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ORCIDBioinformatics, Volume 39
Volume 39, Number 1, January 2023
- Hong Zhang
, Devan V. Mehrotra, Judong Shen:
AWOT and CWOT for genotype and genotype-by-treatment interaction joint analysis in pharmacogenetics GWAS.
- Xuezhi Xie, Pedro A. Valiente, Philip M. Kim:
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures. - Xiaokun Hong, Ningshan Li, Jiyang Lv, Yan Zhang, Jing Li, Jian Zhang, Hai-Feng Chen:
PTMint database of experimentally verified PTM regulation on protein-protein interaction. - Alessandro Vinceti, Lucia Trastulla, Umberto Perron, Andrea Raiconi, Francesco Iorio:
A heuristic algorithm solving the mutual-exclusivity-sorting problem. - Nelle Varoquaux, William S. Noble, Jean-Philippe Vert:
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. - Teresa De Jesus Martinez, Elliot A. Hershberg, Emma Guo, Garrett Stevens, Colin M. Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes:
JBrowse Jupyter: a Python interface to JBrowse 2. - Neda Shokraneh, Mariam Arab, Maxwell W. Libbrecht:
Integrative chromatin domain annotation through graph embedding of Hi-C data. - Shivam Kumar, Dipanka Sarmah, Shailendra Asthana, Samrat Chatterjee:
konnect2prot: a web application to explore the protein properties in a functional protein-protein interaction network. - Ngoc-Quang Nguyen, Gwanghoon Jang, Hajung Kim, Jaewoo Kang:
Perceiver CPI: a nested cross-attention network for compound-protein interaction prediction. - Manuel Glöckler, Andreas Dräger, Reihaneh Mostolizadeh:
Hierarchical modelling of microbial communities. - José Camacho, Raffaele Vitale, David Morales-Jiménez, Carolina Gómez-Llorente:
Variable-selection ANOVA Simultaneous Component Analysis (VASCA). - Filippo Grazioli, Pierre Machart, Anja Mösch, Kai Li, Leonardo V. Castorina, Nico Pfeifer, Martin Renqiang Min:
Attentive Variational Information Bottleneck for TCR-peptide interaction prediction. - Marcus T. Moen, Iain G. Johnston:
HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs. - Xingqi Wu, Yi Shi, Minghui Wang, Ao Li:
CAMR: cross-aligned multimodal representation learning for cancer survival prediction. - Jinding Liu, Yaru Zhang, Yapin Shi, Yiqing Zheng, Yali Zhu, Zhuoran Guan, Danyu Shen, Daolong Dou:
FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing. - Marija Stanojevic, Jovan Andjelkovic, Adrienne Kasprowicz, Louise A. Huuki, Jennifer Chao, S. Blair Hedges, Sudhir Kumar, Zoran Obradovic:
Discovering research articles containing evolutionary timetrees by machine learning. - Correction to: FASTRAL: improving scalability of phylogenomic analysis.
- Jonathan K. Vis, Mark A. Santcroos, Walter A. Kosters, Jeroen F. J. Laros:
A Boolean algebra for genetic variants. - Vamsi Nallapareddy, Nicola Bordin, Ian Sillitoe, Michael Heinzinger, Maria Littmann, Vaishali P. Waman, Neeladri Sen, Burkhard Rost, Christine A. Orengo:
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models. - Chenxi Zhou, Shane A. McCarthy, Richard Durbin:
YaHS: yet another Hi-C scaffolding tool. - Correction to: Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms.
- Marek S. Wiewiórka, Agnieszka Szmurlo, Pawel Stankiewicz, Tomasz Gambin:
Cloud-native distributed genomic pileup operations. - Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf:
mOWL: Python library for machine learning with biomedical ontologies. - Dailin Gan, Jun Li:
SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data. - Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg:
GOThresher: a program to remove annotation biases from protein function annotation datasets. - Yufeng Liu, Ye Zhong, Xuan Zhao, Lijuan Liu, Liya Ding, Hanchuan Peng:
Tracing weak neuron fibers. - Yuwei Wang, Bin Lian, Haohui Zhang, Yuanke Zhong, Jie He, Fashuai Wu, Knut Reinert, Xuequn Shang, Hui Yang, Jialu Hu:
A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. - Abin Abraham, Abigail L. Labella, Mary Lauren Benton, Antonis Rokas, John A. Capra:
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. - Licai Huang, James P. Long, Ehsan Irajizad, James D. Doecke, Kim-Anh Do, Min Jin Ha:
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes. - Jialun Wu, Yuxin Dong, Zeyu Gao, Tieliang Gong, Chen Li:
Dual Attention and Patient Similarity Network for drug recommendation. - Wei Chen, Zhiwei Li, Hongyi Fang, Qianyuan Yao, Cheng Zhong, Jianye Hao, Qi Zhang, Xuanjing Huang, Jiajie Peng, Zhongyu Wei:
A benchmark for automatic medical consultation system: frameworks, tasks and datasets. - Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar:
Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates.
Volume 39, Number 2, February 2023
- Andy Lin, Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A. Bilmes, William Stafford Noble:
MS1Connect: a mass spectrometry run similarity measure. - Xiang Cheng, Md Amanullah, Weigang Liu, Yi Liu, Xiaoqing Pan, Honghe Zhang, Haiming Xu, Peng-Yuan Liu, Yan Lu:
WMDS.net: a network control framework for identifying key players in transcriptome programs. - Kun Zhu, Hong Su, Zhenling Peng, Jianyi Yang:
A unified approach to protein domain parsing with inter-residue distance matrix. - Piotr Klukowski, Roland Riek, Peter Güntert:
NMRtist: an online platform for automated biomolecular NMR spectra analysis. - Xabier Rey-Barreiro, Alejandro F. Villaverde:
Benchmarking tools for a priori identifiability analysis. - Yunhe Wang, Zhuohan Yu, Shaochuan Li, Chuang Bian, Yanchun Liang, Ka-Chun Wong, Xiangtao Li:
scBGEDA: deep single-cell clustering analysis via a dual denoising autoencoder with bipartite graph ensemble clustering.
Volume 39, Number 3, March 2023
- Adam Streck, Tom L. Kaufmann, Roland F. Schwarz:
SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity. - Elisabet Munté, Lidia Feliubadaló, Marta Pineda, Eva Tornero, Maribel González, José Marcos Moreno-Cabrera, Carla Roca, Joan Bales Rubio, Laura Arnaldo, Gabriel Capellá, Jose Luis Mosquera, Conxi Lázaro:
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines. - Zhourun Wu, Mingyue Guo, Xiaopeng Jin, Junjie Chen, Bin Liu:
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction.
Volume 39, Number 4, April 2023
- Mingqian Zhang, Wenke Zhang, Yuzhu Chen, Jin Zhao, Shunyao Wu, Xiaoquan Su:
Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes. - Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori:
Prediction and curation of missing biomedical identifier mappings with Biomappings. - Bansho Masutani, Riki Kawahara, Shinichi Morishita:
Decomposing mosaic tandem repeats accurately from long reads. - Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek:
Boolean network sketches: a unifying framework for logical model inference.
Volume 39, Number 5, May 2023
- Yongxin Ji, Jiayu Shang, Xubo Tang, Yanni Sun:
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer. - Ran Wang, Xubin Zheng, Fangda Song, Man Hon Wong, Kwong-Sak Leung, Lixin Cheng:
Deciphering associations between gut microbiota and clinical factors using microbial modules. - Tianqi Wu, Zhiye Guo, Jianlin Cheng:
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer. - Kijin Kim, Kyungmin Park, Seonghyeon Lee, Seung-Hwan Baek, Tae-Hun Lim, Jongwoo Kim, Balachandran Manavalan, Jin-Won Song, Won-Keun Kim:
VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing. - Correction to: wpLogicNet: logic gate and structure inference in gene regulatory networks.
- Zixuan Wang, Shuwen Xiong, Yun Yu, Jiliu Zhou, Yongqing Zhang:
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency. - Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu:
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs.
Volume 39, Number 8, August 2023
- Tong Xin, Yanan Lv, Haoran Chen, Linlin Li, Lijun Shen, Guangcun Shan, Xi Chen, Hua Han:
A novel registration method for long-serial section images of EM with a serial split technique based on unsupervised optical flow network. - Russell B. Davidson, Mark Coletti, Mu Gao, Bryan Piatkowski, Avinash Sreedasyam, Farhan Quadir, David J. Weston, Jeremy Schmutz, Jianlin Cheng, Jeffrey Skolnick, Jerry M. Parks, Ada Sedova:
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. - Abbi Abdel-Rehim, Oghenejokpeme I. Orhobor, Hang Lou, Hao Ni, Ross D. King:
Protein-ligand binding affinity prediction exploiting sequence constituent homology.
Volume 39, Number 9, September 2023
- Hui Yu, Limin Jiang, Chung-I Li, Scott Ness, Sara G. M. Piccirillo, Yan Guo:
Somatic mutation effects diffused over microRNA dysregulation. - Lechuan Li, Ruth Dannenfelser, Yu Zhu, Nathaniel Hejduk, Santiago Segarra, Vicky Yao:
Joint embedding of biological networks for cross-species functional alignment. - Matthew D. Smith, Marshall A Case, Emily K. Makowski, Peter M. Tessier:
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data. - Pin Lyu, Yijie Zhai, Taibo Li, Jiang Qian:
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server.
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