB/BBAC534},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/TianWYLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianXXTT23,
author = {Lejin Tian and
Yunxiao Xie and
Zhaobin Xie and
Jasmine Tian and
Weidong Tian},
title = {AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad268},
doi = {10.1093/BIB/BBAD268},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TianXXTT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianY23,
author = {Leqi Tian and
Tianwei Yu},
title = {An integrated deep learning framework for the interpretation of untargeted
metabolomics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad244},
doi = {10.1093/BIB/BBAD244},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TianY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianYFXG23,
author = {Zhen Tian and
Yue Yu and
Haichuan Fang and
Weixin Xie and
Maozu Guo},
title = {Predicting microbe-drug associations with structure-enhanced contrastive
learning and self-paced negative sampling strategy},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac634},
doi = {10.1093/BIB/BBAC634},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TianYFXG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianZYWLWFFYZZZ23,
author = {Saisai Tian and
Jinbo Zhang and
Shunling Yuan and
Qun Wang and
Chao Lv and
Jinxing Wang and
Jiansong Fang and
Lu Fu and
Jian Yang and
Xianpeng Zu and
Jing Zhao and
Weidong Zhang},
title = {Exploring pharmacological active ingredients of traditional Chinese
medicine by pharmacotranscriptomic map in {ITCM}},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad027},
doi = {10.1093/BIB/BBAD027},
timestamp = {Thu, 11 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TianZYWLWFFYZZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TiengZSMLM23,
author = {Francis Yew Fu Tieng and
Muhammad Redha Abdullah Zawawi and
Nur Alyaa Afifah Md Shahri and
Zeti{-}Azura Mohamed{-}Hussein and
Learn{-}Han Lee and
Nurul{-}Syakima Ab Mutalib},
title = {A Hitchhiker's guide to {RNA-RNA} structure and interaction prediction
tools},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad421},
doi = {10.1093/BIB/BBAD421},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TiengZSMLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TippenhauerPLS23,
author = {Kevin Tippenhauer and
Marwin Philips and
Carlo R. Largiad{\`{e}}r and
Murat Sariyar},
title = {Using the PharmCAT tool for Pharmacogenetic clinical decision support},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad452},
doi = {10.1093/BIB/BBAD452},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/TippenhauerPLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TognonGP23,
author = {Manuel Tognon and
Rosalba Giugno and
Luca Pinello},
title = {A survey on algorithms to characterize transcription factor binding
sites},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad156},
doi = {10.1093/BIB/BBAD156},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TognonGP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TongLYSZXTLLHY23,
author = {Mengsha Tong and
Yuxiang Lin and
Wenxian Yang and
Jinsheng Song and
Zheyang Zhang and
Jiajing Xie and
Jingyi Tian and
Shijie Luo and
Chenyu Liang and
Jialiang Huang and
Rongshan Yu},
title = {Prioritizing prognostic-associated subpopulations and individualized
recurrence risk signatures from single-cell transcriptomes of colorectal
cancer},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad078},
doi = {10.1093/BIB/BBAD078},
timestamp = {Sun, 06 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TongLYSZXTLLHY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ToroDominguezMMLCBGPCA23,
author = {Daniel Toro{-}Dom{\'{\i}}nguez and
Jordi Martorell{-}Marugan and
Manuel Mart{\'{\i}}nez{-}Bueno and
Ra{\'{u}}l L{\'{o}}pez{-}Dom{\'{\i}}nguez and
Elena Carnero{-}Montoro and
Guillermo Barturen and
Daniel Goldman and
Michelle Petri and
Pedro Carmona{-}Saez and
Marta E. Alarc{\'{o}}n{-}Riquelme},
title = {Response to the letter 'testing the effectiveness of MyPROSLE in classifying
patients with lupus nephritis'},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad454},
doi = {10.1093/BIB/BBAD454},
timestamp = {Fri, 26 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ToroDominguezMMLCBGPCA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ToseefPWRLLW23,
author = {Muhammad Toseef and
Olutomilayo Olayemi Petinrin and
Fuzhou Wang and
Saifur Rahaman and
Zhe Liu and
Xiangtao Li and
Ka{-}Chun Wong},
title = {Deep transfer learning for clinical decision-making based on high-throughput
data: comprehensive survey with benchmark results},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad254},
doi = {10.1093/BIB/BBAD254},
timestamp = {Wed, 24 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ToseefPWRLLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TrinidadVCECNGHM23,
author = {Eva Mar{\'{\i}}a Trinidad and
Enrique Vidal and
Esther Coronado and
Anna Esteve{-}Codina and
Victoria Castel and
Adela Ca{\~{n}}ete Nieto and
Marta Gut and
Simon Heath and
Jaime Font de Mora},
title = {Liquidhope: methylome and genomic profiling from very limited quantities
of plasma-derived {DNA}},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac575},
doi = {10.1093/BIB/BBAC575},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/TrinidadVCECNGHM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TuJH23,
author = {Yueh{-}Hua Tu and
Hsueh{-}Fen Juan and
Hsuan{-}Cheng Huang},
title = {Context-dependent gene regulatory network reveals regulation dynamics
and cell trajectories using unspliced transcripts},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac633},
doi = {10.1093/BIB/BBAC633},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TuJH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TurzoSLL23,
author = {S. M. Bargeen Alam Turzo and
Justin T. Seffernick and
Sergey Lyskov and
Steffen Lindert},
title = {Predicting ion mobility collision cross sections using projection
approximation with {ROSIE-PARCS} webserver},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad308},
doi = {10.1093/BIB/BBAD308},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TurzoSLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ValizadehAslaniSRWZHZL23,
author = {Taha ValizadehAslani and
Yiwen Shi and
Ping Ren and
Jing Wang and
Yi Zhang and
Meng Hu and
Liang Zhao and
Hualou Liang},
title = {PharmBERT: a domain-specific {BERT} model for drug labels},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad226},
doi = {10.1093/BIB/BBAD226},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ValizadehAslaniSRWZHZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Wang23,
author = {Kai Wang},
title = {{GPDOCK:} highly accurate docking strategy for metalloproteins based
on geometric probability},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac620},
doi = {10.1093/BIB/BBAC620},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/Wang23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangC23,
author = {Wengang Wang and
Hailin Chen},
title = {Predicting miRNA-disease associations based on lncRNA-miRNA interactions
and graph convolution networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac495},
doi = {10.1093/BIB/BBAC495},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangC23a,
author = {Yiwen Wang and
Kim{-}Anh L{\^{e}} Cao},
title = {PLSDA-batch: a multivariate framework to correct for batch effects
in microbiome data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac622},
doi = {10.1093/BIB/BBAC622},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangC23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangCHL23,
author = {Rulan Wang and
Chia{-}Ru Chung and
Hsien{-}Da Huang and
Tzong{-}Yi Lee},
title = {Identification of species-specific {RNA} N6-methyladinosine modification
sites from {RNA} sequences},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac573},
doi = {10.1093/BIB/BBAC573},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangCHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangCWGY23,
author = {Jun Wang and
Xi Chen and
Zhengtian Wu and
Maozu Guo and
Guoxian Yu},
title = {Cooperative driver pathways discovery by multiplex network embedding},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad112},
doi = {10.1093/BIB/BBAD112},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangCWGY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangDWL23,
author = {Xiao Wang and
Zhao{-}Yuan Ding and
Rong Wang and
Xi Lin},
title = {Deepro-Glu: combination of convolutional neural network and Bi-LSTM
models using ProtBert and handcrafted features to identify lysine
glutarylation sites},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac631},
doi = {10.1093/BIB/BBAC631},
timestamp = {Thu, 23 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangDWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangDWWLHBP23,
author = {Hong Wang and
Chong Dai and
Yuqi Wen and
Xiaoqi Wang and
Wenjuan Liu and
Song He and
Xiaochen Bo and
Shaoliang Peng},
title = {{GADRP:} graph convolutional networks and autoencoders for cancer
drug response prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac501},
doi = {10.1093/BIB/BBAC501},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangDWWLHBP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangDZLCWWW23,
author = {Zhongyu Wang and
Zhaohong Deng and
Wei Zhang and
Qiongdan Lou and
Kup{-}Sze Choi and
Zhisheng Wei and
Lei Wang and
Jing Wu},
title = {MMSMAPlus: a multi-view multi-scale multi-attention embedding model
for protein function prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad201},
doi = {10.1093/BIB/BBAD201},
timestamp = {Thu, 28 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangDZLCWWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangFLLWSHL23,
author = {Zhen Wang and
Zheng Feng and
Yanjun Li and
Bowen Li and
Yongrui Wang and
Chulin Sha and
Min He and
Xiaolin Li},
title = {BatmanNet: bi-branch masked graph transformer autoencoder for molecular
representation},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad400},
doi = {10.1093/BIB/BBAD400},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangFLLWSHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangGWL23,
author = {Xin Wang and
Xin Gao and
Guohua Wang and
Dan Li},
title = {miProBERT: identification of microRNA promoters based on the pre-trained
model {BERT}},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad093},
doi = {10.1093/BIB/BBAD093},
timestamp = {Wed, 12 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangGWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangHCW23,
author = {Jun Wang and
Marc Horlacher and
Lixin Cheng and
Ole Winther},
title = {{RNA} trafficking and subcellular localization - a review of mechanisms,
experimental and predictive methodologies},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad249},
doi = {10.1093/BIB/BBAD249},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangHCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangHDLWTL23,
author = {Yimeng Wang and
Mengting Huang and
Hua Deng and
Weihua Li and
Zengrui Wu and
Yun Tang and
Guixia Liu},
title = {Identification of vital chemical information via visualization of
graph neural networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac577},
doi = {10.1093/BIB/BBAC577},
timestamp = {Tue, 27 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangHDLWTL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangHELX23,
author = {Robert Wang and
Ingo Helbig and
Andrew C. Edmondson and
Lan Lin and
Yi Xing},
title = {Splicing defects in rare diseases: transcriptomics and machine learning
strategies towards genetic diagnosis},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad284},
doi = {10.1093/BIB/BBAD284},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangHELX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangHGC23,
author = {Qingyong Wang and
Minfan He and
Long{-}Yi Guo and
Hua Chai},
title = {{AFEI:} adaptive optimized vertical federated learning for heterogeneous
multi-omics data integration},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad269},
doi = {10.1093/BIB/BBAD269},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangHGC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangHWC23,
author = {Xiao Wang and
Lijun Han and
Rong Wang and
Haoran Chen},
title = {DaDL-SChlo: protein subchloroplast localization prediction based on
generative adversarial networks and pre-trained protein language model},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad083},
doi = {10.1093/BIB/BBAD083},
timestamp = {Thu, 23 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangHWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangHWXW23,
author = {Lei Wang and
Chen Huang and
Mingxia Wang and
Zhidong Xue and
Yan Wang},
title = {NeuroPred-PLM: an interpretable and robust model for neuropeptide
prediction by protein language model},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad077},
doi = {10.1093/BIB/BBAD077},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangHWXW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangKL23,
author = {Meng Wang and
Lukasz A. Kurgan and
Min Li},
title = {A comprehensive assessment and comparison of tools for {HLA} class
{I} peptide-binding prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad150},
doi = {10.1093/BIB/BBAD150},
timestamp = {Tue, 11 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangKL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLLMWL23,
author = {Zixiao Wang and
Shiyang Liang and
Siwei Liu and
Zhaohan Meng and
Jingjie Wang and
Shangsong Liang},
title = {Sequence pre-training-based graph neural network for predicting lncRNA-miRNA
associations},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad317},
doi = {10.1093/BIB/BBAD317},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangLLMWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLLSXSL23,
author = {Bo Wang and
Jiawei Luo and
Ying Liu and
Wanwan Shi and
Zehao Xiong and
Cong Shen and
Yahui Long},
title = {Spatial-MGCN: a novel multi-view graph convolutional network for identifying
spatial domains with attention mechanism},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad262},
doi = {10.1093/BIB/BBAD262},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangLLSXSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLRWZPZ23,
author = {Shudong Wang and
Tiyao Liu and
Chuanru Ren and
Wenhao Wu and
Zhiyuan Zhao and
Shanchen Pang and
Yuanyuan Zhang},
title = {Predicting potential small molecule-miRNA associations utilizing truncated
schatten p-norm},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad234},
doi = {10.1093/BIB/BBAD234},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangLRWZPZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLSSWSP23,
author = {Yongtian Wang and
Xinmeng Liu and
Yewei Shen and
Xuerui Song and
Tao Wang and
Xuequn Shang and
Jiajie Peng},
title = {Collaborative deep learning improves disease-related circRNA prediction
based on multi-source functional information},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad069},
doi = {10.1093/BIB/BBAD069},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangLSSWSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLTPTL23,
author = {Boshen Wang and
Xue Lei and
Wei Tian and
Alan Perez{-}Rathke and
Yan{-}Yuan Tseng and
Jie Liang},
title = {Structure-based pathogenicity relationship identifier for predicting
effects of single missense variants and discovery of higher-order
cancer susceptibility clusters of mutations},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad206},
doi = {10.1093/BIB/BBAD206},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangLTPTL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangLZPQZW23,
author = {Shudong Wang and
Yunyin Li and
Yuanyuan Zhang and
Shanchen Pang and
Sibo Qiao and
Yu Zhang and
Fuyu Wang},
title = {Generative Adversarial Matrix Completion Network based on Multi-Source
Data Fusion for miRNA-Disease Associations Prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad270},
doi = {10.1093/BIB/BBAD270},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangLZPQZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangPCWCCHLL23,
author = {Zhuo Wang and
Yuxuan Pang and
Chia{-}Ru Chung and
Hsin{-}Yao Wang and
Haiyan Cui and
Ying{-}Chih Chiang and
Jorng{-}Tzong Horng and
Jang{-}Jih Lu and
Tzong{-}Yi Lee},
title = {A risk assessment framework for multidrug-resistant \emph{Staphylococcus
aureus} using machine learning and mass spectrometry technology},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad330},
doi = {10.1093/BIB/BBAD330},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangPCWCCHLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangQA23,
author = {Yishu Wang and
Juan Qi and
Dongmei Ai},
title = {{DPADM:} a novel algorithm for detecting drug-pathway associations
based on high-throughput transcriptional response to compounds},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac517},
doi = {10.1093/BIB/BBAC517},
timestamp = {Wed, 06 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangQA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangRZLPS23,
author = {Shudong Wang and
Chuanru Ren and
Yulin Zhang and
YunYin Li and
Shanchen Pang and
Tao Song},
title = {Identifying potential small molecule-miRNA associations via Robust
{PCA} based on \emph{{\(\gamma\)}}-norm regularization},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad312},
doi = {10.1093/BIB/BBAD312},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangRZLPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangSLZLLDLHC23,
author = {Lei Wang and
Shao{-}Hua Shi and
Hui Li and
Xiangxiang Zeng and
Su{-}You Liu and
Zhao{-}Qian Liu and
Yafeng Deng and
Ai{-}Ping Lu and
Tingjun Hou and
Dong{-}Sheng Cao},
title = {Reducing false positive rate of docking-based virtual screening by
active learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac626},
doi = {10.1093/BIB/BBAC626},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangSLZLLDLHC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangSWWHZ23,
author = {Yu Mei Wang and
Yuzhi Sun and
Beiying Wang and
Zhiping Wu and
Xiao{-}Ying He and
Yuansong Zhao},
title = {Transfer learning for clustering single-cell RNA-seq data crossing-species
and batch, case on uterine fibroids},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad426},
doi = {10.1093/BIB/BBAD426},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangSWWHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangVFHXLZ23,
author = {Jingjing Wang and
Werner Pieter Veldsman and
Xiaodong Fang and
Yufen Huang and
Xuefeng Xie and
Aiping Lyu and
Lu Zhang},
title = {Benchmarking multi-platform sequencing technologies for human genome
assembly},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad300},
doi = {10.1093/BIB/BBAD300},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangVFHXLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangWNDSWWCXL23,
author = {Guangshuai Wang and
Tao Wu and
Wei Ning and
Kaixuan Diao and
Xiaoqin Sun and
Jinyu Wang and
Chenxu Wu and
Jing Chen and
Dongliang Xu and
Xue{-}Song Liu},
title = {TLimmuno2: predicting {MHC} class {II} antigen immunogenicity through
transfer learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad116},
doi = {10.1093/BIB/BBAD116},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangWNDSWWCXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangWSBLWYKLH23,
author = {Dong Wang and
Zhenxing Wu and
Chao Shen and
Lingjie Bao and
Hao Luo and
Zhe Wang and
Hucheng Yao and
De{-}Xin Kong and
Cheng Luo and
Tingjun Hou},
title = {Learning with uncertainty to accelerate the discovery of histone lysine-specific
demethylase 1A {(KDM1A/LSD1)} inhibitors},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac592},
doi = {10.1093/BIB/BBAC592},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangWSBLWYKLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangWXZWG23,
author = {Liugen Wang and
Yan Wang and
Chenxu Xuan and
Bai Zhang and
Hanwen Wu and
Jie Gao},
title = {Predicting potential microbe-disease associations based on multi-source
features and deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad255},
doi = {10.1093/BIB/BBAD255},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangWXZWG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangWXZXSHXZLWWJCLH23,
author = {Xuebin Wang and
Taifu Wang and
Zhihao Xie and
Youjin Zhang and
Shiqiang Xia and
Ruixue Sun and
Xinqiu He and
Ruizhi Xiang and
Qiwen Zheng and
Zhencheng Liu and
Jin'an Wang and
Honglong Wu and
Xiangqian Jin and
Weijun Chen and
Dongfang Li and
Zengquan He},
title = {GPMeta: a GPU-accelerated method for ultrarapid pathogen identification
from metagenomic sequences},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad092},
doi = {10.1093/BIB/BBAD092},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangWXZXSHXZLWWJCLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangXWHHS23,
author = {Lingling Wang and
Lei Xu and
Zhe Wang and
Tingjun Hou and
Haiping Hao and
Huiyong Sun},
title = {Cooperation of structural motifs controls drug selectivity in cyclin-dependent
kinases: an advanced theoretical analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac544},
doi = {10.1093/BIB/BBAC544},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangXWHHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangXWSZ23,
author = {Jing Wang and
Junfeng Xia and
Haiyun Wang and
Yansen Su and
Chun{-}Hou Zheng},
title = {scDCCA: deep contrastive clustering for single-cell RNA-seq data based
on auto-encoder network},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac625},
doi = {10.1093/BIB/BBAC625},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangXWSZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangXWZDG23,
author = {Yan Wang and
Chenxu Xuan and
Hanwen Wu and
Bai Zhang and
Tao Ding and
Jie Gao},
title = {{P-CSN:} single-cell {RNA} sequencing data analysis by partial cell-specific
network},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad180},
doi = {10.1093/BIB/BBAD180},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangXWZDG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangYWCSZXPWH23,
author = {Cheng Wang and
Chuang Yuan and
Yahui Wang and
Ranran Chen and
Yuying Shi and
Tao Zhang and
Fuzhong Xue and
Gary J. Patti and
Leyi Wei and
Qingzhen Hou},
title = {{MPI-VGAE:} protein-metabolite enzymatic reaction link learning by
variational graph autoencoders},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad189},
doi = {10.1093/BIB/BBAD189},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangYWCSZXPWH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangYYLHRLM23,
author = {Xin{-}Fei Wang and
Changqing Yu and
Zhu{-}Hong You and
Li{-}Ping Li and
Wenzhun Huang and
Zhong{-}Hao Ren and
Yue{-}Chao Li and
Weixiao Meng},
title = {A feature extraction method based on noise reduction for circRNA-miRNA
interaction prediction combining multi-structure features in the association
networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad111},
doi = {10.1093/BIB/BBAD111},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangYYLHRLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZKHLWY23,
author = {Shuaiqun Wang and
Kai Zheng and
Wei Kong and
Ruiwen Huang and
Lulu Liu and
Gen Wen and
Yaling Yu},
title = {Multimodal data fusion based on {IGERNNC} algorithm for detecting
pathogenic brain regions and genes in Alzheimer's disease},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac515},
doi = {10.1093/BIB/BBAC515},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangZKHLWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZKZZZ23,
author = {He Wang and
Yongjian Zang and
Ying Kang and
Jianwen Zhang and
Lei Zhang and
Shengli Zhang},
title = {{ETLD:} an encoder-transformation layer-decoder architecture for protein
contact and mutation effects prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad290},
doi = {10.1093/BIB/BBAD290},
timestamp = {Tue, 19 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangZKZZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZLDL23,
author = {Qilin Wang and
Junyou Zhang and
Zhaoshuo Liu and
Yingying Duan and
Chunyan Li},
title = {Integrative approaches based on genomic techniques in the functional
studies on enhancers},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad442},
doi = {10.1093/BIB/BBAD442},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangZLDL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZSZWZW23,
author = {Ying Wang and
Min Zhang and
Jian Shi and
Yue Zhu and
Xin Wang and
Shaojun Zhang and
Fang Wang},
title = {Cracking the pattern of tumor evolution based on single-cell copy
number alterations},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad341},
doi = {10.1093/BIB/BBAD341},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangZSZWZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZVZZ23,
author = {Chonghao Wang and
Jing Zhang and
Werner Pieter Veldsman and
Xin Zhou and
Lu Zhang},
title = {A comprehensive investigation of statistical and machine learning
approaches for predicting complex human diseases on genomic variants},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac552},
doi = {10.1093/BIB/BBAC552},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangZVZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZWL23,
author = {Kaili Wang and
Renyi Zhou and
Yifan Wu and
Min Li},
title = {RLBind: a deep learning method to predict RNA-ligand binding sites},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac486},
doi = {10.1093/BIB/BBAC486},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangZWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZWLWKMWL23,
author = {Zechen Wang and
Liangzhen Zheng and
Sheng Wang and
Mingzhi Lin and
Zhihao Wang and
Adams Wai{-}Kin Kong and
Yuguang Mu and
Yanjie Wei and
Weifeng Li},
title = {A fully differentiable ligand pose optimization framework guided by
deep learning and a traditional scoring function},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac520},
doi = {10.1093/BIB/BBAC520},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangZWLWKMWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZWYWWSZTZN23,
author = {Weixu Wang and
Xiaolan Zhou and
Jing Wang and
Jun Yao and
Haimei Wen and
Yi Wang and
Mingwan Sun and
Chao Zhang and
Wei Tao and
Jiahua Zou and
Ting Ni},
title = {Approximate estimation of cell-type resolution transcriptome in bulk
tissue through matrix completion},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad273},
doi = {10.1093/BIB/BBAD273},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WangZWYWWSZTZN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZYZYXZ23,
author = {Lihua Wang and
Tao Zhang and
Lihong Yu and
Chun{-}Hou Zheng and
Wenguang Yin and
Junfeng Xia and
Tiejun Zhang},
title = {Deleterious synonymous mutation identification based on selective
ensemble strategy},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac598},
doi = {10.1093/BIB/BBAC598},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangZYZYXZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WangZZS23,
author = {Hai{-}Yun Wang and
Jian{-}Ping Zhao and
Chun{-}Hou Zheng and
Yan{-}Sen Su},
title = {scGMAAE: Gaussian mixture adversarial autoencoders for diversification
analysis of scRNA-seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac585},
doi = {10.1093/BIB/BBAC585},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WangZZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WeiHLWW23,
author = {Hailin Wei and
Tong Han and
Taiwen Li and
Qiu Wu and
Chenfei Wang},
title = {{SCREE:} a comprehensive pipeline for single-cell multi-modal {CRISPR}
screen data processing and analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad123},
doi = {10.1093/BIB/BBAD123},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WeiHLWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WeiLZYSCC23,
author = {Yifang Wei and
Lingmei Li and
Xin Zhao and
Haitao Yang and
Jian Sa and
Hongyan Cao and
Yuehua Cui},
title = {Cancer subtyping with heterogeneous multi-omics data via hierarchical
multi-kernel learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac488},
doi = {10.1093/BIB/BBAC488},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WeiLZYSCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WeiZZLFY23,
author = {Jinhang Wei and
Linlin Zhuo and
Zhecheng Zhou and
Xinze Lian and
Xiangzheng Fu and
Xiaojun Yao},
title = {{GCFMCL:} predicting miRNA-drug sensitivity using graph collaborative
filtering and multi-view contrastive learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad247},
doi = {10.1093/BIB/BBAD247},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WeiZZLFY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WongKPG23,
author = {Bertrand Jern Han Wong and
Weijia Kong and
Hui Peng and
Wilson Wen Bin Goh},
title = {{PROSE:} phenotype-specific network signatures from individual proteomic
samples},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad075},
doi = {10.1093/BIB/BBAD075},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WongKPG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuDXZCZTZW23,
author = {Tao Wu and
Yao Dai and
Yue Xu and
Jie Zheng and
Shuting Chen and
Yinuo Zhang and
Peng Tian and
Xiaoqi Zheng and
Haiyun Wang},
title = {ExosomePurity: tumour purity deconvolution in serum exosomes based
on miRNA signatures},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad119},
doi = {10.1093/BIB/BBAD119},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WuDXZCZTZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuH23,
author = {Qilong Wu and
Sheng{-}You Huang},
title = {HCovDock: an efficient docking method for modeling covalent protein-ligand
interactions},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac559},
doi = {10.1093/BIB/BBAC559},
timestamp = {Mon, 27 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WuH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuHZGML23,
author = {Haonan Wu and
Jiyun Han and
Shizhuo Zhang and
Xin Gao and
Chaozhou Mou and
Juntao Liu},
title = {Spatom: a graph neural network for structure-based protein-protein
interaction site prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad345},
doi = {10.1093/BIB/BBAD345},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WuHZGML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuNDWPF23,
author = {Jinyang Wu and
Zhiwei Ning and
Yidong Ding and
Ying Wang and
Qinke Peng and
Laiyi Fu},
title = {{KGETCDA:} an efficient representation learning framework based on
knowledge graph encoder from transformer for predicting circRNA-disease
associations},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad292},
doi = {10.1093/BIB/BBAD292},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WuNDWPF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuPKKP23,
author = {Andy J. Wu and
Akila Perera and
Linganesan Kularatnarajah and
Anna Korsakova and
Jason J. Pitt},
title = {Mutational signature assignment heterogeneity is widespread and can
be addressed by ensemble approaches},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad331},
doi = {10.1093/BIB/BBAD331},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WuPKKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuQOZGMLS23,
author = {Jun Wu and
Haipeng Qing and
Jian Ouyang and
Jiajia Zhou and
Zihao Gao and
Christopher E. Mason and
Zhichao Liu and
Tieliu Shi},
title = {HiFun: homology independent protein function prediction by a novel
protein-language self-attention model},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad311},
doi = {10.1093/BIB/BBAD311},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WuQOZGMLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuSFCJWYDPSW23,
author = {Peike Wu and
Renliang Sun and
Aamir Fahira and
Yongzhou Chen and
Huiting Jiangzhou and
Ke Wang and
Qiangzhen Yang and
Yang Dai and
Dun Pan and
Yongyong Shi and
Zhuo Wang},
title = {{DROEG:} a method for cancer drug response prediction based on omics
and essential genes integration},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad003},
doi = {10.1093/BIB/BBAD003},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WuSFCJWYDPSW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuSWCJJGWLXFGY23,
author = {Guiying Wu and
Mengmeng Song and
Ke Wang and
Tianyu Cui and
Zicong Jiao and
Liyan Ji and
Xuan Gao and
Jiayin Wang and
Tao Liu and
Xuefeng Xia and
Huan Fang and
Yanfang Guan and
Xin Yi},
title = {{DELFMUT:} duplex sequencing-oriented depth estimation model for stable
detection of low-frequency mutations},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad277},
doi = {10.1093/BIB/BBAD277},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WuSWCJJGWLXFGY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuXYWKZH23,
author = {Sijia Wu and
Qiuping Xue and
Mengyuan Yang and
Yanfei Wang and
Pora Kim and
Xiaobo Zhou and
Liyu Huang},
title = {Genetic control of {RNA} editing in neurodegenerative disease},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad007},
doi = {10.1093/BIB/BBAD007},
timestamp = {Fri, 15 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WuXYWKZH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuZC23,
author = {Kevin E. Wu and
James Y. Zou and
Howard Chang},
title = {Machine learning modeling of {RNA} structures: methods, challenges
and future perspectives},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad210},
doi = {10.1093/BIB/BBAD210},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WuZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/WuZYLWYZFWX23,
author = {Cuiling Wu and
Yiyi Zhang and
Zhiwen Ying and
Ling Li and
Jun Wang and
Hui Yu and
Mengchen Zhang and
Xianzhong Feng and
Xinghua Wei and
Xiaogang Xu},
title = {A transformer-based genomic prediction method fused with knowledge-guided
module},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad438},
doi = {10.1093/BIB/BBAD438},
timestamp = {Wed, 17 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/WuZYLWYZFWX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23,
title = {Correction to: siGCD: a web server to explore survival interaction
of genes, cells and drugs in human cancers},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac618},
doi = {10.1093/BIB/BBAC618},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/X23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23a,
title = {Correction to: VPatho: a deep learning-based two-stage approach for
accurate prediction of gain-of-function and loss-of-function variants},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad019},
doi = {10.1093/BIB/BBAD019},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/X23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23b,
title = {Correction to: \emph{m}CNN-ETC: identifying electron transporters
and their functional families by using multiple windows scanning techniques
in convolutional neural networks with evolutionary information of
protein sequences},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad089},
doi = {10.1093/BIB/BBAD089},
timestamp = {Wed, 19 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X23b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23c,
title = {Correction to: kTWAS: integrating kernel machine with transcriptome-wide
association studies improves statistical power and reveals novel genes},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad091},
doi = {10.1093/BIB/BBAD091},
timestamp = {Wed, 19 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X23c.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23d,
title = {Correction to: Prediction of transcript structure and concentration
using RNA-Seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad055},
doi = {10.1093/BIB/BBAD055},
timestamp = {Wed, 19 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X23d.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23e,
title = {Correction to: Molecular persistent spectral image (Mol-PSI) representation
for machine learning models in drug design},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad128},
doi = {10.1093/BIB/BBAD128},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X23e.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23f,
title = {Correction to: Quantum computing algorithms: getting closer to critical
problems in computational biology},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad134},
doi = {10.1093/BIB/BBAD134},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X23f.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23g,
title = {Correction to: DeepFormer: a hybrid network based on convolutional
neural network and flow-attention mechanism for identifying the function
of {DNA} sequences},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad211},
doi = {10.1093/BIB/BBAD211},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X23g.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23h,
title = {Correction: Comparison and benchmark of structural variants detected
from long read and long-read assembly},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad224},
doi = {10.1093/BIB/BBAD224},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X23h.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23i,
title = {Correction to: An automatic immunofluorescence pattern classification
framework for HEp-2 image based on supervised learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad350},
doi = {10.1093/BIB/BBAD350},
timestamp = {Mon, 23 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/X23i.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/X23j,
title = {Correction to: Breaking the barriers of data scarcity in drug-target
affinity prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad477},
doi = {10.1093/BIB/BBAD477},
timestamp = {Mon, 01 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/X23j.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XiaFXPS23,
author = {Chun{-}Qiu Xia and
Shi{-}Hao Feng and
Ying Xia and
Xiaoyong Pan and
Hong{-}Bin Shen},
title = {Leveraging scaffold information to predict protein-ligand binding
affinity with an empirical graph neural network},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac603},
doi = {10.1093/BIB/BBAC603},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XiaFXPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XiaoWDZ23,
author = {Kaixuan Xiao and
Yu Wang and
Kangning Dong and
Shihua Zhang},
title = {SmartGate is a spatial metabolomics tool for resolving tissue structures},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad141},
doi = {10.1093/BIB/BBAD141},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XiaoWDZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XieCLGYLCLC23,
author = {Guobo Xie and
Rui{-}Bin Chen and
Zhiyi Lin and
Guosheng Gu and
Jun{-}Rui Yu and
Zhen{-}Guo Liu and
Ji Cui and
Lieqing Lin and
Lang{-}Cheng Chen},
title = {Predicting lncRNA-disease associations based on combining selective
similarity matrix fusion and bidirectional linear neighborhood label
propagation},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac595},
doi = {10.1093/BIB/BBAC595},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XieCLGYLCLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XieXZLWPJ23,
author = {Shijie Xie and
Xiaojun Xie and
Xin Zhao and
Fei Liu and
Yiming Wang and
Jihui Ping and
Zhiwei Ji},
title = {{HNSPPI:} a hybrid computational model combing network and sequence
information for predicting protein-protein interaction},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad261},
doi = {10.1093/BIB/BBAD261},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XieXZLWPJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XieZGZ23,
author = {Ailin Xie and
Ziqiao Zhang and
Jihong Guan and
Shuigeng Zhou},
title = {Self-supervised learning with chemistry-aware fragmentation for effective
molecular property prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad296},
doi = {10.1093/BIB/BBAD296},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XieZGZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XingZLHD23,
author = {Wenxuan Xing and
Jie Zhang and
Chen Li and
Yujia Huo and
Gaifang Dong},
title = {iAMP-Attenpred: a novel antimicrobial peptide predictor based on {BERT}
feature extraction method and CNN-BiLSTM-Attention combination model},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad443},
doi = {10.1093/BIB/BBAD443},
timestamp = {Mon, 01 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XingZLHD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuCVLCZ23,
author = {Ke Xu and
Chinwang Cheong and
Werner Pieter Veldsman and
Aiping Lyu and
William K. Cheung and
Lu Zhang},
title = {Accurate and interpretable gene expression imputation on scRNA-seq
data using IGSimpute},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad124},
doi = {10.1093/BIB/BBAD124},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XuCVLCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuL23,
author = {Xinyi Xu and
Xiangjie Li},
title = {Structure-preserved dimension reduction using joint triplets sampling
for multi-batch integration of single-cell transcriptomic data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac608},
doi = {10.1093/BIB/BBAC608},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XuL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuLHLLL23,
author = {Chao Xu and
Runduo Liu and
Shuheng Huang and
Wenchao Li and
Zhe Li and
Hai{-}Bin Luo},
title = {3D-SMGE: a pipeline for scaffold-based molecular generation and evaluation},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad327},
doi = {10.1093/BIB/BBAD327},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XuLHLLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuLLGLSPLIYAS23,
author = {Jing Xu and
Fuyi Li and
Chen Li and
Xudong Guo and
Cornelia B. Landersdorfer and
Hsin{-}Hui Shen and
Anton Y. Peleg and
Jian Li and
Seiya Imoto and
Jianhua Yao and
Tatsuya Akutsu and
Jiangning Song},
title = {iAMPCN: a deep-learning approach for identifying antimicrobial peptides
and their functional activities},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad240},
doi = {10.1093/BIB/BBAD240},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XuLLGLSPLIYAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuWWZZJCN23,
author = {Wei Xu and
Teng Wang and
Nan Wang and
Haohong Zhang and
Yuguo Zha and
Lei Ji and
Yuwen Chu and
Kang Ning},
title = {Artificial intelligence-enabled microbiome-based diagnosis models
for a broad spectrum of cancer types},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad178},
doi = {10.1093/BIB/BBAD178},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XuWWZZJCN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuYWML23,
author = {Fanding Xu and
Zhiwei Yang and
Lizhuo Wang and
Deyu Meng and
Jiangang Long},
title = {MESPool: Molecular Edge Shrinkage Pooling for hierarchical molecular
representation learning and property prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad423},
doi = {10.1093/BIB/BBAD423},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XuYWML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuZLCZ23,
author = {Jing Xu and
Aidi Zhang and
Fang Liu and
Liang Chen and
Xiujun Zhang},
title = {CIForm as a Transformer-based model for cell-type annotation of large-scale
single-cell RNA-seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad195},
doi = {10.1093/BIB/BBAD195},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/XuZLCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XuZLWJWLZLSJWRC23,
author = {Yiming Xu and
Bowen Zheng and
Xiaohong Liu and
Tao Wu and
Jinxiu Ju and
Shi{-}jie Wang and
Yufan Lian and
Hongjun Zhang and
Tong Liang and
Ye Sang and
Rui Jiang and
Guangyu Wang and
Jie Ren and
Ting Chen},
title = {Improving artificial intelligence pipeline for liver malignancy diagnosis
using ultrasound images and video frames},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac569},
doi = {10.1093/BIB/BBAC569},
timestamp = {Wed, 08 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/XuZLWJWLZLSJWRC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YanFHW23,
author = {Ke Yan and
Jiawei Feng and
Jing Huang and
Hao Wu},
title = {iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins
based on subfunction classifiers},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad251},
doi = {10.1093/BIB/BBAD251},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YanFHW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YanLZHZ23,
author = {Junyu Yan and
Shuai Li and
Ying Zhang and
Aimin Hao and
Qinping Zhao},
title = {ZetaDesign: an end-to-end deep learning method for protein sequence
design and side-chain packing},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad257},
doi = {10.1093/BIB/BBAD257},
timestamp = {Tue, 16 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YanLZHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YanYCW23,
author = {Zi{-}Jun Yan and
Chu{-}Ting Yu and
Lei Chen and
Hong{-}Yang Wang},
title = {Development of a TMErisk model based on immune infiltration in tumour
microenvironment to predict prognosis of immune checkpoint inhibitor
treatment in hepatocellular carcinoma},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad067},
doi = {10.1093/BIB/BBAD067},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YanYCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YanYYLZLQ23,
author = {Jiaxian Yan and
Zhaofeng Ye and
Ziyi Yang and
Chengqiang Lu and
Shengyu Zhang and
Qi Liu and
Jiezhong Qiu},
title = {Multi-task bioassay pre-training for protein-ligand binding affinity
prediction},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad451},
doi = {10.1093/BIB/BBAD451},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YanYYLZLQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangBXXWZ23,
author = {Maohua Yang and
Zonghua Bo and
Tao Xu and
Bo Xu and
Dongdong Wang and
Hang Zheng},
title = {Uni-GBSA: an open-source and web-based automatic workflow to perform
{MM/GB(PB)SA} calculations for virtual screening},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad218},
doi = {10.1093/BIB/BBAD218},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangBXXWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangC23,
author = {Lu Yang and
Jun Chen},
title = {Benchmarking differential abundance analysis methods for correlated
microbiome sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac607},
doi = {10.1093/BIB/BBAC607},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangC23a,
author = {Bo Yang and
Hailin Chen},
title = {Predicting circRNA-drug sensitivity associations by learning multimodal
networks using graph auto-encoders and attention mechanism},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac596},
doi = {10.1093/BIB/BBAC596},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangC23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangCRMSCT23,
author = {Zikun Yang and
Basilio Cieza and
Dolly Reyes{-}Dumeyer and
Rosa Montesinos and
Marcio Soto{-}A{\~{n}}ari and
Nilton Custodio and
Giuseppe Tosto},
title = {A benchmark study on current {GWAS} models in admixed populations},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad437},
doi = {10.1093/BIB/BBAD437},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangCRMSCT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangGCLZW23,
author = {Hai Yang and
Lipeng Gan and
Rui Chen and
Dongdong Li and
Jing Zhang and
Zhe Wang},
title = {From multi-omics data to the cancer druggable gene discovery: a novel
machine learning-based approach},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac528},
doi = {10.1093/BIB/BBAC528},
timestamp = {Sat, 18 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangGCLZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangGZSCZL23,
author = {Shuang Yang and
Weikang Gong and
Tong Zhou and
Xiaohan Sun and
Lei Chen and
Wenxue Zhou and
Chunhua Li},
title = {emPDBA: protein-DNA binding affinity prediction by combining features
from binding partners and interface learned with ensemble regression
model},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad192},
doi = {10.1093/BIB/BBAD192},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangGZSCZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangHCYL23,
author = {Cheng{-}Hong Yang and
Ming{-}Feng Hou and
Li{-}Yeh Chuang and
Cheng{-}San Yang and
Yu{-}Da Lin},
title = {Dimensionality reduction approach for many-objective epistasis analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac512},
doi = {10.1093/BIB/BBAC512},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangHCYL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangLLZXC23,
author = {Yongjian Yang and
Yu{-}Te Lin and
Guanxun Li and
Yan Zhong and
Qian Xu and
James J. Cai},
title = {Interpretable modeling of time-resolved single-cell gene-protein expression
with CrossmodalNet},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad342},
doi = {10.1093/BIB/BBAD342},
timestamp = {Thu, 23 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangLLZXC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangLLZZYMKLLP23,
author = {Yifan Yang and
Haoyuan Liu and
Yi Liu and
Liyuan Zhou and
Xiaoqi Zheng and
Rongxian Yue and
David L. Mattson and
Srividya Kidambi and
Mingyu Liang and
Pengyuan Liu and
Xiaoqing Pan},
title = {\emph{E}-value: a superior alternative to \emph{P}-value and its adjustments
in {DNA} methylation studies},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad241},
doi = {10.1093/BIB/BBAD241},
timestamp = {Wed, 04 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangLLZZYMKLLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangLY23,
author = {Yang Yang and
Yuwei Lu and
Wenying Yan},
title = {A comprehensive review on knowledge graphs for complex diseases},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac543},
doi = {10.1093/BIB/BBAC543},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangLYLW23,
author = {Hai Yang and
Yawen Liu and
Yijing Yang and
Dongdong Li and
Zhe Wang},
title = {InDEP: an interpretable machine learning approach to predict cancer
driver genes from multi-omics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad318},
doi = {10.1093/BIB/BBAD318},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangLYLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangSLXDW23,
author = {Minjian Yang and
Hanyu Sun and
Xue Liu and
Xi Xue and
Yafeng Deng and
Xiaojian Wang},
title = {{CMGN:} a conditional molecular generation net to design target-specific
molecules with desired properties},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad185},
doi = {10.1093/BIB/BBAD185},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangSLXDW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangXZWJJ23,
author = {Qi Yang and
Zhaochun Xu and
Wenyang Zhou and
Pingping Wang and
Qinghua Jiang and
Liran Juan},
title = {An interpretable single-cell {RNA} sequencing data clustering method
based on latent Dirichlet allocation},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad199},
doi = {10.1093/BIB/BBAD199},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangXZWJJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangYFXZDLLLZLGZLWZ23,
author = {Kuo Yang and
Yuxia Yang and
Shuyue Fan and
Jianan Xia and
Qiguang Zheng and
Xin Dong and
Jun Liu and
Qiong Liu and
Lei Lei and
Yingying Zhang and
Bing Li and
Zhuye Gao and
Runshun Zhang and
Baoyan Liu and
Zhong Wang and
Xuezhong Zhou},
title = {DRONet: effectiveness-driven drug repositioning framework using network
embedding and ranking learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac518},
doi = {10.1093/BIB/BBAC518},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangYFXZDLLLZLGZLWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangYHCL23,
author = {Lifang Yang and
Ye Yang and
Luqi Huang and
Xiuming Cui and
Yuan Liu},
title = {From single- to multi-omics: future research trends in medicinal plants},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac485},
doi = {10.1093/BIB/BBAC485},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YangYHCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YangZWLCLSZ23,
author = {Xiaobo Yang and
Bei Zhang and
Siqi Wang and
Ye Lu and
Kaixian Chen and
Cheng Luo and
Aihua Sun and
Hao Zhang},
title = {{OTTM:} an automated classification tool for translational drug discovery
from omics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad301},
doi = {10.1093/BIB/BBAD301},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YangZWLCLSZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YaoZSHL23,
author = {Zhou Yao and
Wenjing Zhang and
Peng Song and
Yuxue Hu and
Jianxiao Liu},
title = {DeepFormer: a hybrid network based on convolutional neural network
and flow-attention mechanism for identifying the function of {DNA}
sequences},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad095},
doi = {10.1093/BIB/BBAD095},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YaoZSHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YeLMSDDFSSX23,
author = {Zheng Ye and
Shaohao Li and
Xue Mi and
Baoyi Shao and
Zhu Dai and
Bo Ding and
Songwei Feng and
Bo Sun and
Yang Shen and
Zhongdang Xiao},
title = {STMHCpan, an accurate Star-Transformer-based extensible framework
for predicting {MHC} {I} allele binding peptides},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad164},
doi = {10.1093/BIB/BBAD164},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YeLMSDDFSSX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YeungZLK23,
author = {Wayland Yeung and
Zhongliang Zhou and
Sheng Li and
Natarajan Kannan},
title = {Alignment-free estimation of sequence conservation for identifying
functional sites using protein sequence embeddings},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac599},
doi = {10.1093/BIB/BBAC599},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YeungZLK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YeungZMGTOSVLLK23,
author = {Wayland Yeung and
Zhongliang Zhou and
Liju Mathew and
Nathan Gravel and
Rahil Taujale and
Brady O'boyle and
Mariah Salcedo and
Aarya Venkat and
William Lanzilotta and
Sheng Li and
Natarajan Kannan},
title = {Tree visualizations of protein sequence embedding space enable improved
functional clustering of diverse protein superfamilies},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac619},
doi = {10.1093/BIB/BBAC619},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YeungZMGTOSVLLK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YiLCJ23,
author = {Huiguang Yi and
Yanling Lin and
Qing Chang and
Wenfei Jin},
title = {A fast and globally optimal solution for RNA-seq quantification},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad298},
doi = {10.1093/BIB/BBAD298},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YiLCJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YiNJ23,
author = {Dohun Yi and
Jin{-}Wu Nam and
Hyobin Jeong},
title = {Toward the functional interpretation of somatic structural variations:
bulk- and single-cell approaches},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad297},
doi = {10.1093/BIB/BBAD297},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YiNJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YinC23,
author = {Qingyang Yin and
Liang Chen},
title = {CellTICS: an explainable neural network for cell-type identification
and interpretation based on single-cell RNA-seq data},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad449},
doi = {10.1093/BIB/BBAD449},
timestamp = {Mon, 01 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YinC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YinLG23,
author = {Zhen{-}Ning Yin and
Fei{-}Liao Lai and
Feng Gao},
title = {Unveiling human origins of replication using deep learning: accurate
prediction and comprehensive analysis},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad432},
doi = {10.1093/BIB/BBAD432},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YinLG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YoonN23,
author = {Sang{-}Ho Yoon and
Jin{-}Wu Nam},
title = {Clustering malignant cell states using universally variable genes},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad460},
doi = {10.1093/BIB/BBAD460},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YoonN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YorkiSCWLMEW23,
author = {Sosie Yorki and
Terrance Shea and
Christina Cuomo and
Bruce J. Walker and
Regina C. Larocque and
Abigail L. Manson and
Ashlee M. Earl and
Colin J. Worby},
title = {Comparison of long- and short-read metagenomic assembly for low-abundance
species and resistance genes},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad050},
doi = {10.1093/BIB/BBAD050},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YorkiSCWLMEW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YousefiYTKNBGBSG23,
author = {Niloofar Yousefi and
Mehdi Yazdani{-}Jahromi and
Aida Tayebi and
Elayaraja Kolanthai and
Craig J. Neal and
Tanumoy Banerjee and
Agnivo Gosai and
Ganesh Balasubramanian and
Sudipta Seal and
{\"{O}}zlem {\"{O}}zmen Garibay},
title = {BindingSite-AugmentedDTA: enabling a next-generation pipeline for
interpretable prediction models in drug repurposing},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad136},
doi = {10.1093/BIB/BBAD136},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YousefiYTKNBGBSG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuAS23,
author = {Runzhou Yu and
Syed Muhammad Umer Abdullah and
Yanni Sun},
title = {HMMPolish: a coding region polishing tool for TGS-sequenced {RNA}
viruses},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad264},
doi = {10.1093/BIB/BBAD264},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YuAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuDGLZY23,
author = {Yutong Yu and
Pengju Ding and
Hongli Gao and
Guozhu Liu and
Fa Zhang and
Bin Yu},
title = {Cooperation of local features and global representations by a dual-branch
network for transcription factor binding sites prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad036},
doi = {10.1093/BIB/BBAD036},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YuDGLZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuL23,
author = {Han Yu and
Xiaozhou Luo},
title = {{IPPF-FE:} an integrated peptide and protein function prediction framework
based on fused features and ensemble models},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac476},
doi = {10.1093/BIB/BBAC476},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YuL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuLCLZLJZZKL23,
author = {Kai Yu and
Zekun Liu and
Haoyang Cheng and
Shihua Li and
Qingfeng Zhang and
Jia Liu and
Huai{-}Qiang Ju and
Zhixiang Zuo and
Qi Zhao and
Shiyang Kang and
Zexian Liu},
title = {dSCOPE: a software to detect sequences critical for liquid-liquid
phase separation},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac550},
doi = {10.1093/BIB/BBAC550},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YuLCLZLJZZKL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuLDSGS23,
author = {Hui Yu and
Kangkang Li and
Wenmin Dong and
Shuanghong Song and
Chen Gao and
Jianyu Shi},
title = {Attention-based cross domain graph neural network for prediction of
drug-drug interactions},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad155},
doi = {10.1093/BIB/BBAD155},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YuLDSGS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuLSD23,
author = {Zhenhua Yu and
Furui Liu and
Fangyuan Shi and
Fang Du},
title = {rcCAE: a convolutional autoencoder method for detecting intra-tumor
heterogeneity and single-cell copy number alterations},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad108},
doi = {10.1093/BIB/BBAD108},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YuLSD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuanCYLC23,
author = {Qitong Yuan and
Keyi Chen and
Yimin Yu and
Nguyen{-}Quoc{-}Khanh Le and
Matthew Chin Heng Chua},
title = {Prediction of anticancer peptides based on an ensemble model of deep
learning and machine learning using ordinal positional encoding},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac630},
doi = {10.1093/BIB/BBAC630},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YuanCYLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuanLLNK23,
author = {Le Yuan and
Hongzhong Lu and
Feiran Li and
Jens Nielsen and
Eduard J. Kerkhoven},
title = {HGTphyloDetect: facilitating the identification and phylogenetic analysis
of horizontal gene transfer},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad035},
doi = {10.1093/BIB/BBAD035},
timestamp = {Sat, 19 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YuanLLNK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuanWWY23,
author = {Guo{-}Hua Yuan and
Ying Wang and
Guang{-}Zhong Wang and
Li Yang},
title = {RNAlight: a machine learning model to identify nucleotide features
determining {RNA} subcellular localization},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac509},
doi = {10.1093/BIB/BBAC509},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YuanWWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YuanXXZY23,
author = {Qianmu Yuan and
Junjie Xie and
Jiancong Xie and
Huiying Zhao and
Yuedong Yang},
title = {Fast and accurate protein function prediction from sequence through
pretrained language model and homology-based label diffusion},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad117},
doi = {10.1093/BIB/BBAD117},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YuanXXZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YueLHLH23,
author = {Yang Yue and
Yongxuan Liu and
Luoying Hao and
Huangshu Lei and
Shan He},
title = {Improving therapeutic synergy score predictions with adverse effects
using multi-task heterogeneous network learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac564},
doi = {10.1093/BIB/BBAC564},
timestamp = {Mon, 09 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YueLHLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YueLWLTH23,
author = {Yang Yue and
Shu Li and
Lingling Wang and
Huanxiang Liu and
Henry H. Y. Tong and
Shan He},
title = {MpbPPI: a multi-task pre-training-based equivariant approach for the
prediction of the effect of amino acid mutations on protein-protein
interactions},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad310},
doi = {10.1093/BIB/BBAD310},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/YueLWLTH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZengHZL23,
author = {Yanping Zeng and
Yongxin He and
Ruiqing Zheng and
Min Li},
title = {Inferring single-cell gene regulatory network by non-redundant mutual
information},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad326},
doi = {10.1093/BIB/BBAD326},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZengHZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZengYLCPLYY23,
author = {Yuansong Zeng and
Rui Yin and
Mai Luo and
Jianing Chen and
Zixiang Pan and
Yutong Lu and
Weijiang Yu and
Yuedong Yang},
title = {Identifying spatial domain by adapting transcriptomics with histology
through contrastive learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad048},
doi = {10.1093/BIB/BBAD048},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZengYLCPLYY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaiCD23,
author = {Yuyao Zhai and
Liang Chen and
Minghua Deng},
title = {scGAD: a new task and end-to-end framework for generalized cell type
annotation and discovery},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad045},
doi = {10.1093/BIB/BBAD045},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaiCD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaiGWMS23,
author = {Song Zhai and
Bin Guo and
Baolin Wu and
Devan V. Mehrotra and
Judong Shen},
title = {Integrating multiple traits for improving polygenic risk prediction
in disease and pharmacogenomics {GWAS}},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad181},
doi = {10.1093/BIB/BBAD181},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaiGWMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaiHSZ23,
author = {Weiqi Zhai and
Xiaodi Huang and
Nan Shen and
Shanfeng Zhu},
title = {Phen2Disease: a phenotype-driven model for disease and gene prioritization
by bidirectional maximum matching semantic similarities},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad172},
doi = {10.1093/BIB/BBAD172},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaiHSZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhanGCM23,
author = {Yongkang Zhan and
Jifeng Guo and
C. L. Philip Chen and
Xian{-}Bing Meng},
title = {iBT-Net: an incremental broad transformer network for cancer drug
response prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad256},
doi = {10.1093/BIB/BBAD256},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhanGCM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangCL23,
author = {Zheng Zhang and
Shengquan Chen and
Zhixiang Lin},
title = {RefTM: reference-guided topic modeling of single-cell chromatin accessibility
data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac540},
doi = {10.1093/BIB/BBAC540},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangCL23a,
author = {Qiyiwen Zhang and
Changgee Chang and
Qi Long},
title = {Robust knowledge-guided biclustering for multi-omics data},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad446},
doi = {10.1093/BIB/BBAD446},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangCL23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangCYZCN23,
author = {Haohong Zhang and
Hui Chong and
Qingyang Yu and
Yuguo Zha and
Mingyue Cheng and
Kang Ning},
title = {Tracing human life trajectory using gut microbial communities by context-aware
deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac629},
doi = {10.1093/BIB/BBAC629},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangCYZCN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangGLNGY23,
author = {Mingxiang Zhang and
Hongli Gao and
Xin Liao and
Baoxing Ning and
Haiming Gu and
Bin Yu},
title = {{DBGRU-SE:} predicting drug-drug interactions based on double BiGRU
and squeeze-and-excitation attention mechanism},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad184},
doi = {10.1093/BIB/BBAD184},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangGLNGY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangGYWLLL23,
author = {Ge Zhang and
Zhijie Gao and
Chaokun Yan and
Jianlin Wang and
Wenjuan Liang and
Junwei Luo and
Huimin Luo},
title = {KGANSynergy: knowledge graph attention network for drug synergy prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad167},
doi = {10.1093/BIB/BBAD167},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangGYWLLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangJWYLWTZSL23,
author = {Feng Zhang and
Huiyuan Jiao and
Yihao Wang and
Chen Yang and
Linying Li and
Zhiming Wang and
Ran Tong and
Junmei Zhou and
Jianfeng Shen and
Lingjie Li},
title = {InferLoop: leveraging single-cell chromatin accessibility for the
signal of chromatin loop},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad166},
doi = {10.1093/BIB/BBAD166},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangJWYLWTZSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangJZXWLLLLLL23,
author = {Wei Zhang and
Jia Ju and
Yong Zhou and
Teng Xiong and
Mengyao Wang and
Chaohui Li and
Shixin Lu and
Zefeng Lu and
Liya Lin and
Xiao Liu and
Shuaicheng Li},
title = {IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for
sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad080},
doi = {10.1093/BIB/BBAD080},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangJZXWLLLLLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLBFUI23,
author = {Yao{-}zhong Zhang and
Yunjie Liu and
Zeheng Bai and
Kosuke Fujimoto and
Satoshi Uematsu and
Seiya Imoto},
title = {Zero-shot-capable identification of phage-host relationships with
whole-genome sequence representation by contrastive learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad239},
doi = {10.1093/BIB/BBAD239},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangLBFUI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLD23,
author = {Ying{-}Ying Zhang and
De{-}Min Liang and
Pu{-}Feng Du},
title = {iEssLnc: quantitative estimation of lncRNA gene essentialities with
meta-path-guided random walks on the lncRNA-protein interaction network},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad097},
doi = {10.1093/BIB/BBAD097},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangLD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLDD23,
author = {Guishan Zhang and
Ye Luo and
Xianhua Dai and
Zhiming Dai},
title = {Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA
on- and off-target activities},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad333},
doi = {10.1093/BIB/BBAD333},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangLDD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLHWS23,
author = {Chuanchao Zhang and
Xinxing Li and
Wendong Huang and
Lequn Wang and
Qianqian Shi},
title = {Spatially aware self-representation learning for tissue structure
characterization and spatial functional genes identification},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad197},
doi = {10.1093/BIB/BBAD197},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangLHWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLLZZXZ23,
author = {Hongning Zhang and
Mingkun Lu and
Gaole Lin and
Lingyan Zheng and
Wei Zhang and
Zhijian Xu and
Feng Zhu},
title = {SoCube: an innovative end-to-end doublet detection algorithm for analyzing
scRNA-seq data},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad104},
doi = {10.1093/BIB/BBAD104},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangLLZZXZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLSXW23,
author = {Tianjiao Zhang and
Liangyu Li and
Hailong Sun and
Dali Xu and
Guohua Wang},
title = {DeepICSH: a complex deep learning framework for identifying cell-specific
silencers and their strength from the human genome},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad316},
doi = {10.1093/BIB/BBAD316},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangLSXW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLZLW23,
author = {Lishen Zhang and
Chengqian Lu and
Min Zeng and
Yaohang Li and
Jianxin Wang},
title = {{CRMSS:} predicting circRNA-RBP binding sites based on multi-scale
characterizing sequence and structure features},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac530},
doi = {10.1093/BIB/BBAC530},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangLZLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangLZZ23,
author = {Hui Zhang and
Hongjia Li and
Fa Zhang and
Ping Zhu},
title = {A strategy combining denoising and cryo-EM single particle analysis},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad148},
doi = {10.1093/BIB/BBAD148},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangLZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangMY23,
author = {Jiawei Zhang and
Wang Ma and
Hui Yao},
title = {Accurate TCR-pMHC interaction prediction using a BERT-based transfer
learning method},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad436},
doi = {10.1093/BIB/BBAD436},
timestamp = {Mon, 01 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangMY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangSWDKLHP23,
author = {Xujun Zhang and
Chao Shen and
Tianyue Wang and
Yafeng Deng and
Yu Kang and
Dan Li and
Tingjun Hou and
Peichen Pan},
title = {{ML-PLIC:} a web platform for characterizing protein-ligand interactions
and developing machine learning-based scoring functions},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad295},
doi = {10.1093/BIB/BBAD295},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangSWDKLHP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangWWMC23,
author = {Ran Zhang and
Zhanjie Wang and
Xuezhi Wang and
Zhen Meng and
Wenjuan Cui},
title = {{MHTAN-DTI:} Metapath-based hierarchical transformer and attention
network for drug-target interaction prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad079},
doi = {10.1093/BIB/BBAD079},
timestamp = {Tue, 30 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangWWMC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangWWMCZ23,
author = {Ran Zhang and
Xuezhi Wang and
Pengfei Wang and
Zhen Meng and
Wenjuan Cui and
Yuanchun Zhou},
title = {{HTCL-DDI:} a hierarchical triple-view contrastive learning framework
for drug-drug interaction prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad324},
doi = {10.1093/BIB/BBAD324},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangWWMCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangWYZTLJKSCMW23,
author = {Xin Zhang and
Lesong Wei and
Xiucai Ye and
Kai Zhang and
Saisai Teng and
Zhongshen Li and
Junru Jin and
Min Jae Kim and
Tetsuya Sakurai and
Lizhen Cui and
Balachandran Manavalan and
Leyi Wei},
title = {SiameseCPP: a sequence-based Siamese network to predict cell-penetrating
peptides by contrastive learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac545},
doi = {10.1093/BIB/BBAC545},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhangWYZTLJKSCMW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangXS23,
author = {Pei{-}Dong Zhang and
Chun{-}Qiu Xia and
Hong{-}Bin Shen},
title = {High-accuracy protein model quality assessment using attention graph
neural networks},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac614},
doi = {10.1093/BIB/BBAC614},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangXS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangXWCZ23,
author = {Wentao Zhang and
Yanchao Xu and
Aowen Wang and
Gang Chen and
Junbo Zhao},
title = {Fuse feeds as one: cross-modal framework for general identification
of AMPs},
journal = {Briefings Bioinform.},
volume = {24},
number = {6},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad336},
doi = {10.1093/BIB/BBAD336},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangXWCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangXWLWL23,
author = {Ze{-}Qun Zhang and
Junlin Xu and
Yanan Wu and
Nian{-}Nian Liu and
Ying{-}Long Wang and
Ying Liang},
title = {CapsNet-LDA: predicting lncRNA-disease associations using attention
mechanism and capsule network based on multi-view data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac531},
doi = {10.1093/BIB/BBAC531},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangXWLWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangYLLYZL23,
author = {Siqin Zhang and
Kuo Yang and
Zhenhong Liu and
Xinxing Lai and
Zhen Yang and
Jianyang Zeng and
Shao Li},
title = {DrugAI: a multi-view deep learning model for predicting drug-target
activating/inhibiting mechanisms},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac526},
doi = {10.1093/BIB/BBAC526},
timestamp = {Wed, 02 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangYLLYZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangYTAZC23,
author = {Chengming Zhang and
Yiwen Yang and
Shijie Tang and
Kazuyuki Aihara and
Chuanchao Zhang and
Luonan Chen},
title = {Contrastively generative self-expression model for single-cell and
spatial multimodal data},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad265},
doi = {10.1093/BIB/BBAD265},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangYTAZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangYVFZ23,
author = {Zhenmiao Zhang and
Chao Yang and
Werner Pieter Veldsman and
Xiaodong Fang and
Lu Zhang},
title = {Benchmarking genome assembly methods on metagenomic sequencing data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad087},
doi = {10.1093/BIB/BBAD087},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangYVFZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangZXL23,
author = {Tong Zhang and
Shao{-}Wu Zhang and
Ming{-}Yu Xie and
Yan Li},
title = {A novel heterophilic graph diffusion convolutional network for identifying
cancer driver genes},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad137},
doi = {10.1093/BIB/BBAD137},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangZXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoCCQ23,
author = {Yuanchun Zhao and
Xingqi Chen and
Jiajia Chen and
Xin Qi},
title = {Decoding Connectivity Map-based drug repurposing for oncotherapy},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad142},
doi = {10.1093/BIB/BBAD142},
timestamp = {Thu, 22 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoCCQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoCJCW23,
author = {Tingting Zhao and
Lihua Cao and
Jiafu Ji and
David K. Chang and
Jianmin Wu},
title = {ReProMSig: an integrative platform for development and application
of reproducible multivariable models for cancer prognosis supporting
guideline-based transparent reporting},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad267},
doi = {10.1093/BIB/BBAD267},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoCJCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoCLFHZ23,
author = {Ming{-}Xiao Zhao and
Qiang Chen and
Fulai Li and
Songsen Fu and
Biling Huang and
Yufen Zhao},
title = {Protein phosphorylation database and prediction tools},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad090},
doi = {10.1093/BIB/BBAD090},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoCLFHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoDYHZY23,
author = {Hang Zhao and
Pin{-}yuan Dai and
Xiao{-}jin Yu and
Jieyu He and
Chao Zhao and
Li{-}hong Yin},
title = {Evaluation of graphical models for multi-group metabolomics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad096},
doi = {10.1093/BIB/BBAD096},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoDYHZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoFZN23,
author = {Zhangxin Zhao and
Qianjin Feng and
Yu Zhang and
Zhenyuan Ning},
title = {Adaptive risk-aware sharable and individual subspace learning for
cancer survival analysis with multi-modality data},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac489},
doi = {10.1093/BIB/BBAC489},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoFZN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoHXZZHYWDSY23,
author = {Yu Zhao and
Bing He and
Zhimeng Xu and
Yidan Zhang and
Xuan Zhao and
Zhi{-}An Huang and
Fan Yang and
Liang Wang and
Lei Duan and
Jiangning Song and
Jianhua Yao},
title = {Interpretable artificial intelligence model for accurate identification
of medical conditions using immune repertoire},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac555},
doi = {10.1093/BIB/BBAC555},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoHXZZHYWDSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoQCQBWLWZZ23,
author = {Lianhe Zhao and
Xiaoning Qi and
Yang Chen and
Yixuan Qiao and
Dechao Bu and
Yang Wu and
Yufan Luo and
Sheng Wang and
Rui Zhang and
Yi Zhao},
title = {Biological knowledge graph-guided investigation of immune therapy
response in cancer with graph neural network},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad023},
doi = {10.1093/BIB/BBAD023},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoQCQBWLWZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoSSZS23,
author = {Jingxuan Zhao and
Jianqiang Sun and
Stella C. Shuai and
Qi Zhao and
Jianwei Shuai},
title = {Predicting potential interactions between lncRNAs and proteins via
combined graph auto-encoder methods},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac527},
doi = {10.1093/BIB/BBAC527},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoSSZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoSZMXQYHY23,
author = {Yu Zhao and
Xiaona Su and
Weitong Zhang and
Sijie Mai and
Zhimeng Xu and
Chenchen Qin and
Rongshan Yu and
Bing He and
Jianhua Yao},
title = {{SC-AIR-BERT:} a pre-trained single-cell model for predicting the
antigen-binding specificity of the adaptive immune receptor},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad191},
doi = {10.1093/BIB/BBAD191},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoSZMXQYHY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoWCGLL23,
author = {Yanpeng Zhao and
Jingjing Wang and
Fubin Chang and
Weikang Gong and
Yang Liu and
Chunhua Li},
title = {Identification of metal ion-binding sites in {RNA} structures using
deep learning method},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad049},
doi = {10.1093/BIB/BBAD049},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoWCGLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoWH23,
author = {Yanping Zhao and
Kui Wang and
Gang Hu},
title = {{DIST:} spatial transcriptomics enhancement using deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad013},
doi = {10.1093/BIB/BBAD013},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoWH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoWZY23,
author = {Xiaosa Zhao and
Jun Wu and
Xiaowei Zhao and
Minghao Yin},
title = {Multi-view contrastive heterogeneous graph attention network for lncRNA-disease
association prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac548},
doi = {10.1093/BIB/BBAC548},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoWZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoYSJSHH23,
author = {Weizhong Zhao and
Xueling Yuan and
Xianjun Shen and
Xingpeng Jiang and
Chuan Shi and
Tingting He and
Xiaohua Hu},
title = {Improving drug-drug interactions prediction with interpretability
via meta-path-based information fusion},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad041},
doi = {10.1093/BIB/BBAD041},
timestamp = {Wed, 27 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoYSJSHH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoYZYZ23,
author = {Xingzhong Zhao and
Anyi Yang and
Zi{-}Chao Zhang and
Yucheng T. Yang and
Xing{-}Ming Zhao},
title = {Deciphering the genetic architecture of human brain structure and
function: a brief survey on recent advances of neuroimaging genomics},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad060},
doi = {10.1093/BIB/BBAD060},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoYZYZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoZDF23,
author = {Tingting Zhao and
Guangyu Zhu and
Harsh Vardhan Dubey and
Patrick Flaherty},
title = {Identification of significant gene expression changes in multiple
perturbation experiments using knockoffs},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad084},
doi = {10.1093/BIB/BBAD084},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoZDF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoZSLCXW23,
author = {Jing Zhao and
Bowen Zhao and
Xiaotong Song and
Chujun Lyu and
Weizhi Chen and
Yi Xiong and
Dong{-}Qing Wei},
title = {Subtype-DCC: decoupled contrastive clustering method for cancer subtype
identification based on multi-omics data},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad025},
doi = {10.1093/BIB/BBAD025},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhaoZSLCXW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhengHD23,
author = {Rongtao Zheng and
Zhijian Huang and
Lei Deng},
title = {Large-scale predicting protein functions through heterogeneous feature
fusion},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad243},
doi = {10.1093/BIB/BBAD243},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhengHD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhengTWYLL23,
author = {Zixi Zheng and
Yanyan Tan and
Hong Wang and
Shengpeng Yu and
Tianyu Liu and
Cheng Liang},
title = {CasANGCL: pre-training and fine-tuning model based on cascaded attention
network and graph contrastive learning for molecular property prediction},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac566},
doi = {10.1093/BIB/BBAC566},
timestamp = {Thu, 02 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhengTWYLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhengYD23,
author = {Jiahao Zheng and
Yuedong Yang and
Zhiming Dai},
title = {Subgraph extraction and graph representation learning for single cell
Hi-C imputation and clustering},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad379},
doi = {10.1093/BIB/BBAD379},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhengYD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhengZWYJLL23,
author = {Kai Zheng and
Xin{-}Lu Zhang and
Lei Wang and
Zhu{-}Hong You and
Bo{-}Ya Ji and
Xiao Liang and
Zheng{-}Wei Li},
title = {{SPRDA:} a link prediction approach based on the structural perturbation
to infer disease-associated Piwi-interacting RNAs},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac498},
doi = {10.1093/BIB/BBAC498},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhengZWYJLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhongCLMS23,
author = {Wujuan Zhong and
Aparna Chhibber and
Lan Luo and
Devan V. Mehrotra and
Judong Shen},
title = {A fast and powerful linear mixed model approach for genotype-environment
interaction tests in large-scale {GWAS}},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac547},
doi = {10.1093/BIB/BBAC547},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhongCLMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhongDLLC23,
author = {Jiayuan Zhong and
Dandan Ding and
Juntan Liu and
Rui Liu and
Pei Chen},
title = {{SPNE:} sample-perturbed network entropy for revealing critical states
of complex biological systems},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad028},
doi = {10.1093/BIB/BBAD028},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhongDLLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhongWLZZG23,
author = {Tengwei Zhong and
Wenqing Wang and
Houyan Liu and
Maolin Zeng and
Xinyu Zhao and
Zhiyun Guo},
title = {eccDNA Atlas: a comprehensive resource of eccDNA catalog},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad037},
doi = {10.1093/BIB/BBAD037},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhongWLZZG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhouDFJHZYCYZW23,
author = {Bailing Zhou and
Maolin Ding and
Jing Feng and
Baohua Ji and
Pingping Huang and
Junye Zhang and
Xue Yu and
Zanxia Cao and
Yuedong Yang and
Yaoqi Zhou and
Jihua Wang},
title = {EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs
by deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac583},
doi = {10.1093/BIB/BBAC583},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhouDFJHZYCYZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhouJY23,
author = {Yuting Zhou and
Yongquan Jiang and
Yan Yang},
title = {{AGAT-PPIS:} a novel protein-protein interaction site predictor based
on augmented graph attention network with initial residual and identity
mapping},
journal = {Briefings Bioinform.},
volume = {24},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad122},
doi = {10.1093/BIB/BBAD122},
timestamp = {Sat, 20 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhouJY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhouST23,
author = {Jiayin Zhou and
Wen Song and
Qichao Tu},
title = {To assemble or not to assemble: metagenomic profiling of microbially
mediated biogeochemical pathways in complex communities},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac594},
doi = {10.1093/BIB/BBAC594},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhouST23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhouTS23,
author = {Haiwei Zhou and
Wenxi Tan and
Shao{-}Ping Shi},
title = {DeepGpgs: a novel deep learning framework for predicting arginine
methylation sites combined with Gaussian prior and gated self-attention
mechanism},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad018},
doi = {10.1093/BIB/BBAD018},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhouTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhouYYYQG23,
author = {Zhi{-}Jian Zhou and
Chen{-}Hui Yang and
Sheng{-}Bao Ye and
Xiao{-}Wei Yu and
Ye Qiu and
Xing{-}Yi Ge},
title = {VirusRecom: an information-theory-based method for recombination detection
of viral lineages and its application on SARS-CoV-2},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac513},
doi = {10.1093/BIB/BBAC513},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhouYYYQG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhouZLZJ23,
author = {Shengming Zhou and
Yetong Zhou and
Tian Liu and
Jia Zheng and
Cangzhi Jia},
title = {PredLLPS{\_}PSSM: a novel predictor for liquid-liquid protein separation
identification based on evolutionary information and a deep neural
network},
journal = {Briefings Bioinform.},
volume = {24},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad299},
doi = {10.1093/BIB/BBAD299},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhouZLZJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhuBXX23,
author = {Xi{-}Liang Zhu and
Lin{-}Xia Bao and
Min{-}Qi Xue and
Ying{-}Ying Xu},
title = {Automatic recognition of protein subcellular location patterns in
single cells from immunofluorescence images based on deep learning},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac609},
doi = {10.1093/BIB/BBAC609},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhuBXX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhuDDZMLHL23,
author = {Fei Zhu and
Lei Deng and
Yuhao Dai and
Guangyu Zhang and
Fanwang Meng and
Cheng Luo and
Guang Hu and
Zhongjie Liang},
title = {{PPICT:} an integrated deep neural network for predicting inter-protein
{PTM} cross-talk},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad052},
doi = {10.1093/BIB/BBAD052},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhuDDZMLHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhuLGWCWSJ23,
author = {Yan Zhu and
Fuyi Li and
Xudong Guo and
Xiaoyu Wang and
Lachlan J. M. Coin and
Geoffrey I. Webb and
Jiangning Song and
Cangzhi Jia},
title = {{TIMER} is a Siamese neural network-based framework for identifying
both general and species-specific bacterial promoters},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad209},
doi = {10.1093/BIB/BBAD209},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhuLGWCWSJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhuLTLZWC23,
author = {Junjie Zhu and
Zhengxin Li and
Haowei Tong and
Zhouyu Lu and
Ningjie Zhang and
Ting Wei and
Hai{-}Feng Chen},
title = {Phanto-IDP: compact model for precise intrinsically disordered protein
backbone generation and enhanced sampling},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad429},
doi = {10.1093/BIB/BBAD429},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhuLTLZWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhuLW23,
author = {Hao Zhu and
Tong Liu and
Zheng Wang},
title = {scHiMe: predicting single-cell {DNA} methylation levels based on single-cell
Hi-C data},
journal = {Briefings Bioinform.},
volume = {24},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad223},
doi = {10.1093/BIB/BBAD223},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhuLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZouLSXWWSWXZY23,
author = {Min Zou and
Honghao Li and
Dongqing Su and
Yuqiang Xiong and
Haodong Wei and
Shiyuan Wang and
Hongmei Sun and
Tao Wang and
Qilemuge Xi and
Yongchun Zuo and
Lei Yang},
title = {Integrating somatic mutation profiles with structural deep clustering
network for metabolic stratification in pancreatic cancer: a comprehensive
analysis of prognostic and genomic landscapes},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbad430},
doi = {10.1093/BIB/BBAD430},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZouLSXWWSWXZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AbeysingheYBZC22,
author = {Rashmie Abeysinghe and
Yuntao Yang and
Mason Bartels and
W. Jim Zheng and
Licong Cui},
title = {An evidence-based lexical pattern approach for quality assurance of
Gene Ontology relations},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac122},
doi = {10.1093/BIB/BBAC122},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AbeysingheYBZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AdamowiczMBB22,
author = {Klaudia Adamowicz and
Andreas Maier and
Jan Baumbach and
David B. Blumenthal},
title = {Online \emph{in silico} validation of disease and gene sets, clusterings
or subnetworks with {DIGEST}},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac247},
doi = {10.1093/BIB/BBAC247},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AdamowiczMBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AgapitoPNJ22,
author = {Giuseppe Agapito and
Chiara Pastrello and
Yun Niu and
Igor Jurisica},
title = {Pathway integration and annotation: building a puzzle with non-matching
pieces and no reference picture},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac368},
doi = {10.1093/BIB/BBAC368},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AgapitoPNJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AggarwalRKDY22,
author = {Suruchi Aggarwal and
Anurag Raj and
Dhirendra Kumar and
Debasis Dash and
Amit Kumar Yadav},
title = {False discovery rate: the Achilles' heel of proteogenomics},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac163},
doi = {10.1093/BIB/BBAC163},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AggarwalRKDY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AhmedCWDSKLSP22,
author = {Talal Ahmed and
Mark A. Carty and
Stephane Wenric and
Jonathan R. Dry and
Ameen A. Salahudeen and
Aly A. Khan and
Eric Lefkofsky and
Martin C. Stumpe and
Raphael Pelossof},
title = {Privacy preserving validation for multiomic prediction models},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac110},
doi = {10.1093/BIB/BBAC110},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AhmedCWDSKLSP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AlghamdiAAUK22,
author = {Wajdi Alghamdi and
Muhammad Attique and
Ebraheem Alzahrani and
Malik Zaka Ullah and
Yaser Daanial Khan},
title = {LBCEPred: a machine learning model to predict linear B-cell epitopes},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac035},
doi = {10.1093/BIB/BBAC035},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AlghamdiAAUK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AlsaffarHMS22,
author = {Muhalb M. Alsaffar and
Mohammad Hasan and
Gavin P. McStay and
Mohamed Sedky},
title = {Digital {DNA} lifecycle security and privacy: an overview},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab607},
doi = {10.1093/BIB/BBAB607},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AlsaffarHMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AmerifarNG22,
author = {Sare Amerifar and
Mohammad Norouzi and
Mahmoud Ghandi},
title = {A tool for feature extraction from biological sequences},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac108},
doi = {10.1093/BIB/BBAC108},
timestamp = {Thu, 20 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AmerifarNG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AnCYLG22,
author = {Xin An and
Xi Chen and
Daiyao Yi and
Hongyang Li and
Yuanfang Guan},
title = {Representation of molecules for drug response prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab393},
doi = {10.1093/BIB/BBAB393},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AnCYLG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AnEYP22,
author = {Hyunsu An and
Minho Eun and
Jawoon Yi and
Jihwan Park},
title = {{CRESSP:} a comprehensive pipeline for prediction of immunopathogenic
SARS-CoV-2 epitopes using structural properties of proteins},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac056},
doi = {10.1093/BIB/BBAC056},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AnEYP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AnchangMXACHPML22,
author = {Benedict Anchang and
Raul Mendez{-}Giraldez and
Xiaojiang Xu and
Trevor K. Archer and
Qing Chen and
Guang Hu and
Sylvia K. Plevritis and
Alison Anne Motsinger{-}Reif and
Jian{-}Liang Li},
title = {Visualization, benchmarking and characterization of nested single-cell
heterogeneity as dynamic forest mixtures},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac017},
doi = {10.1093/BIB/BBAC017},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AnchangMXACHPML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AndradesM22,
author = {Renan Andrades and
Mariana Recamonde Mendoza},
title = {Machine learning methods for prediction of cancer driver genes: a
survey paper},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac062},
doi = {10.1093/BIB/BBAC062},
timestamp = {Tue, 31 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AndradesM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AoZY22,
author = {Chunyan Ao and
Quan Zou and
Liang Yu},
title = {NmRF: identification of multispecies {RNA} 2'-O-methylation modification
sites from {RNA} sequences},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab480},
doi = {10.1093/BIB/BBAB480},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AoZY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ArendBMKLBBL22,
author = {Lis Arend and
Judith Bernett and
Quirin Manz and
Melissa Klug and
Olga Lazareva and
Jan Baumbach and
Dario Bongiovanni and
Markus List},
title = {A systematic comparison of novel and existing differential analysis
methods for CyTOF data},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab471},
doi = {10.1093/BIB/BBAB471},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ArendBMKLBBL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AromolaranAIO22,
author = {Olufemi Aromolaran and
Damilare Aromolaran and
Itunuoluwa Isewon and
Jelili Oyelade},
title = {Corrigendum to: Machine learning approach to gene essentiality prediction:
a review},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab419},
doi = {10.1093/BIB/BBAB419},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AromolaranAIO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AyyalaLO22,
author = {Deepak Nag Ayyala and
Jianan Lin and
Zhengqing Ouyang},
title = {Differential {RNA} methylation using multivariate statistical methods},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab309},
doi = {10.1093/BIB/BBAB309},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/AyyalaLO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BaiTAX22,
author = {Jun Bai and
Renbo Tan and
Zheng An and
Ying Xu},
title = {Quantitative estimation of intracellular oxidative stress in human
tissues},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac206},
doi = {10.1093/BIB/BBAC206},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BaiTAX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Balague-DobonCG22,
author = {Laura Balagu{\'{e}}{-}Dob{\'{o}}n and
Alejandro C{\'{a}}ceres and
Juan R. Gonz{\'{a}}lez},
title = {Fully exploiting {SNP} arrays: a systematic review on the tools to
extract underlying genomic structure},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac043},
doi = {10.1093/BIB/BBAC043},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Balague-DobonCG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BaoLYZQZ22,
author = {Siqi Bao and
Ke Li and
Congcong Yan and
Zicheng Zhang and
Jia Qu and
Meng Zhou},
title = {Deep learning-based advances and applications for single-cell RNA-sequencing
data analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab473},
doi = {10.1093/BIB/BBAB473},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BaoLYZQZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BartasVBPCBSBP22,
author = {Martin Bartas and
Adriana Voln{\'{a}} and
Christopher A. Beaudoin and
Ebbe Toftgaard Poulsen and
Jir{\'{\i}} Cerven and
V{\'{a}}clav Br{\'{a}}zda and
Vladim{\'{\i}}r Spunda and
Tom L. Blundell and
Petr Pecinka},
title = {Unheeded SARS-CoV-2 proteins? {A} deep look into negative-sense {RNA}},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac045},
doi = {10.1093/BIB/BBAC045},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BartasVBPCBSBP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BasithLM22,
author = {Shaherin Basith and
Gwang Lee and
Balachandran Manavalan},
title = {{STALLION:} a stacking-based ensemble learning framework for prokaryotic
lysine acetylation site prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab376},
doi = {10.1093/BIB/BBAB376},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BasithLM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Ben-CohenDDLSR22,
author = {Gil Ben{-}Cohen and
Flora Doffe and
Michal Devir and
Bernard Leroy and
Thierry Soussi and
Shai Rosenberg},
title = {TP53{\_}PROF: a machine learning model to predict impact of missense
mutations in \emph{TP53}},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab524},
doi = {10.1093/BIB/BBAB524},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Ben-CohenDDLSR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BiLGWPGWYJS22,
author = {Yue Bi and
Fuyi Li and
Xudong Guo and
Zhikang Wang and
Tong Pan and
Yuming Guo and
Geoffrey I. Webb and
Jianhua Yao and
Cangzhi Jia and
Jiangning Song},
title = {Clarion is a multi-label problem transformation method for identifying
mRNA subcellular localizations},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac467},
doi = {10.1093/BIB/BBAC467},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BiLGWPGWYJS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BiLWWLX22,
author = {Xia{-}an Bi and
Lou Li and
Zizheng Wang and
Yu Wang and
Xun Luo and
Luyun Xu},
title = {{IHGC-GAN:} influence hypergraph convolutional generative adversarial
network for risk prediction of late mild cognitive impairment based
on imaging genetic data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac093},
doi = {10.1093/BIB/BBAC093},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BiLWWLX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BiMLWZLX22,
author = {Xia{-}an Bi and
Yuhua Mao and
Sheng Luo and
Hao Wu and
Lixia Zhang and
Xun Luo and
Luyun Xu},
title = {A novel generation adversarial network framework with characteristics
aggregation and diffusion for brain disease classification and feature
selection},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac454},
doi = {10.1093/BIB/BBAC454},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BiMLWZLX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BiZLMHZX22,
author = {Xia{-}an Bi and
Wenyan Zhou and
Sheng Luo and
Yuhua Mao and
Xi Hu and
Bin Zeng and
Luyun Xu},
title = {Feature aggregation graph convolutional network based on imaging genetic
data for diagnosis and pathogeny identification of Alzheimer's disease},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac137},
doi = {10.1093/BIB/BBAC137},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BiZLMHZX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BlecuaDVMMCE22,
author = {Pedro Blecua and
Veronica Davalos and
Izar de Villasante and
Angelika Merkel and
Eva Musulen and
Laia Coll{-}Sanmartin and
Manel Esteller},
title = {Refinement of computational identification of somatic copy number
alterations using {DNA} methylation microarrays illustrated in cancers
of unknown primary},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac161},
doi = {10.1093/BIB/BBAC161},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BlecuaDVMMCE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BommertWSR22,
author = {Andrea Bommert and
Thomas Welchowski and
Matthias Schmid and
J{\"{o}}rg Rahnenf{\"{u}}hrer},
title = {Benchmark of filter methods for feature selection in high-dimensional
gene expression survival data},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab354},
doi = {10.1093/BIB/BBAB354},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BommertWSR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BondhusVHA22,
author = {Leroy Bondhus and
Roshni Varma and
Yenifer Hernandez and
Valerie A. Arboleda},
title = {Balancing the transcriptome: leveraging sample similarity to improve
measures of gene specificity},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac158},
doi = {10.1093/BIB/BBAC158},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BondhusVHA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BonidiaAASRSC22,
author = {Robson Bonidia and
Anderson P. Avila{-}Santos and
Breno L{\'{\i}}vio Silva de Almeida and
Peter F. Stadler and
Ulisses Nunes da Rocha and
Danilo Sipoli Sanches and
Andr{\'{e}} C. P. L. F. de Carvalho},
title = {BioAutoML: automated feature engineering and metalearning to predict
noncoding RNAs in bacteria},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac218},
doi = {10.1093/BIB/BBAC218},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BonidiaAASRSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BonidiaDSC22,
author = {Robson Bonidia and
Douglas Silva Domingues and
Danilo Sipoli Sanches and
Andr{\'{e}} C. P. L. F. de Carvalho},
title = {MathFeature: feature extraction package for DNA, {RNA} and protein
sequences based on mathematical descriptors},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab434},
doi = {10.1093/BIB/BBAB434},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BonidiaDSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BonnerBYSEBHH22,
author = {Stephen Bonner and
Ian P. Barrett and
Cheng Ye and
Rowan Swiers and
Ola Engkvist and
Andreas Bender and
Charles Tapley Hoyt and
William L. Hamilton},
title = {A review of biomedical datasets relating to drug discovery: a knowledge
graph perspective},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac404},
doi = {10.1093/BIB/BBAC404},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BonnerBYSEBHH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BonnerKETB22,
author = {Stephen Bonner and
Ufuk Kirik and
Ola Engkvist and
Jian Tang and
Ian P. Barrett},
title = {Implications of topological imbalance for representation learning
on biomedical knowledge graphs},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac279},
doi = {10.1093/BIB/BBAC279},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BonnerKETB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BonomoGGR22,
author = {Mariella Bonomo and
Raffaele Giancarlo and
Daniele Greco and
Simona E. Rombo},
title = {Topological ranks reveal functional knowledge encoded in biological
networks: a comparative analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac101},
doi = {10.1093/BIB/BBAC101},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BonomoGGR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BoyrazPEA22,
author = {Asli Boyraz and
Vera Pawlowsky{-}Glahn and
Juan Jos{\'{e}} Egozcue and
Aybar Can Acar},
title = {Principal microbial groups: compositional alternative to phylogenetic
grouping of microbiome data},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac328},
doi = {10.1093/BIB/BBAC328},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BoyrazPEA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BuWWSSBC22,
author = {Kevin Bu and
David S. Wallach and
Zach Wilson and
Nan Shen and
Leopoldo N. Segal and
Emilia Bagiella and
Jos{\'{e}} Carlos Clemente},
title = {Identifying correlations driven by influential observations in large
datasets},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab482},
doi = {10.1093/BIB/BBAB482},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BuWWSSBC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BuckleyLMWWTSAS22,
author = {Paul R. Buckley and
Chloe H. Lee and
Ruichong Ma and
Isaac Woodhouse and
Jeongmin Woo and
Vasily Tsvetkov and
Dmitrii S. Shcherbinin and
Agne Antanaviciute and
Mikhail Shughay and
Margarida Rei and
Alison Simmons and
Hashem Koohy},
title = {Evaluating performance of existing computational models in predicting
{CD8+} {T} cell pathogenic epitopes and cancer neoantigens},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac141},
doi = {10.1093/BIB/BBAC141},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BuckleyLMWWTSAS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BugnonEPGRFRCGA22,
author = {Leandro A Bugnon and
Alejandro A. Edera and
Santiago Prochetto and
Matias Gerard and
Jonathan Raad and
Emilio Fenoy and
Mariano Rubiolo and
Uciel Chorostecki and
Toni Gabald{\'{o}}n and
Federico Ariel and
Leandro E. Di Persia and
Diego H. Milone and
Georgina Stegmayer},
title = {Secondary structure prediction of long noncoding {RNA:} review and
experimental comparison of existing approaches},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac205},
doi = {10.1093/BIB/BBAC205},
timestamp = {Fri, 16 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BugnonEPGRFRCGA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BurenHCWWSLW22,
author = {Eric Van Buren and
Ming Hu and
Liang Cheng and
John Wrobel and
Kirk Wilhelmsen and
Lishan Su and
Yun Li and
Di Wu},
title = {{TWO-SIGMA-G:} a new competitive gene set testing framework for scRNA-seq
data accounting for inter-gene and cell-cell correlation},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac084},
doi = {10.1093/BIB/BBAC084},
timestamp = {Tue, 31 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BurenHCWWSLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BurnsSGHMBSFF22,
author = {Josh J. R. Burns and
Benjamin T. Shealy and
Mitchell S. Greer and
John A. Hadish and
Matthew McGowan and
Tyler Biggs and
Melissa C. Smith and
F. Alex Feltus and
Stephen P. Ficklin},
title = {Addressing noise in co-expression network construction},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab495},
doi = {10.1093/BIB/BBAB495},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BurnsSGHMBSFF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaiFQWZWJGZP22,
author = {Zena Cai and
Ping Fu and
Ye Qiu and
Aiping Wu and
Gaihua Zhang and
Yirong Wang and
Taijiao Jiang and
Xing{-}Yi Ge and
Haizhen Zhu and
Yousong Peng},
title = {vsRNAfinder: a novel method for identifying high-confidence viral
small RNAs from small RNA-Seq data},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac496},
doi = {10.1093/BIB/BBAC496},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CaiFQWZWJGZP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaiVCLG22,
author = {Menglan Cai and
Anna Vesely and
Xu Chen and
Limin Li and
Jelle J. Goeman},
title = {NetTDP: permutation-based true discovery proportions for differential
co-expression network analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac417},
doi = {10.1093/BIB/BBAC417},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CaiVCLG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaiZZWW22,
author = {Hanxuan Cai and
Huimin Zhang and
Duancheng Zhao and
Jingxing Wu and
Ling Wang},
title = {{FP-GNN:} a versatile deep learning architecture for enhanced molecular
property prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac408},
doi = {10.1093/BIB/BBAC408},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CaiZZWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaoHDJQZ22,
author = {Zhen Cao and
Yanting Huang and
Ran Duan and
Peng Jin and
Zhaohui S. Qin and
Shihua Zhang},
title = {Disease category-specific annotation of variants using an ensemble
learning framework},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab438},
doi = {10.1093/BIB/BBAB438},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CaoHDJQZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaoYZFWSWLW22,
author = {Yi Cao and
Zhen{-}Qun Yang and
Xu{-}Lu Zhang and
Wenqi Fan and
Yaowei Wang and
Jiajun Shen and
Dong{-}Qing Wei and
Qing Li and
Xiao{-}Yong Wei},
title = {Identifying the kind behind {SMILES} - anatomical therapeutic chemical
classification using structure-only representations},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac346},
doi = {10.1093/BIB/BBAC346},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/CaoYZFWSWLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CarpiGHSV22,
author = {Giovanna Carpi and
Lev Gorenstein and
Timothy T. Harkins and
Mehrzad Samadi and
Pankaj Vats},
title = {A GPU-accelerated compute framework for pathogen genomic variant identification
to aid genomic epidemiology of infectious disease: a malaria case
study},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac314},
doi = {10.1093/BIB/BBAC314},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/CarpiGHSV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChaiGYLLCSYWXY22,
author = {Mengya Chai and
Yajuan Guo and
Liu Yang and
Jianhui Li and
Shuo Liu and
Lei Chen and
Yuelei Shen and
Yi Yang and
Youchun Wang and
Lida Xu and
Changyuan Yu},
title = {A high-throughput single cell-based antibody discovery approach against
the full-length SARS-CoV-2 spike protein suggests a lack of neutralizing
antibodies targeting the highly conserved {S2} domain},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac070},
doi = {10.1093/BIB/BBAC070},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChaiGYLLCSYWXY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChangZC22,
author = {Wennan Chang and
Chi Zhang and
Sha Cao},
title = {Response to 'Letter to the Editor: on the stability and internal consistency
of component-wise sparse mixture regression based clustering', Zhang
\emph{et al.}},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac262},
doi = {10.1093/BIB/BBAC262},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChangZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChatzigoulasC22,
author = {Alexios Chatzigoulas and
Zoe Cournia},
title = {Predicting protein-membrane interfaces of peripheral membrane proteins
using ensemble machine learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab518},
doi = {10.1093/BIB/BBAB518},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChatzigoulasC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChelliahBKWEYSO22,
author = {Ramachandran Chelliah and
Eric Banan{-}Mwinedaliri and
Imran Khan and
Shuai Wei and
Fazle Elahi and
Su{-}Jung Yeon and
Vijayalakshmi Selvakumar and
Fred Kwame Ofosu and
Momna Rubab and
Hum Hun Ju and
Harikrishna Reddy Rallabandi and
Inamul Hasan Madar and
Ghazala Sultan and
Deog Hwan Oh},
title = {A review on the application of bioinformatics tools in food microbiome
studies},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac007},
doi = {10.1093/BIB/BBAC007},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChelliahBKWEYSO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenGWM22,
author = {Ziwei Chen and
Fuzhou Gong and
Lin Wan and
Liang Ma},
title = {\emph{BiTSC} 2: Bayesian inference of tumor clonal tree by joint analysis
of single-cell {SNV} and {CNA} data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac092},
doi = {10.1093/BIB/BBAC092},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenGWM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenH22,
author = {Xing Chen and
Li Huang},
title = {Computational model for ncRNA research},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac472},
doi = {10.1093/BIB/BBAC472},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenHMDHY22,
author = {Yaowen Chen and
Zhen He and
Yahui Men and
Guohua Dong and
Shuofeng Hu and
Xiaomin Ying},
title = {MetaLogo: a heterogeneity-aware sequence logo generator and aligner},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab591},
doi = {10.1093/BIB/BBAB591},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenHMDHY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenJZZQSZS22,
author = {Zhao Chen and
Yin Jiang and
Xiaoyu Zhang and
Rui Zheng and
Ruijin Qiu and
Yang Sun and
Chen Zhao and
Hongcai Shang},
title = {ResNet18DNN: prediction approach of drug-induced liver injury by deep
neural network with ResNet18},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab503},
doi = {10.1093/BIB/BBAB503},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenJZZQSZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenJZZQSZS22a,
author = {Zhao Chen and
Yin Jiang and
Xiaoyu Zhang and
Rui Zheng and
Ruijin Qiu and
Yang Sun and
Chen Zhao and
Hongcai Shang},
title = {The prediction approach of drug-induced liver injury: response to
the issues of reproducible science of artificial intelligence in real-world
applications},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac196},
doi = {10.1093/BIB/BBAC196},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenJZZQSZS22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenLLYJWGGZYL22,
author = {Jiawen Chen and
Weifang Liu and
Tianyou Luo and
Zhentao Yu and
Minzhi Jiang and
Jia Wen and
Gaorav P. Gupta and
Paola Giusti and
Hongtu Zhu and
Yuchen Yang and
Yun Li},
title = {A comprehensive comparison on cell-type composition inference for
spatial transcriptomics data},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac245},
doi = {10.1093/BIB/BBAC245},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenLLYJWGGZYL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenLYZJXL22,
author = {Siqi Chen and
Tiancheng Li and
Luna Yang and
Fei Zhai and
Xiwei Jiang and
Rongwu Xiang and
Guixia Ling},
title = {Artificial intelligence-driven prediction of multiple drug interactions},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac427},
doi = {10.1093/BIB/BBAC427},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenLYZJXL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenLZBZ22,
author = {Shouzhi Chen and
Qing Li and
Jianping Zhao and
Yannan Bin and
Chunhou Zheng},
title = {NeuroPred-CLQ: incorporating deep temporal convolutional networks
and multi-head attention mechanism to predict neuropeptides},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac319},
doi = {10.1093/BIB/BBAC319},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenLZBZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenQLLLFL22,
author = {Lingxi Chen and
Yuhao Qing and
Ruikang Li and
Chaohui Li and
Hechen Li and
Xikang Feng and
Shuai Cheng Li},
title = {Somatic variant analysis suite: copy number variation clonal visualization
online platform for large-scale single-cell genomics},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab452},
doi = {10.1093/BIB/BBAB452},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenQLLLFL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenT22,
author = {Jen{-}Hao Chen and
Yufeng Jane Tseng},
title = {A general optimization protocol for molecular property prediction
using a deep learning network},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab367},
doi = {10.1093/BIB/BBAB367},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenWRWZBZYZ22,
author = {Qingjian Chen and
Qi{-}Nian Wu and
Yu{-}Ming Rong and
Shixiang Wang and
Zhixiang Zuo and
Long Bai and
Bei Zhang and
Shuqiang Yuan and
Qi Zhao},
title = {Deciphering clonal dynamics and metastatic routines in a rare patient
of synchronous triple-primary tumors and multiple metastases with
MPTevol},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac175},
doi = {10.1093/BIB/BBAC175},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenWRWZBZYZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenWWLZ22,
author = {Yaojia Chen and
Jiacheng Wang and
Chuyu Wang and
Mingxin Liu and
Quan Zou},
title = {Deep learning models for disease-associated circRNA prediction: a
review},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac364},
doi = {10.1093/BIB/BBAC364},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenWWLZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenXHJL22,
author = {Ruolan Chen and
Feng Xia and
Bing Hu and
Shuting Jin and
Xiangrong Liu},
title = {Drug-target interactions prediction via deep collaborative filtering
with multiembeddings},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab520},
doi = {10.1093/BIB/BBAB520},
timestamp = {Tue, 26 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenXHJL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZ22,
author = {Yurui Chen and
Louxin Zhang},
title = {How much can deep learning improve prediction of the responses to
drugs in cancer cell lines?},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab378},
doi = {10.1093/BIB/BBAB378},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZY22,
author = {Ken Chen and
Huiying Zhao and
Yuedong Yang},
title = {Capturing large genomic contexts for accurately predicting enhancer-promoter
interactions},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab577},
doi = {10.1093/BIB/BBAB577},
timestamp = {Wed, 21 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChenZY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChenZYZCL22,
author = {Pei Chen and
Jiayuan Zhong and
Kun Yang and
Xuhang Zhang and
Yingqi Chen and
Rui Liu},
title = {{TPD:} a web tool for tipping-point detection based on dynamic network
biomarker},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac399},
doi = {10.1093/BIB/BBAC399},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChenZYZCL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Cheng22,
author = {Liang Cheng},
title = {Omics data analysis and integration for {COVID-19} patients - editorial},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac471},
doi = {10.1093/BIB/BBAC471},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/Cheng22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChengJXWXZZYMW22,
author = {Qian Cheng and
Shuqing Jiang and
Feng Xu and
Qian Wang and
Yingjie Xiao and
Ruyang Zhang and
Jiuran Zhao and
Jianbing Yan and
Chuang Ma and
Xiangfeng Wang},
title = {Genome optimization via virtual simulation to accelerate maize hybrid
breeding},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab447},
doi = {10.1093/BIB/BBAB447},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChengJXWXZZYMW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChengLSWWDSW22,
author = {Shanshan Cheng and
Jingjing Lyu and
Xian Shi and
Kai Wang and
Zengmiao Wang and
Minghua Deng and
Baoluo Sun and
Chaolong Wang},
title = {Rare variant association tests for ancestry-matched case-control data
based on conditional logistic regression},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab572},
doi = {10.1093/BIB/BBAB572},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChengLSWWDSW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChengLWCRZJT22,
author = {Xuanjin Cheng and
Yongxing Liu and
Jiahe Wang and
Yujie Chen and
Andrew Gordon Robertson and
Xuekui Zhang and
Steven J. M. Jones and
Stefan Taubert},
title = {cSurvival: a web resource for biomarker interactions in cancer outcomes
and in cell lines},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac090},
doi = {10.1093/BIB/BBAC090},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChengLWCRZJT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChengSYDYZQLYX22,
author = {Hang Cheng and
Yuhong Sun and
Qing Yang and
Minggui Deng and
Zhijian Yu and
Gang Zhu and
Jiuxin Qu and
Lei Liu and
Liang Yang and
Yu Xia},
title = {A rapid bacterial pathogen and antimicrobial resistance diagnosis
workflow using Oxford nanopore adaptive sequencing method},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac453},
doi = {10.1093/BIB/BBAC453},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChengSYDYZQLYX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChengXLWCJZXJ22,
author = {Rui Cheng and
Zhaochun Xu and
Meng Luo and
Pingping Wang and
Huimin Cao and
Xiyun Jin and
Wenyang Zhou and
Lixing Xiao and
Qinghua Jiang},
title = {Identification of alternative splicing-derived cancer neoantigens
for mRNA vaccine development},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab553},
doi = {10.1093/BIB/BBAB553},
timestamp = {Fri, 19 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChengXLWCJZXJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChiromMMSS22,
author = {Keilash Chirom and
Md. Zubbair Malik and
Irengbam Rocky Mangangcha and
Pallavi Somvanshi and
R. K. Brojen Singh},
title = {Network medicine in ovarian cancer: topological properties to drug
discovery},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac085},
doi = {10.1093/BIB/BBAC085},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChiromMMSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChongZYCXWHHSWC22,
author = {Hui Chong and
Yuguo Zha and
Qingyang Yu and
Mingyue Cheng and
Guangzhou Xiong and
Nan Wang and
Xinhe Huang and
Shijuan Huang and
Chuqing Sun and
Sicheng Wu and
Wei{-}Hua Chen and
Lu{\'{\i}}s Pedro Coelho and
Kang Ning},
title = {{EXPERT:} transfer learning-enabled context-aware microbial community
classification},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac396},
doi = {10.1093/BIB/BBAC396},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChongZYCXWHHSWC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChuZSL22,
author = {Shih{-}Kai Chu and
Shilin Zhao and
Yu Shyr and
Qi Liu},
title = {Comprehensive evaluation of noise reduction methods for single-cell
{RNA} sequencing data},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab565},
doi = {10.1093/BIB/BBAB565},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChuZSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Dahal-KoiralaBN22,
author = {Shiva Dahal{-}Koirala and
Gabriel Balaban and
Ralf Stefan Neumann and
Lonneke Scheffer and
Knut Erik Aslaksen Lundin and
Victor Greiff and
Ludvig Magne Sollid and
Shuo{-}Wang Qiao and
Geir Kjetil Sandve},
title = {TCRpower: quantifying the detection power of T-cell receptor sequencing
with a novel computational pipeline calibrated by spike-in sequences},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab566},
doi = {10.1093/BIB/BBAB566},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Dahal-KoiralaBN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DaiJPZL22,
author = {Jianhua Dai and
Chao Jiang and
Ruoyao Peng and
Daojian Zeng and
Yangding Li},
title = {Chinese medical dialogue information extraction via contrastive multi-utterance
inference},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac284},
doi = {10.1093/BIB/BBAC284},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DaiJPZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DaiLWDG22,
author = {Qiguo Dai and
Ziqiang Liu and
Zhaowei Wang and
Xiaodong Duan and
Maozu Guo},
title = {GraphCDA: a hybrid graph representation learning framework based on
{GCN} and {GAT} for predicting disease-associated circRNAs},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac379},
doi = {10.1093/BIB/BBAC379},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DaiLWDG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DaiPW22,
author = {Min Dai and
Xiaobing Pei and
Xiu{-}Jie Wang},
title = {Accurate and fast cell marker gene identification with {COSG}},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab579},
doi = {10.1093/BIB/BBAB579},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DaiPW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DaiWLDSG22,
author = {Qiguo Dai and
Zhaowei Wang and
Ziqiang Liu and
Xiaodong Duan and
Jinmiao Song and
Maozu Guo},
title = {Predicting miRNA-disease associations using an ensemble learning framework
with resampling method},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab543},
doi = {10.1093/BIB/BBAB543},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DaiWLDSG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DanilevskyPS22,
author = {Artem Danilevsky and
Avital Luba Polsky and
Noam Shomron},
title = {Adaptive sequencing using nanopores and deep learning of mitochondrial
{DNA}},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac251},
doi = {10.1093/BIB/BBAC251},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DanilevskyPS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DasKGPLPK22,
author = {Trishala Das and
Harbinder Kaur and
Pratibha Gour and
Kartikay Prasad and
Andrew M. Lynn and
Amresh Prakash and
Vijay Kumar},
title = {Intersection of network medicine and machine learning towards investigating
the key biomarkers and pathways underlying amyotrophic lateral sclerosis:
a systematic review},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac442},
doi = {10.1093/BIB/BBAC442},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DasKGPLPK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DengCC22,
author = {Yidi Deng and
Jarny Choi and
Kim{-}Anh L{\^{e}} Cao},
title = {Sincast: a computational framework to predict cell identities in single-cell
transcriptomes using bulk atlases as references},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac088},
doi = {10.1093/BIB/BBAC088},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DengCC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DengQXLZZZ22,
author = {Yifan Deng and
Yang Qiu and
Xinran Xu and
Shichao Liu and
Zhongfei Zhang and
Shanfeng Zhu and
Wen Zhang},
title = {{META-DDIE:} predicting drug-drug interaction events with few-shot
learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab514},
doi = {10.1093/BIB/BBAB514},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DengQXLZZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DengYOSW22,
author = {Jianyuan Deng and
Zhibo Yang and
Iwao Ojima and
Dimitris Samaras and
Fusheng Wang},
title = {Artificial intelligence in drug discovery: applications and techniques},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab430},
doi = {10.1093/BIB/BBAB430},
timestamp = {Mon, 04 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DengYOSW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DeySM22,
author = {Ashmita Dey and
Sagnik Sen and
Ujjwal Maulik},
title = {Study of transcription factor druggabilty for prostate cancer using
structure information, gene regulatory networks and protein moonlighting},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab465},
doi = {10.1093/BIB/BBAB465},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DeySM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DhakalMTC22,
author = {Ashwin Dhakal and
Cole McKay and
John J. Tanner and
Jianlin Cheng},
title = {Artificial intelligence in the prediction of protein-ligand interactions:
recent advances and future directions},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab476},
doi = {10.1093/BIB/BBAB476},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DhakalMTC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DhallPR22,
author = {Anjali Dhall and
Sumeet Patiyal and
Gajendra P. S. Raghava},
title = {HLAncPred: a method for predicting promiscuous non-classical {HLA}
binding sites},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac192},
doi = {10.1093/BIB/BBAC192},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DhallPR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DhandaMG22,
author = {Sandeep Kumar Dhanda and
Jitendra Malviya and
Sudheer Gupta},
title = {Not all {T} cell epitopes are equally desired: a review of \emph{in
silico} tools for the prediction of cytokine-inducing potential of
T-cell epitopes},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac382},
doi = {10.1093/BIB/BBAC382},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DhandaMG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingL22,
author = {Hongyu Ding and
Junwei Luo},
title = {MAMnet: detecting and genotyping deletions and insertions based on
long reads and a deep learning approach},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac195},
doi = {10.1093/BIB/BBAC195},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingLLW22,
author = {Yulian Ding and
Xiujuan Lei and
Bo Liao and
Fang{-}Xiang Wu},
title = {{MLRDFM:} a multi-view Laplacian regularized DeepFM model for predicting
miRNA-disease associations},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac079},
doi = {10.1093/BIB/BBAC079},
timestamp = {Tue, 31 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingLLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingNG22,
author = {Wenze Ding and
Kenta Nakai and
Haipeng Gong},
title = {Protein design via deep learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac102},
doi = {10.1093/BIB/BBAC102},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingNG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingTGZ22,
author = {Yijie Ding and
Jijun Tang and
Fei Guo and
Quan Zou},
title = {Identification of drug-target interactions via multiple kernel-based
triple collaborative matrix factorization},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab582},
doi = {10.1093/BIB/BBAB582},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingTGZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DingYLXXPCASCJ22,
author = {Qian Ding and
Wenyi Yang and
Meng Luo and
Chang Xu and
Zhaochun Xu and
Fenglan Pang and
Yideng Cai and
Anastasia A. Anashkina and
Xi Su and
Na Chen and
Qinghua Jiang},
title = {{CBLRR:} a cauchy-based bounded constraint low-rank representation
method to cluster single-cell RNA-seq data},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac300},
doi = {10.1093/BIB/BBAC300},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DingYLXXPCASCJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DongCCWCDWHHH22,
author = {Xin Dong and
Ke Chen and
Wenbo Chen and
Jun Wang and
Liuping Chang and
Jin Deng and
Lei Wei and
Leng Han and
Chunhua Huang and
Chunjiang He},
title = {circRIP: an accurate tool for identifying circRNA-RBP interactions},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac186},
doi = {10.1093/BIB/BBAC186},
timestamp = {Wed, 30 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DongCCWCDWHHH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DongZFZ22,
author = {Guiying Dong and
Zi{-}Chao Zhang and
Jianfeng Feng and
Xing{-}Ming Zhao},
title = {MorbidGCN: prediction of multimorbidity with a graph convolutional
network based on integration of population phenotypes and disease
network},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac255},
doi = {10.1093/BIB/BBAC255},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DongZFZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DongZLSZ22,
author = {Jingxin Dong and
Mingyi Zhao and
Yuansheng Liu and
Yansen Su and
Xiangxiang Zeng},
title = {Deep learning in retrosynthesis planning: datasets, models and tools},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab391},
doi = {10.1093/BIB/BBAB391},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DongZLSZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DongZWCXGLYZWLT22,
author = {Ji Dong and
Peijie Zhou and
Yichong Wu and
Yidong Chen and
Haoling Xie and
Yuan Gao and
Jiansen Lu and
Jingwei Yang and
Xiannian Zhang and
Lu Wen and
Tiejun Li and
Fuchou Tang},
title = {Integrating single-cell datasets with ambiguous batch information
by incorporating molecular network features},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab366},
doi = {10.1093/BIB/BBAB366},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DongZWCXGLYZWLT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DuWHCPHYL22,
author = {Zhihua Du and
Yang{-}Han Wu and
Yu{-}An Huang and
Jie Chen and
Gui{-}Qing Pan and
Lun Hu and
Zhu{-}Hong You and
Jian{-}Qiang Li},
title = {GraphTGI: an attention-based graph embedding model for predicting
TF-target gene interactions},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac148},
doi = {10.1093/BIB/BBAC148},
timestamp = {Sun, 03 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DuWHCPHYL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DubocPMBDPB22,
author = {V{\'{e}}ronique Duboc and
David Pratella and
Marco Milanesio and
John Boudjarane and
St{\'{e}}phane Descombes and
V{\'{e}}ronique Paquis{-}Flucklinger and
Silvia Bottini},
title = {NiPTUNE: an automated pipeline for noninvasive prenatal testing in
an accurate, integrative and flexible framework},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab380},
doi = {10.1093/BIB/BBAB380},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/DubocPMBDPB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DuhanNK22,
author = {Naveen Duhan and
Jeanette M. Norton and
Rakesh Kaundal},
title = {deepNEC: a novel alignment-free tool for the identification and classification
of nitrogen biochemical network-related enzymes using deep learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac071},
doi = {10.1093/BIB/BBAC071},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DuhanNK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/EderaMS22,
author = {Alejandro A. Edera and
Diego H. Milone and
Georgina Stegmayer},
title = {Anc2vec: embedding gene ontology terms by preserving ancestors relationships},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac003},
doi = {10.1093/BIB/BBAC003},
timestamp = {Fri, 25 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/EderaMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FanCP22,
author = {Yongxian Fan and
Meijun Chen and
Xiaoyong Pan},
title = {{GCRFLDA:} scoring lncRNA-disease associations using graph convolution
matrix completion with conditional random field},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab361},
doi = {10.1093/BIB/BBAB361},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FanCP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FanKDMSW22,
author = {Peihao Fan and
Julia Kofler and
Ying Ding and
Michael Marks and
Robert A. Sweet and
Lirong Wang},
title = {Efficacy difference of antipsychotics in Alzheimer's disease and schizophrenia:
explained with network efficiency and pathway analysis methods},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac394},
doi = {10.1093/BIB/BBAC394},
timestamp = {Wed, 20 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FanKDMSW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FanLZWLX22,
author = {Jiaxin Fan and
Yafei Lyu and
Qihuang Zhang and
Xuran Wang and
Mingyao Li and
Rui Xiao},
title = {MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac430},
doi = {10.1093/BIB/BBAC430},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FanLZWLX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FangLL22,
author = {Yiming Fang and
Xuejun Liu and
Hui Liu},
title = {Attention-aware contrastive learning for predicting {T} cell receptor-antigen
binding specificity},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac378},
doi = {10.1093/BIB/BBAC378},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FangLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FangSAIJH22,
author = {Mingyan Fang and
Zheng Su and
Hassan Abolhassani and
Yuval Itan and
Xin Jin and
Lennart Hammarstr{\"{o}}m},
title = {{VIPPID:} a gene-specific single nucleotide variant pathogenicity
prediction tool for primary immunodeficiency diseases},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac176},
doi = {10.1093/BIB/BBAC176},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FangSAIJH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FengHLZZ22,
author = {Qiongqiong Feng and
Minghua Hou and
Jun Liu and
Kai{-}Long Zhao and
Guijun Zhang},
title = {Construct a variable-length fragment library for de novo protein structure
prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac086},
doi = {10.1093/BIB/BBAC086},
timestamp = {Tue, 31 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FengHLZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FengSLL22,
author = {Ziyan Feng and
Zihao Shen and
Honglin Li and
Shiliang Li},
title = {e-TSN: an interactive visual exploration platform for target-disease
knowledge mapping from literature},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac465},
doi = {10.1093/BIB/BBAC465},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FengSLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FengWYAQXG22,
author = {Jitong Feng and
Shengbo Wu and
Hongpeng Yang and
Chengwei Ai and
Jianjun Qiao and
Junhai Xu and
Fei Guo},
title = {Microbe-bridged disease-metabolite associations identification by
heterogeneous graph fusion},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac423},
doi = {10.1093/BIB/BBAC423},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FengWYAQXG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FengYFS22,
author = {Yi{-}Yang Feng and
Hui Yu and
Yue{-}Hua Feng and
Jian{-}Yu Shi},
title = {Directed graph attention networks for predicting asymmetric drug-drug
interactions},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac151},
doi = {10.1093/BIB/BBAC151},
timestamp = {Thu, 27 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FengYFS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FenoyES22,
author = {Emilio Fenoy and
Alejandro A. Edera and
Georgina Stegmayer},
title = {Transfer learning in proteins: evaluating novel protein learned representations
for bioinformatics tasks},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac232},
doi = {10.1093/BIB/BBAC232},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FenoyES22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Fernandez-OrthR22,
author = {Dietmar Fern{\'{a}}ndez{-}Orth and
Manuel Rueda and
Babita Singh and
Mauricio Moldes and
Aina Jene and
Marta Ferri and
Claudia Vasallo and
Lauren A. Fromont and
Arcadi Navarro and
Jordi Rambla},
title = {A quality control portal for sequencing data deposited at the European
genome-phenome archive},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac136},
doi = {10.1093/BIB/BBAC136},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Fernandez-OrthR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FiroozbakhtYS22,
author = {Farzaneh Firoozbakht and
Behnam Yousefi and
Benno Schwikowski},
title = {An overview of machine learning methods for monotherapy drug response
prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab408},
doi = {10.1093/BIB/BBAB408},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/FiroozbakhtYS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FloresLZHCYPJZG22,
author = {Mario Flores and
Zhentao Liu and
Tinghe Zhang and
Md Musaddaqui Hasib and
Yu{-}Chiao Chiu and
Zhenqing Ye and
Karla Paniagua and
Sumin Jo and
Jianqiu Zhang and
Shou{-}Jiang Gao and
Yu{-}Fang Jin and
Yidong Chen and
Yufei Huang},
title = {Deep learning tackles single-cell analysis - a survey of deep learning
for scRNA-seq analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab531},
doi = {10.1093/BIB/BBAB531},
timestamp = {Mon, 27 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FloresLZHCYPJZG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ForniCPCS22,
author = {Diego Forni and
Rachele Cagliani and
Chiara Pontremoli and
Mario Clerici and
Manuela Sironi},
title = {The substitution spectra of coronavirus genomes},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab382},
doi = {10.1093/BIB/BBAB382},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ForniCPCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GabellaDD22,
author = {Chiara Gabella and
Severine Duvaud and
Christine Durinx},
title = {Managing the life cycle of a portfolio of open data resources at the
{SIB} Swiss Institute of Bioinformatics},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab478},
doi = {10.1093/BIB/BBAB478},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GabellaDD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GableSLRM22,
author = {Annika L. Gable and
Damian Szklarczyk and
David Lyon and
Jo{\~{a}}o F. Matias Rodrigues and
Christian von Mering},
title = {Systematic assessment of pathway databases, based on a diverse collection
of user-submitted experiments},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac355},
doi = {10.1093/BIB/BBAC355},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GableSLRM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaffoBMB22,
author = {Enrico Gaffo and
Alessia Buratin and
Anna Dal Molin and
Stefania Bortoluzzi},
title = {Sensitive, reliable and robust circRNA detection from RNA-seq with
CirComPara2},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab418},
doi = {10.1093/BIB/BBAB418},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaffoBMB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GanGGXZ22,
author = {Yanglan Gan and
Cheng Guo and
Wenjing Guo and
Guangwei Xu and
Guobing Zou},
title = {Entropy-based inference of transition states and cellular trajectory
for single-cell transcriptomics},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac225},
doi = {10.1093/BIB/BBAC225},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GanGGXZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GanHZZG22,
author = {Yanglan Gan and
Xingyu Huang and
Guobing Zou and
Shuigeng Zhou and
Jihong Guan},
title = {Deep structural clustering for single-cell RNA-seq data jointly through
autoencoder and graph neural network},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac018},
doi = {10.1093/BIB/BBAC018},
timestamp = {Fri, 25 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GanHZZG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GanYZ22,
author = {Dailin Gan and
Guosheng Yin and
Yan Dora Zhang},
title = {The {GR2D2} estimator for the precision matrices},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac426},
doi = {10.1093/BIB/BBAC426},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GanYZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoCZSX22,
author = {Ling Gao and
Hui Cui and
Tiangang Zhang and
Nan Sheng and
Ping Xuan},
title = {Prediction of drug-disease associations by integrating common topologies
of heterogeneous networks and specific topologies of subnets},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab467},
doi = {10.1093/BIB/BBAB467},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaoCZSX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoLQGS22,
author = {Meihong Gao and
Shuhui Liu and
Yang Qi and
Xinpeng Guo and
Xuequn Shang},
title = {{GAE-LGA:} integration of multi-omics data with graph autoencoders
to identify lncRNA-PCG associations},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac452},
doi = {10.1093/BIB/BBAC452},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GaoLQGS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoSGWZSGZLNZ22,
author = {Yue Gao and
Shipeng Shang and
Shuang Guo and
Xinyue Wang and
Hanxiao Zhou and
Yue Sun and
Jing Gan and
Yakun Zhang and
Xia Li and
Shangwei Ning and
Yunpeng Zhang},
title = {AgingBank: a manually curated knowledgebase and high-throughput analysis
platform that provides experimentally supported multi-omics data relevant
to aging in multiple species},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac438},
doi = {10.1093/BIB/BBAC438},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GaoSGWZSGZLNZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoYLC22,
author = {Rong Gao and
Jinling Yan and
Peiluan Li and
Luonan Chen},
title = {Detecting the critical states during disease development based on
temporal network flow entropy},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac164},
doi = {10.1093/BIB/BBAC164},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaoYLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GaoZSW22,
author = {Qian Gao and
Yu Zhang and
Hongwei Sun and
Tong Wang},
title = {Evaluation of propensity score methods for causal inference with high-dimensional
covariates},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac227},
doi = {10.1093/BIB/BBAC227},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GaoZSW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Garcia-JacasGMT22,
author = {C{\'{e}}sar R. Garc{\'{\i}}a{-}Jacas and
Luis A. Garc{\'{\i}}a{-}Gonz{\'{a}}lez and
Felix Martinez{-}Rios and
Issac P. Tapia{-}Contreras and
Carlos A. Brizuela},
title = {Handcrafted versus non-handcrafted (self-supervised) features for
the classification of antimicrobial peptides: complementary or redundant?},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac428},
doi = {10.1093/BIB/BBAC428},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Garcia-JacasGMT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Garcia-JacasPGB22,
author = {C{\'{e}}sar R. Garc{\'{\i}}a{-}Jacas and
Sergio Alejandro Pinacho{-}Castellanos and
Luis A. Garc{\'{\i}}a{-}Gonz{\'{a}}lez and
Carlos A. Brizuela},
title = {Do deep learning models make a difference in the identification of
antimicrobial peptides?},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac094},
doi = {10.1093/BIB/BBAC094},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/Garcia-JacasPGB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GautamGGRMMAGSS22,
author = {Vishakha Gautam and
Rahul Gupta and
Deepti Gupta and
Anubhav Ruhela and
Aayushi Mittal and
Sanjay Kumar Mohanty and
Sakshi Arora and
Ria Gupta and
Chandan Saini and
Debarka Sengupta and
Natarajan Arul Murugan and
Gaurav Ahuja},
title = {\emph{deepGraphh}: AI-driven web service for graph-based quantitative
structure-activity relationship analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac288},
doi = {10.1093/BIB/BBAC288},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GautamGGRMMAGSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GeZXASY22,
author = {Fang Ge and
Ying Zhang and
Jian Xu and
Muhammad Arif and
Jiangning Song and
Dong{-}Jun Yu},
title = {Prediction of disease-associated nsSNPs by integrating multi-scale
ResNet models with deep feature fusion},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab530},
doi = {10.1093/BIB/BBAB530},
timestamp = {Tue, 15 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GeZXASY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GelhausenMSASEB22,
author = {Rick Gelhausen and
Teresa M{\"{u}}ller and
Sarah L. Svensson and
Omer S. Alkhnbashi and
Cynthia M. Sharma and
Florian Eggenhofer and
Rolf Backofen},
title = {RiboReport - benchmarking tools for ribosome profiling-based identification
of open reading frames in bacteria},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab549},
doi = {10.1093/BIB/BBAB549},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GelhausenMSASEB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GliozzoMNPPGPVC22,
author = {Jessica Gliozzo and
Marco Mesiti and
Marco Notaro and
Alessandro Petrini and
Alex Patak and
Antonio Puertas Gallardo and
Alberto Paccanaro and
Giorgio Valentini and
Elena Casiraghi},
title = {Heterogeneous data integration methods for patient similarity networks},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac207},
doi = {10.1093/BIB/BBAC207},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GliozzoMNPPGPVC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Gomez-GonzalezC22,
author = {Paula J. G{\'{o}}mez{-}Gonz{\'{a}}lez and
Susana G. Campino and
Jody Phelan and
Taane G. Clark},
title = {Portable sequencing of \emph{Mycobacterium tuberculosis} for clinical
and epidemiological applications},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac256},
doi = {10.1093/BIB/BBAC256},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Gomez-GonzalezC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GongWWSLX22,
author = {Weikang Gong and
Junjie Wee and
Min{-}Chun Wu and
Xiaohan Sun and
Chunhua Li and
Kelin Xia},
title = {Persistent spectral simplicial complex-based machine learning for
chromosomal structural analysis in cellular differentiation},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac168},
doi = {10.1093/BIB/BBAC168},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GongWWSLX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GoossensHVDVWR22,
author = {Sander N. Goossens and
Tim H. Heupink and
Elise De Vos and
Anzaan Dippenaar and
Margaretha De Vos and
Rob Warren and
Annelies Van Rie},
title = {Detection of minor variants in Mycobacterium tuberculosis whole genome
sequencing data},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab541},
doi = {10.1093/BIB/BBAB541},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GoossensHVDVWR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GoudeyGVZ22,
author = {Benjamin Goudey and
Nicholas Geard and
Karin Verspoor and
Justin Zobel},
title = {Propagation, detection and correction of errors using the sequence
database network},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac416},
doi = {10.1093/BIB/BBAC416},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GoudeyGVZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GrzesikAWM22,
author = {Piotr Grzesik and
Dariusz Rafal Augustyn and
Lukasz Wycislik and
Dariusz Mrozek},
title = {Serverless computing in omics data analysis and integration},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab349},
doi = {10.1093/BIB/BBAB349},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GrzesikAWM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuH22,
author = {Zuguang Gu and
Daniel H{\"{u}}bschmann},
title = {Improve consensus partitioning via a hierarchical procedure},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac048},
doi = {10.1093/BIB/BBAC048},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuZXYLL22,
author = {Yaowen Gu and
Si Zheng and
Zidu Xu and
Qijin Yin and
Liang Li and
Jiao Li},
title = {An efficient curriculum learning-based strategy for molecular graph
learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac099},
doi = {10.1093/BIB/BBAC099},
timestamp = {Wed, 02 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuZXYLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuanPLSGXF22,
author = {Renchu Guan and
Haoyu Pang and
Yanchun Liang and
Zhongjun Shao and
Xin Gao and
Dong Xu and
Xiaoyue Feng},
title = {Discovering trends and hotspots of biosafety and biosecurity research
via machine learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac194},
doi = {10.1093/BIB/BBAC194},
timestamp = {Tue, 20 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuanPLSGXF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuanWSLHZ22,
author = {Xiaoyu Guan and
Yuqin Wang and
Wei Shao and
Zhongnian Li and
Shuo Huang and
Daoqiang Zhang},
title = {S2Snet: deep learning for low molecular weight {RNA} identification
with nanopore},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac098},
doi = {10.1093/BIB/BBAC098},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuanWSLHZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoESSTXZ22,
author = {Yang Guo and
Fatemeh Esfahani and
Xiaojian Shao and
Venkatesh Srinivasan and
Alex Thomo and
Li Xing and
Xuekui Zhang},
title = {Integrative {COVID-19} biological network inference with probabilistic
core decomposition},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab455},
doi = {10.1093/BIB/BBAB455},
timestamp = {Mon, 25 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuoESSTXZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoHYS22,
author = {Xinyun Guo and
Huan He and
Jialin Yu and
Shaoping Shi},
title = {{PKSPS:} a novel method for predicting kinase of specific phosphorylation
sites based on maximum weighted bipartite matching algorithm and phosphorylation
sequence enrichment analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab436},
doi = {10.1093/BIB/BBAB436},
timestamp = {Tue, 22 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuoHYS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoJZ22,
author = {Xiaoyi Guo and
Yizhang Jiang and
Quan Zou},
title = {Structured Sparse Regularized {TSK} Fuzzy System for predicting therapeutic
peptides},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac135},
doi = {10.1093/BIB/BBAC135},
timestamp = {Mon, 09 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuoJZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoSA22,
author = {Margaret G. Guo and
Daniel N. Sosa and
Russ B. Altman},
title = {Challenges and opportunities in network-based solutions for biological
questions},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab437},
doi = {10.1093/BIB/BBAB437},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/GuoSA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuoYWYZRP22,
author = {Lu{-}Xiang Guo and
Zhu{-}Hong You and
Lei Wang and
Changqing Yu and
Bo{-}Wei Zhao and
Zhong{-}Hao Ren and
Jie Pan},
title = {A novel circRNA-miRNA association prediction model based on structural
deep neural network embedding},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac391},
doi = {10.1093/BIB/BBAC391},
timestamp = {Thu, 11 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuoYWYZRP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuptaVM22,
author = {Priya Gupta and
Sureshkumar Venkadesan and
Debasisa Mohanty},
title = {Pf-Phospho: a machine learning-based phosphorylation sites prediction
tool for \emph{Plasmodium} proteins},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac249},
doi = {10.1093/BIB/BBAC249},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuptaVM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GuzziPM22,
author = {Pietro Hiram Guzzi and
Francesco Petrizzelli and
Tommaso Mazza},
title = {Disease spreading modeling and analysis: a survey},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac230},
doi = {10.1093/BIB/BBAC230},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GuzziPM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GwakR22,
author = {Ho{-}Jin Gwak and
Mina Rho},
title = {ViBE: a hierarchical {BERT} model to identify eukaryotic viruses using
metagenome sequencing data},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac204},
doi = {10.1093/BIB/BBAC204},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GwakR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HaberSP22,
author = {Anna Christine Haber and
Ulrich Sax and
Fabian Prasser},
title = {Open tools for quantitative anonymization of tabular phenotype data:
literature review},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac440},
doi = {10.1093/BIB/BBAC440},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HaberSP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HamamotoTMKTBSS22,
author = {Ryuji Hamamoto and
Ken Takasawa and
Hidenori Machino and
Kazuma Kobayashi and
Satoshi Takahashi and
Amina Bolatkan and
Norio Shinkai and
Akira Sakai and
Rina Aoyama and
Masayoshi Yamada and
Ken Asada and
Masaaki Komatsu and
Koji Okamoto and
Hirokazu Kameoka and
Syuzo Kaneko},
title = {Application of non-negative matrix factorization in oncology: one
approach for establishing precision medicine},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac246},
doi = {10.1093/BIB/BBAC246},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HamamotoTMKTBSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanCCZHCZHCKGL22,
author = {Wenkai Han and
Yuqi Cheng and
Jiayang Chen and
Huawen Zhong and
Zhihang Hu and
Siyuan Chen and
Licheng Zong and
Liang Hong and
Ting{-}Fung Chan and
Irwin King and
Xin Gao and
Yu Li},
title = {Self-supervised contrastive learning for integrative single cell RNA-seq
data analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac377},
doi = {10.1093/BIB/BBAC377},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HanCCZHCZHCKGL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanHFPASLMSGPW22,
author = {Siyu Han and
Jialing Huang and
Francesco Foppiano and
Cornelia Prehn and
Jerzy Adamski and
Karsten Suhre and
Ying Li and
Giuseppe Matullo and
Freimut Schliess and
Christian Gieger and
Annette Peters and
Rui Wang{-}Sattler},
title = {{TIGER:} technical variation elimination for metabolomics data using
ensemble learning architecture},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab535},
doi = {10.1093/BIB/BBAB535},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HanHFPASLMSGPW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanSZXSY22,
author = {Ke Han and
Long{-}Chen Shen and
Yi{-}Heng Zhu and
Jian Xu and
Jiangning Song and
Dong{-}Jun Yu},
title = {MAResNet: predicting transcription factor binding sites by combining
multi-scale bottom-up and top-down attention and residual network},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab445},
doi = {10.1093/BIB/BBAB445},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HanSZXSY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanWCACYL22,
author = {Yanqiang Han and
Zhilong Wang and
An Chen and
Imran Ali and
Junfei Cai and
Simin Ye and
Jin{-}Jin Li},
title = {An inductive transfer learning force field {(ITLFF)} protocol builds
protein force fields in seconds},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab590},
doi = {10.1093/BIB/BBAB590},
timestamp = {Mon, 18 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HanWCACYL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HanYSYZPFL22,
author = {Siyu Han and
Xiao Yang and
Hang Sun and
Hu Yang and
Qi Zhang and
Cheng Peng and
Wensi Fang and
Ying Li},
title = {{LION:} an integrated {R} package for effective prediction of ncRNA-protein
interaction},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac420},
doi = {10.1093/BIB/BBAC420},
timestamp = {Wed, 12 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HanYSYZPFL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HaoLLLXKLLXQLL22,
author = {Yangyang Hao and
Liang Lu and
Anna Liu and
Xue Lin and
Li Xiao and
Xiaoyue Kong and
Kai Li and
Fengji Liang and
Jianghui Xiong and
Lina Qu and
Yinghui Li and
Jian Li},
title = {Integrating bioinformatic strategies in spatial life science research},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac415},
doi = {10.1093/BIB/BBAC415},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HaoLLLXKLLXQLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeCC22,
author = {Haohuai He and
Guanxing Chen and
Calvin Yu{-}Chian Chen},
title = {3DGT-DDI: 3D graph and text based neural network for drug-drug interaction
prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac134},
doi = {10.1093/BIB/BBAC134},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HeCC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeJJLZMSGW22,
author = {Wenjia He and
Yi Jiang and
Junru Jin and
Zhongshen Li and
Jiaojiao Zhao and
Balachandran Manavalan and
Ran Su and
Xin Gao and
Leyi Wei},
title = {Accelerating bioactive peptide discovery via mutual information-based
meta-learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab499},
doi = {10.1093/BIB/BBAB499},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HeJJLZMSGW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeWXBTTGXY22,
author = {Binsheng He and
Kun Wang and
Ju Xiang and
Pingping Bing and
Min Tang and
Geng Tian and
Cheng Guo and
Miao Xu and
Jialiang Yang},
title = {{DGHNE:} network enhancement-based method in identifying disease-causing
genes through a heterogeneous biomedical network},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac405},
doi = {10.1093/BIB/BBAC405},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HeWXBTTGXY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HeYJ22,
author = {Qifan He and
Jian Yang and
Yonghai Jin},
title = {Immune infiltration and clinical significance analyses of the coagulation-related
genes in hepatocellular carcinoma},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac291},
doi = {10.1093/BIB/BBAC291},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HeYJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HicklQWMH22,
author = {Oskar Hickl and
Pedro Queir{\'{o}}s and
Paul Wilmes and
Patrick May and
Anna Heintz{-}Buschart},
title = {\emph{binny}: an automated binning algorithm to recover high-quality
genomes from complex metagenomic datasets},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac431},
doi = {10.1093/BIB/BBAC431},
timestamp = {Sun, 15 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HicklQWMH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HippeLBPKDHSC22,
author = {Kyle Hippe and
Cade Lilley and
Joshua William Berkenpas and
Ciri Chandana Pocha and
Kiyomi Kishaba and
Hui Ding and
Jie Hou and
Dong Si and
Renzhi Cao},
title = {ZoomQA: residue-level protein model accuracy estimation with machine
learning on sequential and 3D structural features},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab384},
doi = {10.1093/BIB/BBAB384},
timestamp = {Tue, 27 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HippeLBPKDHSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HoLO22,
author = {Quang{-}Thai Ho and
Nguyen{-}Quoc{-}Khanh Le and
Yu{-}Yen Ou},
title = {mCNN-ETC: identifying electron transporters and their functional families
by using multiple windows scanning techniques in convolutional neural
networks with evolutionary information of protein sequences},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab352},
doi = {10.1093/BIB/BBAB352},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HoLO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HongFSPJCE22,
author = {Ye Hong and
Dani Flinkman and
Tomi Suomi and
Sami Pietil{\"{a}} and
Peter James and
Eleanor Coffey and
Laura L. Elo},
title = {PhosPiR: an automated phosphoproteomic pipeline in {R}},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab510},
doi = {10.1093/BIB/BBAB510},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HongFSPJCE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HongFSPJCE22a,
author = {Ye Hong and
Dani Flinkman and
Tomi Suomi and
Sami Pietil{\"{a}} and
Peter James and
Eleanor Coffey and
Laura L. Elo},
title = {Correction to: PhosPiR: an automated phosphoproteomic pipeline in
{R}},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac153},
doi = {10.1093/BIB/BBAC153},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HongFSPJCE22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HouPZZZ22,
author = {Minghua Hou and
Chunxiang Peng and
Xiaogen Zhou and
Biao Zhang and
Guijun Zhang},
title = {Multi contact-based folding method for de novo protein structure prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab463},
doi = {10.1093/BIB/BBAB463},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HouPZZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HouZYWMLL22,
author = {Siyu Hou and
Peng Zhang and
Kuo Yang and
Lan Wang and
Changzheng Ma and
Yanda Li and
Shao Li},
title = {Decoding multilevel relationships with the human tissue-cell-molecule
network},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac170},
doi = {10.1093/BIB/BBAC170},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HouZYWMLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuCZSX22,
author = {Kaimiao Hu and
Hui Cui and
Tiangang Zhang and
Chang Sun and
Ping Xuan},
title = {{ALDPI:} adaptively learning importance of multi-scale topologies
and multi-modality similarities for drug-protein interaction prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab606},
doi = {10.1093/BIB/BBAB606},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuCZSX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuGFLWHWZ22,
author = {Jing Hu and
Jie Gao and
Xiaomin Fang and
Zijing Liu and
Fan Wang and
Weili Huang and
Hua Wu and
Guodong Zhao},
title = {DTSyn: a dual-transformer-based neural network to predict synergistic
drug combinations},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac302},
doi = {10.1093/BIB/BBAC302},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuGFLWHWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuLLYP22,
author = {Hang Hu and
Zhong Li and
Xiangjie Li and
Minzhe Yu and
Xiutao Pan},
title = {ScCAEs: deep clustering of single-cell RNA-seq via convolutional autoencoder
embedding and soft K-means},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab321},
doi = {10.1093/BIB/BBAB321},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuLLYP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuRGJTCDY22,
author = {Wei{-}Xin Hu and
Yu Rong and
Yan Guo and
Feng Jiang and
Wen Tian and
Hao Chen and
Shan{-}Shan Dong and
Tie{-}Lin Yang},
title = {ExsgRNA: reduce off-target efficiency by on-target mismatched sgRNA},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac183},
doi = {10.1093/BIB/BBAC183},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuRGJTCDY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuXLMYWWCLXZ22,
author = {Congxue Hu and
Yingqi Xu and
Feng Li and
Wanqi Mi and
He Yu and
Xinran Wang and
Xin Wen and
Shuaijun Chen and
Xia Li and
Yanjun Xu and
Yunpeng Zhang},
title = {Identifying and characterizing drug sensitivity-related lncRNA-TF-gene
regulatory triplets},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac366},
doi = {10.1093/BIB/BBAC366},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuXLMYWWCLXZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuZS22,
author = {Jialu Hu and
Yuanke Zhong and
Xuequn Shang},
title = {A versatile and scalable single-cell data integration algorithm based
on domain-adversarial and variational approximation},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab400},
doi = {10.1093/BIB/BBAB400},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangJGW22,
author = {Xiaotai Huang and
Songwei Jia and
Lin Gao and
Jing Wu},
title = {Reconstruction of human protein-coding gene functional association
network based on machine learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab552},
doi = {10.1093/BIB/BBAB552},
timestamp = {Fri, 25 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangJGW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangKWCW22,
author = {Kai{-}Yao Huang and
Hui{-}Ju Kao and
Tzu{-}Hsiang Weng and
Chia{-}Hung Chen and
Shun{-}Long Weng},
title = {iDVIP: identification and characterization of viral integrase inhibitory
peptides},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac406},
doi = {10.1093/BIB/BBAC406},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangKWCW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangLJL22,
author = {Yuyao Huang and
Jiesi Luo and
Runyu Jing and
Menglong Li},
title = {Multi-model predictive analysis of {RNA} solvent accessibility based
on modified residual attention mechanism},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac470},
doi = {10.1093/BIB/BBAC470},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangLJL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangLLSZW22,
author = {Lei Huang and
Jiecong Lin and
Xiangtao Li and
Linqi Song and
Zetian Zheng and
Ka{-}Chun Wong},
title = {{EGFI:} drug-drug interaction extraction and generation with fusion
of enriched entity and sentence information},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab451},
doi = {10.1093/BIB/BBAB451},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangLLSZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangLLZMCLW22,
author = {Lei Huang and
Jiecong Lin and
Rui Liu and
Zetian Zheng and
Lingkuan Meng and
Xingjian Chen and
Xiangtao Li and
Ka{-}Chun Wong},
title = {CoaDTI: multi-modal co-attention based framework for drug-target interaction
annotation},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac446},
doi = {10.1093/BIB/BBAC446},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangLLZMCLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangNNGLW22,
author = {Neng Huang and
Fan Nie and
Peng Ni and
Xin Gao and
Feng Luo and
Jianxin Wang},
title = {BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab405},
doi = {10.1093/BIB/BBAB405},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangNNGLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangWYG22,
author = {Zimo Huang and
Jun Wang and
Zhongmin Yan and
Maozu Guo},
title = {Differentially expressed genes prediction by multiple self-attention
on epigenetics data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac117},
doi = {10.1093/BIB/BBAC117},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangWYG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangYLJWARHL22,
author = {Le Huang and
Yuchen Yang and
Gang Li and
Minzhi Jiang and
Jia Wen and
Armen Abnousi and
Jonathan D. Rosen and
Ming Hu and
Yun Li},
title = {A systematic evaluation of Hi-C data enhancement methods for enhancing
PLAC-seq and HiChIP data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac145},
doi = {10.1093/BIB/BBAC145},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangYLJWARHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangZC22,
author = {Li Huang and
Li Zhang and
Xing Chen},
title = {Updated review of advances in microRNAs and complex diseases: taxonomy,
trends and challenges of computational models},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac358},
doi = {10.1093/BIB/BBAC358},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangZC22a,
author = {Li Huang and
Li Zhang and
Xing Chen},
title = {Updated review of advances in microRNAs and complex diseases: experimental
results, databases, webservers and data fusion},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac397},
doi = {10.1093/BIB/BBAC397},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangZC22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangZC22b,
author = {Li Huang and
Li Zhang and
Xing Chen},
title = {Updated review of advances in microRNAs and complex diseases: towards
systematic evaluation of computational models},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac407},
doi = {10.1093/BIB/BBAC407},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangZC22b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangZLDWZL22,
author = {Haojie Huang and
Gongming Zhou and
Xuejun Liu and
Lei Deng and
Chen Wu and
Dachuan Zhang and
Hui Liu},
title = {Contrastive learning-based computational histopathology predict differential
expression of cancer driver genes},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac294},
doi = {10.1093/BIB/BBAC294},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HuangZLDWZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuffmanOHDTH22,
author = {Anthony Huffman and
Edison Ong and
Junguk Hur and
Adonis D'mello and
Herv{\'{e}} Tettelin and
Yongqun He},
title = {{COVID-19} vaccine design using reverse and structural vaccinology,
ontology-based literature mining and machine learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac190},
doi = {10.1093/BIB/BBAC190},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuffmanOHDTH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Hussain22,
author = {Waqar Hussain},
title = {sAMP-PFPDeep: Improving accuracy of short antimicrobial peptides prediction
using three different sequence encodings and deep neural networks},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab487},
doi = {10.1093/BIB/BBAB487},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/Hussain22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JaakkolaE22,
author = {Maria K. Jaakkola and
Laura L. Elo},
title = {Estimating cell type-specific differential expression using deconvolution},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab433},
doi = {10.1093/BIB/BBAB433},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JaakkolaE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JacobsenKCRS22,
author = {Julius O. B. Jacobsen and
Catherine Kelly and
Valentina Cipriani and
Peter N. Robinson and
Damian Smedley},
title = {Evaluation of phenotype-driven gene prioritization methods for Mendelian
diseases},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac188},
doi = {10.1093/BIB/BBAC188},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JacobsenKCRS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JarnotZGG22,
author = {Patryk Jarnot and
Joanna Ziemska{-}Legiecka and
Marcin Grynberg and
Aleksandra Gruca},
title = {Insights from analyses of low complexity regions with canonical methods
for protein sequence comparison},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac299},
doi = {10.1093/BIB/BBAC299},
timestamp = {Tue, 04 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JarnotZGG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JeonHPLM22,
author = {Young{-}Jun Jeon and
Md. Mehedi Hasan and
Hyun Woo Park and
Ki Wook Lee and
Balachandran Manavalan},
title = {{TACOS:} a novel approach for accurate prediction of cell-specific
long noncoding RNAs subcellular localization},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac243},
doi = {10.1093/BIB/BBAC243},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JeonHPLM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JeongSTTGBPL22,
author = {Yunhee Jeong and
Lisa Barros de Andrade e Sousa and
Dominik Thalmeier and
Reka Toth and
Marlene Ganslmeier and
Kersten Breuer and
Christoph Plass and
Pavlo Lutsik},
title = {Systematic evaluation of cell-type deconvolution pipelines for sequencing-based
bulk {DNA} methylomes},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac248},
doi = {10.1093/BIB/BBAC248},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JeongSTTGBPL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiAPES22,
author = {Jiahui Ji and
Maryam Anwar and
Enrico Petretto and
Costanza Emanueli and
Prashant Kumar Srivastava},
title = {{PPMS:} {A} framework to Profile Primary MicroRNAs from Single-cell
RNA-sequencing datasets},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac419},
doi = {10.1093/BIB/BBAC419},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JiAPES22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiLZST22,
author = {Hongchao Ji and
Xue Lu and
Zhenxiang Zheng and
Siyuan Sun and
Chris Soon Heng Tan},
title = {ProSAP: a {GUI} software tool for statistical analysis and assessment
of thermal stability data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac057},
doi = {10.1093/BIB/BBAC057},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiLZST22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiaYJLWLHLCZ22,
author = {Lihua Jia and
Wen Yao and
Yingru Jiang and
Yang Li and
Zhizhan Wang and
Haoran Li and
Fangfang Huang and
Jiaming Li and
Tiantian Chen and
Huiyong Zhang},
title = {Development of interactive biological web applications with R/Shiny},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab415},
doi = {10.1093/BIB/BBAB415},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiaYJLWLHLCZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangCLLHX22,
author = {Peiran Jiang and
Ying Chi and
Xiao{-}Shuang Li and
Xiang Liu and
Xian{-}Sheng Hua and
Kelin Xia},
title = {Molecular persistent spectral image (Mol-PSI) representation for machine
learning models in drug design},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab527},
doi = {10.1093/BIB/BBAB527},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JiangCLLHX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangHL22,
author = {Han{-}Jing Jiang and
Yabing Huang and
Qianpeng Li},
title = {Spectral clustering of single cells using Siamese nerual network combined
with improved affinity matrix},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac113},
doi = {10.1093/BIB/BBAC113},
timestamp = {Tue, 31 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangJYFJL22,
author = {Likun Jiang and
Changzhi Jiang and
Xinyu Yu and
Rao Fu and
Shuting Jin and
Xiangrong Liu},
title = {DeepTTA: a transformer-based model for predicting cancer drug response},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac100},
doi = {10.1093/BIB/BBAC100},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangJYFJL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangLLWXDYCS22,
author = {Zhonghua Jiang and
Yongmei Lu and
Zhuochong Liu and
Wei Wu and
Xinyi Xu and
Andr{\'{a}}s Dinny{\'{e}}s and
Zhonghua Yu and
Li Chen and
Qun Sun},
title = {Drug resistance prediction and resistance genes identification in
\emph{Mycobacterium tuberculosis} based on a hierarchical attentive
neural network utilizing genome-wide variants},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac041},
doi = {10.1093/BIB/BBAC041},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangLLWXDYCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangNWWZLLCS22,
author = {Mengyun Jiang and
Weidong Ning and
Shishi Wu and
Xingwei Wang and
Kun Zhu and
Aomei Li and
Yongyao Li and
Shifeng Cheng and
Bo Song},
title = {Three-nucleotide periodicity of nucleotide diversity in a population
enables the identification of open reading frames},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac210},
doi = {10.1093/BIB/BBAC210},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangNWWZLLCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangSWHLWCWH22,
author = {Dejun Jiang and
Huiyong Sun and
Jike Wang and
Chang{-}Yu Hsieh and
Yuquan Li and
Zhenxing Wu and
Dong{-}Sheng Cao and
Jian Wu and
Tingjun Hou},
title = {Out-of-the-box deep learning prediction of quantum-mechanical partial
charges by graph representation and transfer learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab597},
doi = {10.1093/BIB/BBAB597},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangSWHLWCWH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangSWNLY22,
author = {Lu Jiang and
Jiahao Sun and
Yue Wang and
Qiao Ning and
Na Luo and
Minghao Yin},
title = {Identifying drug-target interactions via heterogeneous graph attention
networks combined with cross-modal similarities},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac016},
doi = {10.1093/BIB/BBAC016},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JiangSWNLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JiangXL22,
author = {Zheng Jiang and
Si{-}Rui Xiao and
Rong Liu},
title = {Dissecting and predicting different types of binding sites in nucleic
acids based on structural information},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab411},
doi = {10.1093/BIB/BBAB411},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JiangXL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JinLL22,
author = {Xiaopeng Jin and
Xiaoling Luo and
Bin Liu},
title = {Correction to: PHR-search: a search framework for protein remote homology
detection based on the predicted protein hierarchical relationships},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac103},
doi = {10.1093/BIB/BBAC103},
timestamp = {Fri, 25 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JinLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JinLL22a,
author = {Xiaopeng Jin and
Xiaoling Luo and
Bin Liu},
title = {PHR-search: a search framework for protein remote homology detection
based on the predicted protein hierarchical relationships},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab609},
doi = {10.1093/BIB/BBAB609},
timestamp = {Fri, 25 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JinLL22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JinLSL22,
author = {Chong Jin and
Brian Lee and
Li Shen and
Qi Long},
title = {Integrating multi-omics summary data using a Mendelian randomization
framework},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac376},
doi = {10.1093/BIB/BBAC376},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JinLSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JinSLSPSA22,
author = {Kang Jin and
Daniel J. Schnell and
Guangyuan Li and
Nathan Salomonis and
V. B. Surya Prasath and
Rhonda Szczesniak and
Bruce J. Aronow},
title = {CellDrift: inferring perturbation responses in temporally sampled
single-cell data},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac324},
doi = {10.1093/BIB/BBAC324},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/JinSLSPSA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JjingoMSKKAGKJW22,
author = {Daudi Jjingo and
Gerald Mboowa and
Ivan Sserwadda and
Robert Kakaire and
Davis Kiberu and
Marion Amujal and
Ronald Galiwango and
David Kateete and
Moses Joloba and
Christopher C. Whalen},
title = {Bioinformatics mentorship in a resource limited setting},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab399},
doi = {10.1093/BIB/BBAB399},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JjingoMSKKAGKJW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JoNBS22,
author = {Taeho Jo and
Kwangsik Nho and
Paula Bice and
Andrew J. Saykin},
title = {Deep learning-based identification of genetic variants: application
to Alzheimer's disease classification},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac022},
doi = {10.1093/BIB/BBAC022},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JoNBS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JunttilaSE22,
author = {Sini Junttila and
Johannes Smolander and
Laura L. Elo},
title = {Benchmarking methods for detecting differential states between conditions
from multi-subject single-cell RNA-seq data},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac286},
doi = {10.1093/BIB/BBAC286},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JunttilaSE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KaminskiLJBMSD22,
author = {Kamil Kaminski and
Jan Ludwiczak and
Maciej Jasinski and
Adriana Bukala and
Rafal Madaj and
Krzysztof Szczepaniak and
Stanislaw Dunin{-}Horkawicz},
title = {Rossmann-toolbox: a deep learning-based protocol for the prediction
and design of cofactor specificity in Rossmann fold proteins},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab371},
doi = {10.1093/BIB/BBAB371},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KaminskiLJBMSD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KanJGTG22,
author = {Yingxin Kan and
Limin Jiang and
Yan Guo and
Jijun Tang and
Fei Guo},
title = {Two-stage-vote ensemble framework based on integration of mutation
data and gene interaction network for uncovering driver genes},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab429},
doi = {10.1093/BIB/BBAB429},
timestamp = {Tue, 12 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KanJGTG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KangKM22,
author = {Mingon Kang and
Euiseong Ko and
Tesfaye B. Mersha},
title = {A roadmap for multi-omics data integration using deep learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab454},
doi = {10.1093/BIB/BBAB454},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KangKM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KangLKJYHG22,
author = {Yu{-}Jian Kang and
Jing{-}Yi Li and
Lan Ke and
Shuai Jiang and
Dechang Yang and
Mei Hou and
Ge Gao},
title = {Quantitative model suggests both intrinsic and contextual features
contribute to the transcript coding ability determination in cells},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab483},
doi = {10.1093/BIB/BBAB483},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KangLKJYHG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KangML22,
author = {Qiang Kang and
Jun Meng and
Yushi Luan},
title = {{RNAI-FRID:} novel feature representation method with information
enhancement and dimension reduction for {RNA-RNA} interaction},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac107},
doi = {10.1093/BIB/BBAC107},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KangML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KangMSL22,
author = {Qiang Kang and
Jun Meng and
Chenglin Su and
Yushi Luan},
title = {Mining plant endogenous target mimics from miRNA-lncRNA interactions
based on dual-path parallel ensemble pruning method},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab440},
doi = {10.1093/BIB/BBAB440},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KangMSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KangZLHY22,
author = {Chuanze Kang and
Han Zhang and
Zhuo Liu and
Shenwei Huang and
Yanbin Yin},
title = {{LR-GNN:} a graph neural network based on link representation for
predicting molecular associations},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab513},
doi = {10.1093/BIB/BBAB513},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KangZLHY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KarikomiZN22,
author = {Mathew Karikomi and
Peijie Zhou and
Qing Nie},
title = {{DURIAN:} an integrative deconvolution and imputation method for robust
signaling analysis of single-cell transcriptomics data},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac223},
doi = {10.1093/BIB/BBAC223},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KarikomiZN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KarimiKASS22,
author = {Mohammad Reza Karimi and
Amir{-}Hossein Karimi and
Shamsozoha Abolmaali and
Mehdi Sadeghi and
Ulf Schmitz},
title = {Prospects and challenges of cancer systems medicine: from genes to
disease networks},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab343},
doi = {10.1093/BIB/BBAB343},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KarimiKASS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KaundalLDF22,
author = {Rakesh Kaundal and
Cristian D. Loaiza and
Naveen Duhan and
Nicholas Flann},
title = {deepHPI: a comprehensive deep learning platform for accurate prediction
and visualization of host-pathogen protein-protein interactions},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac125},
doi = {10.1093/BIB/BBAC125},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KaundalLDF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KeurRKM22,
author = {Nick Keur and
Isis Rica{\~{n}}o{-}Ponce and
Vinod Kumar and
Vasiliki Matzaraki},
title = {A systematic review of analytical methods used in genetic association
analysis of the X-chromosome},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac287},
doi = {10.1093/BIB/BBAC287},
timestamp = {Tue, 10 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KeurRKM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KhalighiJBSLGV22,
author = {Sirvan Khalighi and
Peronne Joseph and
Deepak Babu and
Salendra Singh and
Thomas LaFramboise and
Kishore Guda and
Vinay Varadan},
title = {SYSMut: decoding the functional significance of rare somatic mutations
in cancer},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac280},
doi = {10.1093/BIB/BBAC280},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KhalighiJBSLGV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KhaliliRGK22,
author = {Elham Khalili and
Shahin Ramazi and
Faezeh Ghanati and
Samaneh Kouchaki},
title = {Predicting protein phosphorylation sites in soybean using interpretable
deep tabular learning network},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac015},
doi = {10.1093/BIB/BBAC015},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KhaliliRGK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KhanalTZC22,
author = {Jhabindra Khanal and
Hilal Tayara and
Quan Zou and
Kil To Chong},
title = {DeepCap-Kcr: accurate identification and investigation of protein
lysine crotonylation sites based on capsule network},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab492},
doi = {10.1093/BIB/BBAB492},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KhanalTZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KimPLN22,
author = {Hyunho Kim and
Minsu Park and
Ingoo Lee and
Hojung Nam},
title = {BayeshERG: a robust, reliable and interpretable deep learning model
for predicting hERG channel blockers},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac211},
doi = {10.1093/BIB/BBAC211},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KimPLN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KodikaraEC22,
author = {Saritha Kodikara and
Susan Ellul and
Kim{-}Anh L{\^{e}} Cao},
title = {Statistical challenges in longitudinal microbiome data analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac273},
doi = {10.1093/BIB/BBAC273},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KodikaraEC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KowaldBMPESF22,
author = {Axel Kowald and
Israel Barrantes and
Steffen M{\"{o}}ller and
Daniel Palmer and
Hugo Murua Escobar and
Anne Schwerk and
Georg Fuellen},
title = {Transfer learning of clinical outcomes from preclinical molecular
data, principles and perspectives},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac133},
doi = {10.1093/BIB/BBAC133},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KowaldBMPESF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KumarKMMBSD22,
author = {Sanjay Kumar and
Geethu S. Kumar and
Subhrangsu Sundar Maitra and
Petr Mal{\'{y}} and
Shiv Bharadwaj and
Pradeep Sharma and
Vivek Dhar Dwivedi},
title = {Viral informatics: bioinformatics-based solution for managing viral
infections},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac326},
doi = {10.1093/BIB/BBAC326},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KumarKMMBSD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KurataTM22,
author = {Hiroyuki Kurata and
Sho Tsukiyama and
Balachandran Manavalan},
title = {iACVP: markedly enhanced identification of anti-coronavirus peptides
using a dataset-specific word2vec model},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac265},
doi = {10.1093/BIB/BBAC265},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KurataTM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KurucBH22,
author = {Fabrizio Kuruc and
Harald Binder and
Moritz Hess},
title = {Stratified neural networks in a time-to-event setting},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab392},
doi = {10.1093/BIB/BBAB392},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KurucBH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LaiX22,
author = {Boqiao Lai and
Jinbo Xu},
title = {Accurate protein function prediction via graph attention networks
with predicted structure information},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab502},
doi = {10.1093/BIB/BBAB502},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LaiX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LallGRB22,
author = {Snehalika Lall and
Abhik Ghosh and
Sumanta Ray and
Sanghamitra Bandyopadhyay},
title = {sc-REnF: An entropy guided robust feature selection for single-cell
RNA-seq data},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab517},
doi = {10.1093/BIB/BBAB517},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LallGRB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LanDCZLPC22,
author = {Wei Lan and
Yi Dong and
Qingfeng Chen and
Ruiqing Zheng and
Jin Liu and
Yi Pan and
Yi{-}Ping Phoebe Chen},
title = {{KGANCDA:} predicting circRNA-disease associations based on knowledge
graph attention network},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab494},
doi = {10.1093/BIB/BBAB494},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LanDCZLPC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeeST22,
author = {Chien Lee and
Bo{-}Han Su and
Yufeng Jane Tseng},
title = {Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case
study involving the use of G-protein-coupled receptors},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac308},
doi = {10.1093/BIB/BBAC308},
timestamp = {Tue, 04 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LeeST22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LenaSN22,
author = {Pietro Di Lena and
Claudia Sala and
Christine Nardini},
title = {Evaluation of different computational methods for {DNA} methylation-based
biological age},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac274},
doi = {10.1093/BIB/BBAC274},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LenaSN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LengW22,
author = {Jiacheng Leng and
Ling{-}Yun Wu},
title = {Interaction-based transcriptome analysis via differential network
inference},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac466},
doi = {10.1093/BIB/BBAC466},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LengW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeungJZZHHQ22,
author = {Ricky Wai Tak Leung and
Xiaosen Jiang and
Xueqing Zong and
Yanhong Zhang and
Xinlin Hu and
Yaohua Hu and
Jing Qin},
title = {{CORN} - Condition Orientated Regulatory Networks: bridging conditions
to gene networks},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac402},
doi = {10.1093/BIB/BBAC402},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LeungJZZHHQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiCFSGMDSZHW22,
author = {Lei Li and
Siriruk Changrob and
Yanbin Fu and
Olivia Stovicek and
Jenna J. Guthmiller and
Joshua J. C. McGrath and
Haley L. Dugan and
Christopher T. Stamper and
Nai{-}Ying Zheng and
Min Huang and
Patrick C. Wilson},
title = {Librator: a platform for the optimized analysis, design, and expression
of mutable influenza viral antigens},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac028},
doi = {10.1093/BIB/BBAC028},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiCFSGMDSZHW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiDLHGXWPJZWCLS22,
author = {Fuyi Li and
Shuangyu Dong and
Andr{\'{e}} Leier and
Meiya Han and
Xudong Guo and
Jing Xu and
Xiaoyu Wang and
Shirui Pan and
Cangzhi Jia and
Yang Zhang and
Geoffrey I. Webb and
Lachlan J. M. Coin and
Chen Li and
Jiangning Song},
title = {Positive-unlabeled learning in bioinformatics and computational biology:
a brief review},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab461},
doi = {10.1093/BIB/BBAB461},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiDLHGXWPJZWCLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiDYPWSCWWW22,
author = {Hui Li and
Zhaohong Deng and
Haitao Yang and
Xiaoyong Pan and
Zhisheng Wei and
Hong{-}Bin Shen and
Kup{-}Sze Choi and
Lei Wang and
Shitong Wang and
Jing Wu},
title = {circRNA-binding protein site prediction based on multi-view deep learning,
subspace learning and multi-view classifier},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab394},
doi = {10.1093/BIB/BBAB394},
timestamp = {Mon, 04 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiDYPWSCWWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiFWZCP22,
author = {Zutan Li and
Jingya Fang and
Shining Wang and
Liangyun Zhang and
Yuanyuan Chen and
Cong Pian},
title = {Adapt-Kcr: a novel deep learning framework for accurate prediction
of lysine crotonylation sites based on learning embedding features
and attention architecture},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac037},
doi = {10.1093/BIB/BBAC037},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiFWZCP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiGLLW22,
author = {Hongfei Li and
Yue Gong and
Yifeng Liu and
Hao Lin and
Guohua Wang},
title = {Detection of transcription factors binding to methylated {DNA} by
deep recurrent neural network},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab533},
doi = {10.1093/BIB/BBAB533},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiGLLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiGZCLZW22,
author = {Chuanxing Li and
Jing Gao and
Zicheng Zhang and
Lu Chen and
Xun Li and
Meng Zhou and
{\AA}sa M. Wheelock},
title = {Multiomics integration-based molecular characterizations of {COVID-19}},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab485},
doi = {10.1093/BIB/BBAB485},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiGZCLZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiHWLY22,
author = {Yang Li and
Xue{-}Gang Hu and
Lei Wang and
Pei{-}Pei Li and
Zhu{-}Hong You},
title = {{MNMDCDA:} prediction of circRNA-disease associations by learning
mixed neighborhood information from multiple distances},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac479},
doi = {10.1093/BIB/BBAC479},
timestamp = {Fri, 03 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiHWLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiHWQLWJH22,
author = {Xiangmei Li and
Yalan He and
Jiashuo Wu and
Jiayue Qiu and
Ji Li and
Qian Wang and
Ying Jiang and
Junwei Han},
title = {A novel pathway mutation perturbation score predicts the clinical
outcomes of immunotherapy},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac360},
doi = {10.1093/BIB/BBAC360},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiHWQLWJH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiLHZW22,
author = {Xiangtao Li and
Shaochuan Li and
Lei Huang and
Shixiong Zhang and
Ka{-}Chun Wong},
title = {High-throughput single-cell RNA-seq data imputation and characterization
with surrogate-assisted automated deep learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab368},
doi = {10.1093/BIB/BBAB368},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiLHZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiLLHCX22,
author = {Xiao{-}Shuang Li and
Xiang Liu and
Le Lu and
Xian{-}Sheng Hua and
Ying Chi and
Kelin Xia},
title = {Multiphysical graph neural network {(MP-GNN)} for {COVID-19} drug
design},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac231},
doi = {10.1093/BIB/BBAC231},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiLLHCX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiLMCLLCL22,
author = {Xingyu Li and
Xue Lin and
Xueyin Mei and
Pin Chen and
Anna Liu and
Weicheng Liang and
Shan Chang and
Jian Li},
title = {{HLA3D:} an integrated structure-based computational toolkit for immunotherapy},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac076},
doi = {10.1093/BIB/BBAC076},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiLMCLLCL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiLXY22,
author = {Rufeng Li and
Lixin Li and
Yungang Xu and
Juan Yang},
title = {Erratum to: Machine learning meets omics applications and perspectives},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab560},
doi = {10.1093/BIB/BBAB560},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiLXY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiLXY22a,
author = {Rufeng Li and
Lixin Li and
Yungang Xu and
Juan Yang},
title = {Machine learning meets omics: applications and perspectives},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab460},
doi = {10.1093/BIB/BBAB460},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiLXY22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiMWDXSWDLBZYCZ22,
author = {Jianfeng Li and
Benben Miao and
Shixiang Wang and
Wei Dong and
Houshi Xu and
Chenchen Si and
Wei Wang and
Songqi Duan and
Jiacheng Lou and
Zhiwei Bao and
Hailuan Zeng and
Zengzeng Yang and
Wenyan Cheng and
Fei Zhao and
Jianming Zeng and
Xue{-}Song Liu and
Renxie Wu and
Yang Shen and
Zhu Chen and
Saijuan Chen and
Mingjie Wang},
title = {Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready
biomedical data visualization},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac261},
doi = {10.1093/BIB/BBAC261},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiMWDXSWDLBZYCZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiOZYZ22,
author = {Hui{-}Sheng Li and
Le Ou{-}Yang and
Yuan Zhu and
Hong Yan and
Xiao{-}Fei Zhang},
title = {scDEA: differential expression analysis in single-cell RNA-sequencing
data via ensemble learning},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab402},
doi = {10.1093/BIB/BBAB402},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiOZYZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiPZWGSGSXNZL22,
author = {Xin Li and
Xu Pan and
Hanxiao Zhou and
Peng Wang and
Yue Gao and
Shipeng Shang and
Shuang Guo and
Jie Sun and
Zhiying Xiong and
Shangwei Ning and
Hui Zhi and
Xia Li},
title = {Comprehensive characterization genetic regulation and chromatin landscape
of enhancer-associated long non-coding RNAs and their implication
in human cancer},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab401},
doi = {10.1093/BIB/BBAB401},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiPZWGSGSXNZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiQWW22,
author = {Yang Li and
Guanyu Qiao and
Keqi Wang and
Guohua Wang},
title = {Drug-target interaction predication via multi-channel graph neural
networks},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab346},
doi = {10.1093/BIB/BBAB346},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiQWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiWZKJ22,
author = {Jing Li and
Ya{-}Nan Wu and
Sen Zhang and
Xiao{-}Ping Kang and
Tao Jiang},
title = {Deep learning based on biologically interpretable genome representation
predicts two types of human adaptation of SARS-CoV-2 variants},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac036},
doi = {10.1093/BIB/BBAC036},
timestamp = {Thu, 30 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiWZKJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiY22,
author = {Tang Li and
Yanbin Yin},
title = {Critical assessment of pan-genomic analysis of metagenome-assembled
genomes},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac413},
doi = {10.1093/BIB/BBAC413},
timestamp = {Thu, 12 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiYLYZZLQDCZ22,
author = {Fengcheng Li and
Jiayi Yin and
Mingkun Lu and
Qingxia Yang and
Zhenyu Zeng and
Bing Zhang and
Zhaorong Li and
Yunqing Qiu and
Haibin Dai and
Yuzong Chen and
Feng Zhu},
title = {ConSIG: consistent discovery of molecular signature from {OMIC} data},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac253},
doi = {10.1093/BIB/BBAC253},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiYLYZZLQDCZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZ22,
author = {Menglu Li and
Wen Zhang},
title = {{PHIAF:} prediction of phage-host interactions with GAN-based data
augmentation and sequence-based feature fusion},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab348},
doi = {10.1093/BIB/BBAB348},
timestamp = {Fri, 22 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZJ22,
author = {He Li and
Hangxiao Zhang and
Hangjin Jiang},
title = {Combining power of different methods to detect associations in large
data sets},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab488},
doi = {10.1093/BIB/BBAB488},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiZJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZLHY22,
author = {Wei Li and
Han Zhang and
Minghe Li and
Mingjing Han and
Yanbin Yin},
title = {{MGEGFP:} a multi-view graph embedding method for gene function prediction
based on adaptive estimation with {GCN}},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac333},
doi = {10.1093/BIB/BBAC333},
timestamp = {Tue, 11 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiZLHY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZPZZGZX22,
author = {Yongsheng Li and
Yunpeng Zhang and
Tao Pan and
Ping Zhou and
Weiwei Zhou and
Yueying Gao and
Shaojiang Zheng and
Juan Xu},
title = {Shedding light on the hidden human proteome expands immunopeptidome
in cancer},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac034},
doi = {10.1093/BIB/BBAC034},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiZPZZGZX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZSRW22,
author = {Guodong Li and
Ping Zhang and
Weicheng Sun and
Chengjuan Ren and
Lei Wang},
title = {Bridging-BPs: a novel approach to predict potential drug-target interactions
based on a bridging heterogeneous graph and BPs2vec},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab557},
doi = {10.1093/BIB/BBAB557},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiZSRW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZZYQGZ22,
author = {Fengcheng Li and
Ying Zhou and
Ying Zhang and
Jiayi Yin and
Yunqing Qiu and
Jianqing Gao and
Feng Zhu},
title = {{POSREG:} proteomic signature discovered by simultaneously optimizing
its reproducibility and generalizability},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac040},
doi = {10.1093/BIB/BBAC040},
timestamp = {Fri, 03 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiZZYQGZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZZZZWCFZZGC22,
author = {Peng Li and
Haoran Zhang and
Wuxia Zhang and
Yuanyuan Zhang and
Lingmin Zhan and
Ning Wang and
Caiping Chen and
Bangze Fu and
Jinzhong Zhao and
Xuezhong Zhou and
Shuzhen Guo and
Jianxin Chen},
title = {{TMNP:} a transcriptome-based multi-scale network pharmacology platform
for herbal medicine},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab542},
doi = {10.1093/BIB/BBAB542},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiZZZZWCFZZGC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiangJYOXF22,
author = {Tianjian Liang and
Chen Jiang and
Jiayi Yuan and
Yasmin Othman and
Xiang{-}Qun Xie and
Zhiwei Feng},
title = {Differential performance of RoseTTAFold in antibody modeling},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac152},
doi = {10.1093/BIB/BBAC152},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiangJYOXF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiangLKWSWML22,
author = {Lu Liang and
Ye Liu and
Bo Kang and
Ru Wang and
Meng{-}Yu Sun and
Qi Wu and
Xiangfei Meng and
Jianping Lin},
title = {Large-scale comparison of machine learning algorithms for target prediction
of natural products},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac359},
doi = {10.1093/BIB/BBAC359},
timestamp = {Wed, 08 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiangLKWSWML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiangLYHCLG22,
author = {Jing J. Liang and
Zong{-}Wei Li and
Cai{-}Tong Yue and
Zhuo Hu and
Han Cheng and
Zexian Liu and
Weifeng Guo},
title = {Multi-modal optimization to identify personalized biomarkers for disease
prediction of individual patients with cancer},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac254},
doi = {10.1093/BIB/BBAC254},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiangLYHCLG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinHCZW22,
author = {Jiecong Lin and
Lei Huang and
Xingjian Chen and
Shixiong Zhang and
Ka{-}Chun Wong},
title = {DeepMotifSyn: a deep learning approach to synthesize heterodimeric
{DNA} motifs},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab334},
doi = {10.1093/BIB/BBAB334},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LinHCZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinLCMK22,
author = {Yu{-}Da Lin and
Yi{-}Chen Lee and
Chih{-}Po Chiang and
Sin{-}Hua Moi and
Jung{-}Yu Kan},
title = {{MOAI:} a multi-outcome interaction identification approach reveals
an interaction between vaspin and carcinoembryonic antigen on colorectal
cancer prognosis},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab427},
doi = {10.1093/BIB/BBAB427},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LinLCMK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinLDLEWZGWWHW22,
author = {Cui{-}Xiang Lin and
Hong{-}Dong Li and
Chao Deng and
Weisheng Liu and
Shannon Erhardt and
Fang{-}Xiang Wu and
Xing{-}Ming Zhao and
Yuanfang Guan and
Jun Wang and
Daifeng Wang and
Bin Hu and
Jianxin Wang},
title = {An integrated brain-specific network identifies genes associated with
neuropathologic and clinical traits of Alzheimer's disease},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab522},
doi = {10.1093/BIB/BBAB522},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LinLDLEWZGWWHW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinQWLCLLZ22,
author = {Anqi Lin and
Chang Qi and
Ting Wei and
Mengyao Li and
Quan Cheng and
Zaoqu Liu and
Peng Luo and
Jian Zhang},
title = {{CAMOIP:} a web server for comprehensive analysis on multi-omics of
immunotherapy in pan-cancer},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac129},
doi = {10.1093/BIB/BBAC129},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LinQWLCLLZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinWWLLCY22,
author = {Miao{-}Hsia Lin and
Pei{-}Shan Wu and
Tzu{-}Hsuan Wong and
I{-}Ying Lin and
Johnathan Lin and
J{\"{u}}rgen Cox and
Sung{-}Huan Yu},
title = {Benchmarking differential expression, imputation and quantification
methods for proteomics data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac138},
doi = {10.1093/BIB/BBAC138},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LinWWLLCY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinWZCLFJWZXW22,
author = {Shenggeng Lin and
Yanjing Wang and
Lingfeng Zhang and
Yanyi Chu and
Yatong Liu and
Yitian Fang and
Mingming Jiang and
Qiankun Wang and
Bowen Zhao and
Yi Xiong and
Dong{-}Qing Wei},
title = {{MDF-SA-DDI:} predicting drug-drug interaction events based on multi-source
drug fusion, multi-source feature fusion and transformer self-attention
mechanism},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab421},
doi = {10.1093/BIB/BBAB421},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LinWZCLFJWZXW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LinWZWYDLHB22,
author = {Weiping Lin and
Lianlian Wu and
Yixin Zhang and
Yuqi Wen and
Bowei Yan and
Chong Dai and
Kun{-}Hong Liu and
Song He and
Xiaochen Bo},
title = {An enhanced cascade-based deep forest model for drug combination prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab562},
doi = {10.1093/BIB/BBAB562},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LinWZWYDLHB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Liu22,
author = {Yu Liu},
title = {\emph{scDeconv}: an {R} package to deconvolve bulk {DNA} methylation
data with scRNA-seq data and paired bulk {RNA-DNA} methylation data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac150},
doi = {10.1093/BIB/BBAC150},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Liu22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuDLSWWZW22,
author = {Hao Liu and
Jiaqi Dai and
Ke Li and
Yang Sun and
Haoran Wei and
Hong Wang and
Chunxia Zhao and
Dao Wen Wang},
title = {Performance evaluation of computational methods for splice-disrupting
variants and improving the performance using the machine learning-based
framework},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac334},
doi = {10.1093/BIB/BBAC334},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuDLSWWZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuGZZWZL22,
author = {Bao{-}Min Liu and
Ying{-}Lian Gao and
Dai{-}Jun Zhang and
Feng Zhou and
Juan Wang and
Chun{-}Hou Zheng and
Jin{-}Xing Liu},
title = {A new framework for drug-disease association prediction combing light-gated
message passing neural network and gated fusion mechanism},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac457},
doi = {10.1093/BIB/BBAC457},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuGZZWZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuHG22,
author = {Fei Liu and
Monika Heiner and
David R. Gilbert},
title = {Hybrid modelling of biological systems: current progress and future
prospects},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac081},
doi = {10.1093/BIB/BBAC081},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuHG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuHLD22,
author = {Hui Liu and
Yibiao Huang and
Xuejun Liu and
Lei Deng},
title = {Attention-wise masked graph contrastive learning for predicting molecular
property},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac303},
doi = {10.1093/BIB/BBAC303},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuHLD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuHYW22,
author = {Mengfei Liu and
Linlin Hao and
Sien Yang and
Xiaohui Wu},
title = {PolyAtailor: measuring poly(A) tail length from short-read and long-read
sequencing data},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac271},
doi = {10.1093/BIB/BBAC271},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuHYW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuJYTZ22,
author = {Fei Liu and
Xiangkang Jiang and
Jingyuan Yang and
Jiawei Tao and
Mao Zhang},
title = {A chronotherapeutics-applicable multi-target therapeutics based on
{AI:} Example of therapeutic hypothermia},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac365},
doi = {10.1093/BIB/BBAC365},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuJYTZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuLCTRT22,
author = {Zhichao Liu and
Ting Li and
Skylar Connor and
Shraddha Thakkar and
Ruth Roberts and
Weida Tong},
title = {Best practice and reproducible science are required to advance artificial
intelligence in real-world applications},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac237},
doi = {10.1093/BIB/BBAC237},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuLCTRT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuLHPTZY22,
author = {Wei Liu and
Hui Lin and
Li Huang and
Li Peng and
Ting Tang and
Qi Zhao and
Li Yang},
title = {Identification of miRNA-disease associations via deep forest ensemble
learning based on autoencoder},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac104},
doi = {10.1093/BIB/BBAC104},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuLHPTZY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuLLW22,
author = {Qiaoming Liu and
Ximei Luo and
Jie Li and
Guohua Wang},
title = {scESI: evolutionary sparse imputation for single-cell transcriptomes
from nearest neighbor cells},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac144},
doi = {10.1093/BIB/BBAC144},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuLLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuLYLWZLWTY22,
author = {Yachen Liu and
Yalan Lin and
Wenxian Yang and
Yuxiang Lin and
Yujuan Wu and
Zheyang Zhang and
Nuoqi Lin and
Xianlong Wang and
Mengsha Tong and
Rongshan Yu},
title = {Application of individualized differential expression analysis in
human cancer proteome},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac096},
doi = {10.1093/BIB/BBAC096},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuLYLWZLWTY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuPMTP22,
author = {Bin Liu and
Dimitrios Papadopoulos and
Fragkiskos D. Malliaros and
Grigorios Tsoumakas and
Apostolos N. Papadopoulos},
title = {Multiple similarity drug-target interaction prediction with random
walks and matrix factorization},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac353},
doi = {10.1093/BIB/BBAC353},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuPMTP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuPRG22,
author = {Jian Liu and
Yichen Pan and
Zhihan Ruan and
Jun Guo},
title = {{SCDD:} a novel single-cell RNA-seq imputation method with diffusion
and denoising},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac398},
doi = {10.1093/BIB/BBAC398},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuPRG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuSHFXZ22,
author = {Xuan Liu and
Congzhi Song and
Feng Huang and
Haitao Fu and
Wenjie Xiao and
Wen Zhang},
title = {GraphCDR: a graph neural network method with contrastive learning
for cancer drug response prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab457},
doi = {10.1093/BIB/BBAB457},
timestamp = {Fri, 22 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuSHFXZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuSYLYF22,
author = {Wei Liu and
Xingen Sun and
Li Yang and
Kaiwen Li and
Yu Yang and
Xiangzheng Fu},
title = {{NSCGRN:} a network structure control method for gene regulatory network
inference},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac156},
doi = {10.1093/BIB/BBAC156},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuSYLYF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuSZL22,
author = {Mengya Liu and
Zhan{-}Li Sun and
Zhigang Zeng and
Kin{-}Man Lam},
title = {MGF6mARice: prediction of {DNA} N6-methyladenine sites in rice by
exploiting molecular graph feature and residual block},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac082},
doi = {10.1093/BIB/BBAC082},
timestamp = {Tue, 31 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuSZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuTCG22,
author = {Jing Liu and
Xinghua Tang and
Shuanglong Cui and
Xiao Guan},
title = {Predicting the function of rice proteins through Multi-instance Multi-label
Learning based on multiple features fusion},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac095},
doi = {10.1093/BIB/BBAC095},
timestamp = {Tue, 31 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuTCG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuWDHSYZLW22,
author = {Siyuan Liu and
Yusong Wang and
Yifan Deng and
Liang He and
Bin Shao and
Jian Yin and
Nanning Zheng and
Tie{-}Yan Liu and
Tong Wang},
title = {Improved drug-target interaction prediction with intermolecular graph
transformer},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac162},
doi = {10.1093/BIB/BBAC162},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuWDHSYZLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuWDSHZYJ22,
author = {Yusong Liu and
Tongxin Wang and
Ben Duggan and
Michael F. Sharpnack and
Kun Huang and
Jie Zhang and
Xiufen Ye and
Travis S. Johnson},
title = {{SPCS:} a spatial and pattern combined smoothing method for spatial
transcriptomic expression},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac116},
doi = {10.1093/BIB/BBAC116},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuWDSHZYJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuWW22,
author = {Qiaoming Liu and
Jun Wan and
Guohua Wang},
title = {A survey on computational methods in discovering protein inhibitors
of SARS-CoV-2},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab416},
doi = {10.1093/BIB/BBAB416},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuXDLZW22,
author = {Tiantian Liu and
Peirong Xu and
Yueyao Du and
Hui Lu and
Hongyu Zhao and
Tao Wang},
title = {{MZINBVA:} variational approximation for multilevel zero-inflated
negative-binomial models for association analysis in microbiome surveys},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab443},
doi = {10.1093/BIB/BBAB443},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuXDLZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuZWZZ22,
author = {Yue Liu and
Junfeng Zhang and
Shu{-}Lin Wang and
Xiangxiang Zeng and
Wei Zhang},
title = {Are dropout imputation methods for scRNA-seq effective for scATAC-seq
data?},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab442},
doi = {10.1093/BIB/BBAB442},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiuZWZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiuZX22,
author = {Huan Liu and
Quan Zou and
Yun Xu},
title = {A novel fast multiple nucleotide sequence alignment method based on
FM-index},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab519},
doi = {10.1093/BIB/BBAB519},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LiuZX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LopesP22,
author = {Fabr{\'{\i}}cio Martins Lopes and
Matheus Henrique Pimenta{-}Zanon},
title = {Letter on the results of the BASiNET method in the paper 'A systematic
evaluation of computational tools for lncRNA identification'},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac321},
doi = {10.1093/BIB/BBAC321},
timestamp = {Tue, 04 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LopesP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LouCLTLT22,
author = {Zhengzheng Lou and
Zhaoxu Cheng and
Hui Li and
Zhixia Teng and
Yang Liu and
Zhen Tian},
title = {Predicting miRNA-disease associations via learning multimodal networks
and fusing mixed neighborhood information},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac159},
doi = {10.1093/BIB/BBAC159},
timestamp = {Tue, 04 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LouCLTLT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuPWZLXHXWLLZM22,
author = {Dong Lu and
Rongrong Pan and
Wenxuan Wu and
Yanyan Zhang and
Shensuo Li and
Hong Xu and
Jialan Huang and
Jianhua Xia and
Qun Wang and
Xin Luan and
Chao Lv and
Weidong Zhang and
Guofeng Meng},
title = {{FL-DTD:} an integrated pipeline to predict the drug interacting targets
by feedback loop-based network analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac263},
doi = {10.1093/BIB/BBAC263},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuPWZLXHXWLLZM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuXZHYWWMPTLWWP22,
author = {Yong Lu and
Gang Xue and
Ningbo Zheng and
Kun Han and
Wenzhong Yang and
Rui{-}Sheng Wang and
Ling{-}Yun Wu and
Lance D. Miller and
Timothy Pardee and
Pierre L. Triozzi and
Hui{-}Wen Lo and
Kounosuke Watabe and
Stephen T. C. Wong and
Boris C. Pasche and
Wei Zhang and
Guangxu Jin},
title = {hDirect-MAP: projection-free single-cell modeling of response to checkpoint
immunotherapy},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab575},
doi = {10.1093/BIB/BBAB575},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuXZHYWWMPTLWWP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Luo22,
author = {Yuan Luo},
title = {Evaluating the state of the art in missing data imputation for clinical
data},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab489},
doi = {10.1093/BIB/BBAB489},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/Luo22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoGW22,
author = {Liheng Luo and
Michael Gribskov and
Sufang Wang},
title = {Bibliometric review of ATAC-Seq and its application in gene expression},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac061},
doi = {10.1093/BIB/BBAC061},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuoGW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoLWAL22,
author = {Ling Luo and
Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Cecilia N. Arighi and
Zhiyong Lu},
title = {BioRED: a rich biomedical relation extraction dataset},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac282},
doi = {10.1093/BIB/BBAC282},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuoLWAL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoQXC22,
author = {Xizhi Luo and
Fei Qin and
Feifei Xiao and
Guoshuai Cai},
title = {{BISC:} accurate inference of transcriptional bursting kinetics from
single-cell transcriptomic data},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac464},
doi = {10.1093/BIB/BBAC464},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuoQXC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoSXQZPL22,
author = {Renqian Luo and
Liai Sun and
Yingce Xia and
Tao Qin and
Sheng Zhang and
Hoifung Poon and
Tie{-}Yan Liu},
title = {BioGPT: generative pre-trained transformer for biomedical text generation
and mining},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac409},
doi = {10.1093/BIB/BBAC409},
timestamp = {Mon, 29 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuoSXQZPL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoXFLWWW22,
author = {Hongyu Luo and
Yingfei Xiang and
Xiaomin Fang and
Wei Li and
Fan Wang and
Hua Wu and
Haifeng Wang},
title = {BatchDTA: implicit batch alignment enhances deep learning-based drug-target
affinity estimation},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac260},
doi = {10.1093/BIB/BBAC260},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuoXFLWWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoYL22,
author = {Qinhuan Luo and
Yongzhen Yu and
Xun Lan},
title = {{SIGNET:} single-cell RNA-seq-based gene regulatory network prediction
using multiple-layer perceptron bagging},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab547},
doi = {10.1093/BIB/BBAB547},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LuoYL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoZWQLZC22,
author = {Zhi{-}Hui Luo and
Lida Zhu and
Ya{-}Min Wang and
Sheng Hu Qian and
Menglu Li and
Wen Zhang and
Zhen{-}Xia Chen},
title = {{DSEATM:} drug set enrichment analysis uncovering disease mechanisms
by biomedical text mining},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac228},
doi = {10.1093/BIB/BBAC228},
timestamp = {Thu, 08 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuoZWQLZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LvLHJSS22,
author = {Ji Lv and
Guixia Liu and
Junli Hao and
Yuan Ju and
Binwen Sun and
Ying Sun},
title = {Computational models, databases and tools for antibiotic combinations},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac309},
doi = {10.1093/BIB/BBAC309},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LvLHJSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LvXYLLZZCDLSLX22,
author = {Dezhong Lv and
Kang Xu and
Changbo Yang and
Yujie Liu and
Ya Luo and
Weiwei Zhou and
Haozhe Zou and
Yangyang Cai and
Na Ding and
Xia Li and
Tingting Shao and
Yongsheng Li and
Juan Xu},
title = {{PRES:} a webserver for decoding the functional perturbations of {RNA}
editing sites},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac242},
doi = {10.1093/BIB/BBAC242},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LvXYLLZZCDLSLX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LvZWYSDGLD22,
author = {Hao Lv and
Yang Zhang and
Jia{-}Shu Wang and
Shi{-}Shi Yuan and
Zi{-}Jie Sun and
Fu{-}Ying Dao and
Zheng{-}Xing Guan and
Hao Lin and
Ke{-}Jun Deng},
title = {iRice-MS: An integrated XGBoost model for detecting multitype post-translational
modification sites in rice},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab486},
doi = {10.1093/BIB/BBAB486},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LvZWYSDGLD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaLMZ22,
author = {Jiani Ma and
Hui Liu and
Yumeng Mao and
Lin Zhang},
title = {{LRTCLS:} low-rank tensor completion with Laplacian smoothing regularization
for unveiling the post-transcriptional machinery of \emph{N}6-methylation
(m6A)-mediated diseases},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac325},
doi = {10.1093/BIB/BBAC325},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaLMZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaLWLYZW22,
author = {Zhi Ma and
Yang Young Lu and
Yiwen Wang and
Renhao Lin and
Zizi Yang and
Fang Zhang and
Ying Wang},
title = {Metric learning for comparing genomic data with triplet network},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac345},
doi = {10.1093/BIB/BBAC345},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaLWLYZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaNZCX22,
author = {Mingyuan Ma and
Sen Na and
Xiaolu Zhang and
Congzhou Chen and
Jin Xu},
title = {{SFGAE:} a self-feature-based graph autoencoder model for miRNA-disease
associations prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac340},
doi = {10.1093/BIB/BBAC340},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaNZCX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaSJGQ22,
author = {Wenjing Ma and
Sumeet Sharma and
Peng Jin and
Shannon L. Gourley and
Zhaohui S. Qin},
title = {\emph{LRcell}: detecting the source of differential expression at
the sub-cell-type level from bulk RNA-seq data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac063},
doi = {10.1093/BIB/BBAC063},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaSJGQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaSZZL22,
author = {Yuanyuan Ma and
Zexuan Sun and
Pengcheng Zeng and
Wenyu Zhang and
Zhixiang Lin},
title = {{JSNMF} enables effective and accurate integrative analysis of single-cell
multiomics data},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac105},
doi = {10.1093/BIB/BBAC105},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaSZZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaWM22,
author = {Chenjin Ma and
Mengyun Wu and
Shuangge Ma},
title = {Analysis of cancer omics data: a selective review of statistical techniques},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab585},
doi = {10.1093/BIB/BBAB585},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaWM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaghsoudiNTN22,
author = {Zeynab Maghsoudi and
Ha Nguyen and
Alireza Tavakkoli and
Tin Nguyen},
title = {A comprehensive survey of the approaches for pathway analysis using
multi-omics data integration},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac435},
doi = {10.1093/BIB/BBAC435},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MaghsoudiNTN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MahbubB22,
author = {Sazan Mahbub and
Md. Shamsuzzoha Bayzid},
title = {{EGRET:} edge aggregated graph attention networks and transfer learning
improve protein-protein interaction site prediction},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab578},
doi = {10.1093/BIB/BBAB578},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MahbubB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Mahdipour-Shirayeh22,
author = {Ali Mahdipour{-}Shirayeh and
Natalie Erdmann and
Chungyee Leung{-}Hagesteijn and
Rodger E. Tiedemann},
title = {sciCNV: high-throughput paired profiling of transcriptomes and {DNA}
copy number variations at single-cell resolution},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab413},
doi = {10.1093/BIB/BBAB413},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Mahdipour-Shirayeh22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Mahjoubin-Tehran22,
author = {Maryam Mahjoubin{-}Tehran and
Samaneh Rezaei and
Amin Jalili and
Amirhossein Sahebkar and
Seyed Hamid Aghaee{-}Bakhtiari},
title = {A comprehensive review of online resources for microRNA-diseases associations:
the state of the art},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab381},
doi = {10.1093/BIB/BBAB381},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Mahjoubin-Tehran22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MaizonB22,
author = {H{\'{e}}ctor Buena Maiz{\'{o}}n and
Francisco J. Barrantes},
title = {A deep learning-based approach to model anomalous diffusion of membrane
proteins: the case of the nicotinic acetylcholine receptor},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab435},
doi = {10.1093/BIB/BBAB435},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MaizonB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ManavalanBL22,
author = {Balachandran Manavalan and
Shaherin Basith and
Gwang Lee},
title = {Comparative analysis of machine learning-based approaches for identifying
therapeutic peptides targeting SARS-CoV-2},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab412},
doi = {10.1093/BIB/BBAB412},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ManavalanBL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MarchettiNMPCBTMD22,
author = {Laura Marchetti and
Riccardo Nifos{\`{\i}} and
Pier Luigi Martelli and
Eleonora Da Pozzo and
Valentina Cappello and
Francesco Banterle and
Maria Letizia Trincavelli and
Claudia Martini and
Massimo D'elia},
title = {Quantum computing algorithms: getting closer to critical problems
in computational biology},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac437},
doi = {10.1093/BIB/BBAC437},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MarchettiNMPCBTMD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MariniMBNP22,
author = {Simone Marini and
Rodrigo A. Mora and
Christina Boucher and
Noelle Robertson Noyes and
Mattia Prosperi},
title = {Towards routine employment of computational tools for antimicrobial
resistance determination via high-throughput sequencing},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac020},
doi = {10.1093/BIB/BBAC020},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MariniMBNP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MathemaDWJDSKSK22,
author = {Vivek Bhakta Mathema and
Kassaporn Duangkumpha and
Kwanjeera Wanichthanarak and
Narumol Jariyasopit and
Esha Dhakal and
Nuankanya Sathirapongsasuti and
Chagriya Kitiyakara and
Yongyut Sirivatanauksorn and
Sakda Khoomrung},
title = {{CRISP:} a deep learning architecture for {GC} {\texttimes} {GC-TOFMS}
contour {ROI} identification, simulation and analysis in imaging metabolomics},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab550},
doi = {10.1093/BIB/BBAB550},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MathemaDWJDSKSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MehrpooyaMZRSET22,
author = {Adel Mehrpooya and
Farid Saberi Movahed and
Najmeh Azizi Zadeh and
Mohammad Rezaei{-}Ravari and
Farshad Saberi{-}Movahed and
Mahdi Eftekhari and
Iman Tavassoly},
title = {High dimensionality reduction by matrix factorization for systems
pharmacology},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab410},
doi = {10.1093/BIB/BBAB410},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MehrpooyaMZRSET22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MengHCLC22,
author = {Yiwei Meng and
Yanhong Huang and
Xiao Chang and
Xiaoping Liu and
Luonan Chen},
title = {Transcriptome analysis method based on differential distribution evaluation},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab608},
doi = {10.1093/BIB/BBAB608},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MengHCLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MengLJXZY22,
author = {Yajie Meng and
Changcheng Lu and
Min Jin and
Junlin Xu and
Xiangxiang Zeng and
Jialiang Yang},
title = {A weighted bilinear neural collaborative filtering approach for drug
repositioning},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab581},
doi = {10.1093/BIB/BBAB581},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MengLJXZY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MengZZWWLCSL22,
author = {Yanzheng Meng and
Lin Zhang and
Laizhi Zhang and
Ziyu Wang and
Xuanwen Wang and
Chan Li and
Yu Chen and
Shipeng Shang and
Lei Li},
title = {CysModDB: a comprehensive platform with the integration of manually
curated resources and analysis tools for cysteine posttranslational
modifications},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac460},
doi = {10.1093/BIB/BBAC460},
timestamp = {Sun, 25 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MengZZWWLCSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MercatelliCVGG22,
author = {Daniele Mercatelli and
Chiara Cabrelle and
Pierangelo Veltri and
Federico M. Giorgi and
Pietro H. Guzzi},
title = {Detection of pan-cancer surface protein biomarkers via a network-based
approach on transcriptomics data},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac400},
doi = {10.1093/BIB/BBAC400},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MercatelliCVGG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MiaoJCHLHW22,
author = {Shidi Miao and
Haobo Jia and
Ke Cheng and
Xiaohui Hu and
Jing Li and
Wenjuan Huang and
Ruitao Wang},
title = {Deep learning radiomics under multimodality explore association between
muscle/fat and metastasis and survival in breast cancer patients},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac432},
doi = {10.1093/BIB/BBAC432},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MiaoJCHLHW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MingLZWCELYW22,
author = {Jingsi Ming and
Zhixiang Lin and
Jia Zhao and
Xiang Wan and
Tabula Microcebus Consortium and
C. Ezran and
S. Liu and
Can Yang and
Angela Ruohao Wu},
title = {{FIRM:} Flexible integration of single-cell RNA-sequencing data for
large-scale multi-tissue cell atlas datasets},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac167},
doi = {10.1093/BIB/BBAC167},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MingLZWCELYW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MolinGDBPBB22,
author = {Anna Dal Molin and
Enrico Gaffo and
Valeria Difilippo and
Alessia Buratin and
Caterina Tretti Parenzan and
Silvia Bresolin and
Stefania Bortoluzzi},
title = {{CRAFT:} a bioinformatics software for custom prediction of circular
{RNA} functions},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab601},
doi = {10.1093/BIB/BBAB601},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MolinGDBPBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MolinGDBPBB22a,
author = {Anna Dal Molin and
Enrico Gaffo and
Valeria Difilippo and
Alessia Buratin and
Caterina Tretti Parenzan and
Silvia Bresolin and
Stefania Bortoluzzi},
title = {Correction to: {CRAFT} a bioinformatics software for custom prediction
of circular {RNA} functions},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac119},
doi = {10.1093/BIB/BBAC119},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MolinGDBPBB22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MordauntMSL22,
author = {Charles E. Mordaunt and
Julia S. Mouat and
Rebecca J. Schmidt and
Janine M. Lasalle},
title = {Comethyl: a network-based methylome approach to investigate the multivariate
nature of health and disease},
journal = {Briefings Bioinform.},
volume = {23},
number = {2},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab554},
doi = {10.1093/BIB/BBAB554},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/MordauntMSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/MubeenKHD22,
author = {Sarah Mubeen and
Alpha Tom Kodamullil and
Martin Hofmann{-}Apitius and
Daniel Domingo{-}Fern{\'{a}}ndez},
title = {On the influence of several factors on pathway enrichment analysis},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac143},
doi = {10.1093/BIB/BBAC143},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/MubeenKHD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NapolitanoXG22,
author = {Francesco Napolitano and
Xiaopeng Xu and
Xin Gao},
title = {Impact of computational approaches in the fight against {COVID-19:}
an {AI} guided review of 17 000 studies},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab456},
doi = {10.1093/BIB/BBAB456},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NapolitanoXG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NguyenNDV22,
author = {Dat Thanh Nguyen and
Quan Hoang Nguyen and
Nguyen Thuy Duong and
Nam S. Vo},
title = {LmTag: functional-enrichment and imputation-aware tag {SNP} selection
for population-specific genotyping arrays},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac252},
doi = {10.1093/BIB/BBAC252},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/NguyenNDV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NguyenNT22,
author = {Tri Minh Nguyen and
Thin Nguyen and
Truyen Tran},
title = {Mitigating cold-start problems in drug-target affinity prediction
with interaction knowledge transferring},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac269},
doi = {10.1093/BIB/BBAC269},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/NguyenNT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NguyenPA22,
author = {Thanh{-}Binh Nguyen and
Douglas E. V. Pires and
David B. Ascher},
title = {CSM-carbohydrate: protein-carbohydrate binding affinity prediction
and docking scoring function},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab512},
doi = {10.1093/BIB/BBAB512},
timestamp = {Thu, 27 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NguyenPA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NiarakisWGSKNCS22,
author = {Anna Niarakis and
Dagmar Waltemath and
James A. Glazier and
Falk Schreiber and
Sarah M. Keating and
David P. Nickerson and
Claudine Chaouiya and
Anne Siegel and
Vincent No{\"{e}}l and
Henning Hermjakob and
Tom{\'{a}}s Helikar and
Sylvain Soliman and
Laurence Calzone},
title = {Addressing \emph{barriers in comprehensiveness, accessibility, reusability,
interoperability and reproducibility of computational models in systems
biology}},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac212},
doi = {10.1093/BIB/BBAC212},
timestamp = {Wed, 05 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NiarakisWGSKNCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NieD22,
author = {Wenjuan Nie and
Lei Deng},
title = {TSNAPred: predicting type-specific nucleic acid binding residues via
an ensemble approach},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac244},
doi = {10.1093/BIB/BBAC244},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NieD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NingL22,
author = {Qiao Ning and
Jinmou Li},
title = {DLF-Sul: a multi-module deep learning framework for prediction of
S-sulfinylation sites in proteins},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac323},
doi = {10.1093/BIB/BBAC323},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NingL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NingQWDC22,
author = {Qiao Ning and
Zedong Qi and
Yue Wang and
Ansheng Deng and
Chen Chen},
title = {FCCCSR{\_}Glu: a semi-supervised learning model based on {FCCCSR}
algorithm for prediction of glutarylation sites},
journal = {Briefings Bioinform.},
volume = {23},
number = {6},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac421},
doi = {10.1093/BIB/BBAC421},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/NingQWDC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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