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2020 – today
- 2024
[j138]Shuo Li, Yan Liu
, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu:
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Briefings Bioinform. 25(2) (2024)- [j137]Yuchuan Zhang, Zhikang Wang, Fang Ge, Xiaoyu Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu:
MLSNet: a deep learning model for predicting transcription factor binding sites. Briefings Bioinform. 25(6) (2024) - [j136]Yuhan Wang, Zhikang Wang, Xuan Yu, Xiaoyu Wang, Jiangning Song, Dong-Jun Yu, Fang Ge:
MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification. Briefings Bioinform. 26(1) (2024) - [j135]Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori:
DiCleave: a deep learning model for predicting human Dicer cleavage sites. BMC Bioinform. 25(1): 13 (2024) - [j134]Xiaoyu Wang, Nitin Patil, Fuyi Li, Zhikang Wang, Haolan Zhan, Daniel Schmidt, Philip Thompson, Yuming Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Jiangning Song:
PmxPred: A data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria. Comput. Biol. Medicine 168: 107681 (2024) - [j133]Mengmeng Gao, Daokun Zhang, Yi Chen, Yiwen Zhang, Zhikang Wang, Xiaoyu Wang, Shanshan Li, Yuming Guo, Geoffrey I. Webb, Anh T. N. Nguyen, Lauren T. May, Jiangning Song:
GraphormerDTI: A graph transformer-based approach for drug-target interaction prediction. Comput. Biol. Medicine 173: 108339 (2024) - [j132]Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu:
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. J. Chem. Inf. Model. 64(4): 1407-1418 (2024) - [j131]Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu:
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. J. Chem. Inf. Model. 64(15): 6216-6229 (2024) - [j130]Zhikang Wang, Jiani Ma, Qian Gao, Chris Bain, Seiya Imoto, Pietro Liò, Hongmin Cai, Hao Chen, Jiangning Song:
Dual-stream multi-dependency graph neural network enables precise cancer survival analysis. Medical Image Anal. 97: 103252 (2024) - [j129]Dian Liu, Zi Liu, Yunpeng Xia, Zhikang Wang, Jiangning Song, Dong-Jun Yu:
TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 21(5): 1403-1412 (2024) - [j128]Yunpeng Xia, Ying Zhang, Dian Liu, Yi-Heng Zhu, Zhikang Wang, Jiangning Song, Dong-Jun Yu:
BLAM6A-Merge: Leveraging Attention Mechanisms and Feature Fusion Strategies to Improve the Identification of RNA N6-Methyladenosine Sites. IEEE ACM Trans. Comput. Biol. Bioinform. 21(6): 1803-1815 (2024) - [j127]Hongmin Cai, Yi Liao, Lei Zhu, Zhikang Wang, Jiangning Song:
Improving Cancer Survival Prediction via Graph Convolutional Neural Network Learning on Protein-Protein Interaction Networks. IEEE J. Biomed. Health Informatics 28(2): 1134-1143 (2024) - [j126]Cong Wang, Zhijie He, Runchang Jia, Shirui Pan, Lachlan J. M. Coin, Jiangning Song, Fuyi Li:
PLANNER: A Multi-Scale Deep Language Model for the Origins of Replication Site Prediction. IEEE J. Biomed. Health Informatics 28(4): 2445-2454 (2024) - [c13]Guihua Tao, Ziqin Ling, Haojiang Li, Jiangning Song, Hongmin Cai:
Joint Segmentation of Primary Nasopharyngeal Carcinoma Tumors and Lymph Nodes via Global Attention. BIBM 2024: 2489-2496 - [c12]Hongmin Cai, Weiting Yi, Weitian Huang, Zhikang Wang, Yue Zhang, Jiangning Song:
A Hierarchical Hypergraph Attention Network for Survival Analysis from Pathological Images. ISBI 2024: 1-4 - [i7]Zhikang Wang, Yumeng Zhang, Yingxue Xu, Seiya Imoto, Hao Chen, Jiangning Song:
Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images. CoRR abs/2403.10040 (2024) - [i6]Rong Han, Xiaohong Liu, Tong Pan, Jing Xu, Xiaoyu Wang, Wuyang Lan, Zhenyu Li, Zixuan Wang, Jiangning Song, Guangyu Wang, Ting Chen:
CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction. CoRR abs/2409.03773 (2024) - [i5]Yilong Zang, Lingfei Ren, Yue Li, Zhikang Wang, David Antony Selby, Zheng Wang, Sebastian Vollmer, Hongzhi Yin, Jiangning Song, Junhang Wu:
Rethinking Cancer Gene Identification through Graph Anomaly Analysis. CoRR abs/2412.17240 (2024) - 2023
- [j125]Fang Ge, Chen Li, Shahid Iqbal, Muhammad Arif, Fuyi Li, Maha A. Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu:
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings Bioinform. 24(1) (2023) - [j124]Yu Zhao, Bing He, Zhimeng Xu, Yidan Zhang, Xuan Zhao, Zhi-An Huang, Fan Yang, Liang Wang, Lei Duan, Jiangning Song, Jianhua Yao:
Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire. Briefings Bioinform. 24(1) (2023) - [j123]Xiaoti Jia, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song:
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning. Briefings Bioinform. 24(2) (2023) - [j122]Ruyi Chen, Fuyi Li, Xudong Guo, Yue Bi, Chen Li, Shirui Pan, Lachlan J. M. Coin, Jiangning Song:
ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Briefings Bioinform. 24(3) (2023) - [j121]Yan Liu, Guo Wei, Chen Li, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu:
TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level. Briefings Bioinform. 24(3) (2023) - [j120]Jing Xu, Fuyi Li, Chen Li, Xudong Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Seiya Imoto, Jianhua Yao, Tatsuya Akutsu, Jiangning Song:
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Briefings Bioinform. 24(4) (2023) - [j119]Yan Zhu, Fuyi Li, Xudong Guo, Xiaoyu Wang, Lachlan J. M. Coin, Geoffrey I. Webb, Jiangning Song, Cangzhi Jia:
TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters. Briefings Bioinform. 24(4) (2023) - [j118]Yan Cui, Zhikang Wang, Xiaoyu Wang, Yiwen Zhang, Ying Zhang, Tong Pan, Zhe Zhang, Shanshan Li, Yuming Guo, Tatsuya Akutsu, Jiangning Song:
SMG: self-supervised masked graph learning for cancer gene identification. Briefings Bioinform. 24(6) (2023) - [j117]Fuyi Li, Cong Wang, Xudong Guo, Tatsuya Akutsu, Geoffrey I. Webb, Lachlan J. M. Coin, Lukasz A. Kurgan, Jiangning Song:
ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction. Briefings Bioinform. 24(6) (2023) - [j116]Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu:
PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method. Bioinform. 39(1) (2023) - [j115]Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song:
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. Bioinform. 39(3) (2023) - [j114]Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song:
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. Bioinform. 39(3) (2023) - [j113]Jiani Ma, Chen Li, Yiwen Zhang, Zhikang Wang, Shanshan Li, Yuming Guo, Lin Zhang, Hui Liu, Xin Gao, Jiangning Song:
MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning. Bioinform. 39(9) (2023) - [j112]Ying Zhang, Zhikang Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu:
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues. Bioinform. 39(12) (2023) - [j111]Zixuan Wang, Yi Zhou, Tatsuya Takagi, Jiangning Song, Yu-Shi Tian, Tetsuo Shibuya:
Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data. BMC Bioinform. 24(1): 139 (2023) - [j110]Fuyi Li, Xudong Guo, Yue Bi, Runchang Jia, Miranda E. Pitt, Shirui Pan, Shuqin Li, Robin B. Gasser, Lachlan J. M. Coin, Jiangning Song:
Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins. Comput. Biol. Medicine 163: 107155 (2023) - [j109]Zhikang Wang, Qian Gao, Xiaoping Yi, Xinyu Zhang, Yiwen Zhang, Daokun Zhang, Pietro Liò, Chris Bain, Richard Bassed, Shanshan Li, Yuming Guo, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song:
Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. Comput. Methods Programs Biomed. 241: 107733 (2023) - [j108]Fang Wang, Fan Yang, Longkai Huang, Wei Li, Jiangning Song, Robin B. Gasser, Ruedi Aebersold, Guohua Wang, Jianhua Yao:
Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling. Nat. Mac. Intell. 5(11): 1236-1249 (2023) - [j107]Jing Xu, Jiarui Ou, Chen Li, Zheng Zhu, Jian Li, Hailun Zhang, Junchen Chen, Bin Yi, Wu Zhu, Weiru Zhang, Guanxiong Zhang, Qian Gao, Yehong Kuang, Jiangning Song, Xiang Chen, Hong Liu:
Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis. npj Digit. Medicine 6 (2023) - [j106]Ying Zhang, Fang Ge, Fuyi Li, Xibei Yang, Jiangning Song, Dong-Jun Yu:
Prediction of Multiple Types of RNA Modifications via Biological Language Model. IEEE ACM Trans. Comput. Biol. Bioinform. 20(5): 3205-3214 (2023) - 2022
- [j105]Fang Ge, Ying Zhang, Jian Xu, Muhammad Arif, Jiangning Song, Dong-Jun Yu:
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. Briefings Bioinform. 23(1) (2022) - [j104]Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-Jun Yu:
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network. Briefings Bioinform. 23(1) (2022) - [j103]Fuyi Li, Shuangyu Dong, André Leier, Meiya Han, Xudong Guo, Jing Xu, Xiaoyu Wang, Shirui Pan, Cangzhi Jia, Yang Zhang, Geoffrey I. Webb, Lachlan J. M. Coin, Chen Li, Jiangning Song:
Positive-unlabeled learning in bioinformatics and computational biology: a brief review. Briefings Bioinform. 23(1) (2022) - [j102]Yumeng Zhang, Yangming Zhang, Yi Xiong, Hui Wang, Zixin Deng, Jiangning Song, Hong-Yu Ou:
T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model. Briefings Bioinform. 23(1) (2022) - [j101]Xiaoyu Wang, Fuyi Li, Jing Xu, Jia Rong, Geoffrey I. Webb, Zongyuan Ge, Jian Li, Jiangning Song:
ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning. Briefings Bioinform. 23(2) (2022) - [j100]Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li, Yan Zhu, Tatsuya Akutsu, Geoffrey I. Webb, Quan Zou, Lachlan J. M. Coin, Jiangning Song:
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. Briefings Bioinform. 23(2) (2022) - [j99]Xinxin Peng, Xiaoyu Wang, Yuming Guo, Zongyuan Ge, Fuyi Li, Xin Gao, Jiangning Song:
RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins. Briefings Bioinform. 23(4) (2022) - [j98]Varun S. Sharma, Andrea Fossati, Rodolfo Ciuffa, Marija Buljan, Evan G. Williams, Zhen Chen, Wenguang Shao, Patrick G. A. Pedrioli, Anthony W. Purcell, María Rodríguez Martínez, Jiangning Song, Matteo Manica, Ruedi Aebersold, Chen Li:
PCfun: a hybrid computational framework for systematic characterization of protein complex function. Briefings Bioinform. 23(4) (2022) - [j97]Yue Bi, Fuyi Li, Xudong Guo, Zhikang Wang, Tong Pan, Yuming Guo, Geoffrey I. Webb, Jianhua Yao, Cangzhi Jia, Jiangning Song:
Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations. Briefings Bioinform. 23(6) (2022) - [j96]Meng Zhang, Jian Zhao, Chen Li, Fang Ge, Jing Wu, Bin Jiang, Jiangning Song, Xiaofeng Song:
csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames. Briefings Bioinform. 23(6) (2022) - [j95]Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu:
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data. Bioinform. 38(16): 4019-4026 (2022) - [j94]Quanzhong Liu, Honglin Fang, Xiao Wang, Miao Wang, Shuqin Li, Lachlan J. M. Coin, Fuyi Li, Jiangning Song:
DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions. Bioinform. 38(17): 4053-4061 (2022) - [j93]Yanan Wang, Changyuan Hu, Terry Kwok, Christopher A. Bain, Xiangyang Xue, Robin B. Gasser, Geoffrey I. Webb, Alex Boussioutas, Xian Shen, Roger J. Daly, Jiangning Song:
DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images. Bioinform. 38(17): 4206-4213 (2022) - [j92]Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu:
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. Bioinform. 38(23): 5160-5167 (2022) - [j91]Lin Zhu, Xiaoyu Wang, Fuyi Li, Jiangning Song:
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins. BMC Bioinform. 23(1): 444 (2022) - [j90]Xinyu Zhang, Vincent C. S. Lee, Jia Rong, James C. Lee, Jiangning Song, Feng Liu:
A multi-channel deep convolutional neural network for multi-classifying thyroid diseases. Comput. Biol. Medicine 148: 105961 (2022) - [j89]Lu-Xing Zhang, He Yan, Yan Liu, Jian Xu, Jiangning Song, Dong-Jun Yu:
Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA. J. Chem. Inf. Model. 62(7): 1794-1807 (2022) - [j88]Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser, Dong-Jun Yu, Geoffrey I. Webb, Jiangning Song:
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. J. Chem. Inf. Model. 62(17): 4270-4282 (2022) - [j87]Zhen Chen, Xuhan Liu, Pei Zhao, Chen Li, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Chris Bain, Robin B. Gasser, Junzhou Li, Zuoren Yang, Xin Gao, Lukasz A. Kurgan, Jiangning Song:
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. Nucleic Acids Res. 50(W1): 434-447 (2022) - [j86]Guanhua Ye, Hongzhi Yin, Tong Chen, Miao Xu, Quoc Viet Hung Nguyen, Jiangning Song:
Personalized On-Device E-Health Analytics With Decentralized Block Coordinate Descent. IEEE J. Biomed. Health Informatics 26(6): 2778-2786 (2022) - [c11]Hongmin Cai, Weiting Yi, Yucheng Li, Wenxiong Liao, Jiangning Song:
A Regional Multiple Instance Learning Network for Whole Slide Image Segmentation. BIBM 2022: 922-928 - [c10]Zhikang Wang, Feng Zhu, Shixiang Tang, Rui Zhao, Lihuo He, Jiangning Song:
Feature Erasing and Diffusion Network for Occluded Person Re-Identification. CVPR 2022: 4744-4753 - [i4]Xinyu Zhang, Vincent C. S. Lee, Jia Rong, James C. Lee, Jiangning Song, Feng Liu:
Multi-channel deep convolutional neural networks for multi-classifying thyroid disease. CoRR abs/2203.03627 (2022) - [i3]Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Jiangning Song:
Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification. CoRR abs/2208.03526 (2022) - 2021
- [j85]Fuyi Li, Jinxiang Chen, Zongyuan Ge, Ya Wen, Yanwei Yue, Morihiro Hayashida, Abdelkader Baggag, Halima Bensmail, Jiangning Song:
Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework. Briefings Bioinform. 22(2): 2126-2140 (2021) - [j84]Huaming Chen, Fuyi Li, Lei Wang, Yaochu Jin, Chi-Hung Chi, Lukasz A. Kurgan, Jiangning Song, Jun Shen:
Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions. Briefings Bioinform. 22(3) (2021) - [j83]Quanzhong Liu, Jinxiang Chen, Yanze Wang, Shuqin Li, Cangzhi Jia, Jiangning Song, Fuyi Li:
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites. Briefings Bioinform. 22(3) (2021) - [j82]Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang:
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. Briefings Bioinform. 22(3) (2021) - [j81]Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu:
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings Bioinform. 22(3) (2021) - [j80]Xiao Liang, Fuyi Li, Jinxiang Chen, Junlong Li, Hao Wu, Shuqin Li, Jiangning Song, Quanzhong Liu:
Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification. Briefings Bioinform. 22(4) (2021) - [j79]Yan Zhu, Fuyi Li, Dongxu Xiang, Tatsuya Akutsu, Jiangning Song, Cangzhi Jia:
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. Briefings Bioinform. 22(4) (2021) - [j78]Yan Liu, Yi-Heng Zhu, Xiaoning Song, Jiangning Song, Dong-Jun Yu:
Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation. Briefings Bioinform. 22(5) (2021) - [j77]Shutao Mei, Fuyi Li, Dongxu Xiang, Rochelle Ayala, Pouya Faridi, Geoffrey I. Webb, Patricia T. Illing, Jamie Rossjohn, Tatsuya Akutsu, Nathan P. Croft, Anthony W. Purcell, Jiangning Song:
Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules. Briefings Bioinform. 22(5) (2021) - [j76]Long-Chen Shen, Yan Liu, Jiangning Song, Dong-Jun Yu:
SAResNet: self-attention residual network for predicting DNA-protein binding. Briefings Bioinform. 22(5) (2021) - [j75]Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T. Marquez-Lago, Jian Li, Dong-Jun Yu, Jiangning Song:
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. Briefings Bioinform. 22(5) (2021) - [j74]Ying Zhang, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-Jun Yu:
Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites. Briefings Bioinform. 22(6) (2021) - [j73]Yong-Zi Chen, Zhuo-Zhi Wang, Yanan Wang, Guoguang Ying, Zhen Chen, Jiangning Song:
nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Briefings Bioinform. 22(6) (2021) - [j72]Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I. Webb, Jiangning Song:
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings Bioinform. 22(6) (2021) - [j71]Fuyi Li, Xudong Guo, Peipei Jin, Jinxiang Chen, Dongxu Xiang, Jiangning Song, Lachlan J. M. Coin:
Porpoise: a new approach for accurate prediction of RNA pseudouridine sites. Briefings Bioinform. 22(6) (2021) - [j70]Yan Liu, Ke Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-Jun Yu:
Improving protein fold recognition using triplet network and ensemble deep learning. Briefings Bioinform. 22(6) (2021) - [j69]Matee Ullah, Ke Han, Fazal Hadi, Jian Xu, Jiangning Song, Dong-Jun Yu:
PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection. Briefings Bioinform. 22(6) (2021) - [j68]Yanan Wang, Litao Yang, Geoffrey I. Webb, Zongyuan Ge, Jiangning Song:
OCTID: a one-class learning-based Python package for tumor image detection. Bioinform. 37(21): 3986-3988 (2021) - [j67]Yanan Wang, Nicolas Coudray, Yun Zhao, Fuyi Li, Changyuan Hu, Yao-Zhong Zhang, Seiya Imoto, Aristotelis Tsirigos, Geoffrey I. Webb, Roger J. Daly, Jiangning Song:
HEAL: an automated deep learning framework for cancer histopathology image analysis. Bioinform. 37(22): 4291-4295 (2021) - [j66]Sina Ghadermarzi, Bartosz Krawczyk, Jiangning Song, Lukasz A. Kurgan:
XRRpred: accurate predictor of crystal structure quality from protein sequence. Bioinform. 37(23): 4366-4374 (2021) - [j65]Pengyu Liu, Jiangning Song, Chun-Yu Lin, Tatsuya Akutsu:
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites. BMC Bioinform. 22(1): 63 (2021) - [j64]Jinxiang Chen, Fuyi Li, Miao Wang, Junlong Li, Tatiana T. Marquez-Lago, André Leier, Jerico Revote, Shuqin Li, Quanzhong Liu, Jiangning Song:
BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data. Frontiers Big Data 4 (2021) - [j63]Jiawei Wang, Jiahui Li, Yi Hou, Wei Dai, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Tieli Zhou, Von Torres, Iain Hay, Christopher Stubenrauch, Yanju Zhang, Jiangning Song, Trevor Lithgow:
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. Nucleic Acids Res. 49(Database-Issue): D651-D659 (2021) - [j62]Menglu Li, Yanan Wang, Fuyi Li, Yun Zhao, Mengya Liu, Sijia Zhang, Yannan Bin, Alexander Ian Smith, Geoffrey I. Webb, Jian Li, Jiangning Song, Junfeng Xia:
A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction. IEEE ACM Trans. Comput. Biol. Bioinform. 18(5): 1801-1810 (2021) - [j61]Cangzhi Jia, Meng Zhang, Cunshuo Fan, Fuyi Li, Jiangning Song:
Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling. IEEE ACM Trans. Comput. Biol. Bioinform. 18(5): 1937-1945 (2021) - [i2]Zhikang Wang, Feng Zhu, Shixiang Tang, Rui Zhao, Lihuo He, Jiangning Song:
Feature Erasing and Diffusion Network for Occluded Person Re-Identification. CoRR abs/2112.08740 (2021) - [i1]Guanhua Ye, Hongzhi Yin, Tong Chen, Miao Xu, Quoc Viet Hung Nguyen, Jiangning Song:
Personalized On-Device E-health Analytics with Decentralized Block Coordinate Descent. CoRR abs/2112.09341 (2021) - 2020
- [j60]Leyi Wei, Jie Hu, Fuyi Li, Jiangning Song, Ran Su, Quan Zou:
Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms. Briefings Bioinform. 21(1): 106-119 (2020) - [j59]Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song:
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Briefings Bioinform. 21(3): 1047-1057 (2020) - [j58]Fuyi Li, Cunshuo Fan, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Cangzhi Jia, Yan Zhu, Alexander Ian Smith, Geoffrey I. Webb, Quanzhong Liu, Leyi Wei, Jian Li, Jiangning Song:
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. Briefings Bioinform. 21(3): 1069-1079 (2020) - [j57]Shutao Mei, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, Alexander Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song:
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Briefings Bioinform. 21(4): 1119-1135 (2020) - [j56]Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, Alexander Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song:
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. Briefings Bioinform. 21(5): 1676-1696 (2020) - [j55]Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li,