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Briefings in Bioinformatics is now fully open access
 
Oxford University Press is pleased to announce that Briefings in Bioinformatics is fully open access as of January 2024. Visit the journal's open access page to learn more about this change, and what it will mean for accessing content and submitting to the journal.
 
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Briefings in Bioinformatics  
Volume 25 Issue 6
 
November 2024
 
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Articles
 
 
 
 
COFFEE: consensus single cell-type specific inference for gene regulatory networks border= 
 
Musaddiq K Lodi, Anna Chernikov, Preetam Ghosh
 
 
 
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility border= 
 
Wen Wen, Jiaxin Zhong, Zhaoxi Zhang, Lijuan Jia, Tinyi Chu ...
 
 
 
3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data border= 
 
Francesco Tabaro, Matthieu Boulard
 
 
 
NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm border= 
 
Zilin Ren, Jiarong Zhang, Yixiang Zhang, Tingting Yang, Pingping Sun ...
 
 
 
Multi-Cover Persistence (MCP)-based machine learning for polymer property prediction border= 
 
Yipeng Zhang, Cong Shen, Kelin Xia
 
 
 
 
Algorithm-agnostic significance testing in supervised learning with multimodal data border= 
 
Lucas Kook, Anton Rask Lundborg
 
 
 
nsDCC: dual-level contrastive clustering with nonuniform sampling for scRNA-seq data analysis border= 
 
Linjie Wang, Wei Li, Fanghui Zhou, Kun Yu, Chaolu Feng ...
 
 
 
Protein language models are performant in structure-free virtual screening border=  
 
Hilbert Yuen In Lam, Jia Sheng Guan, Xing Er Ong, Robbe Pincket, Yuguang Mu
 
 
 
CMFHMDA: a prediction framework for human disease-microbe associations based on cross-domain matrix factorization border= 
 
Jing Chen, Ran Tao, Yi Qiu, Qun Yuan
 
 
 
miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data border= 
 
Miao Cui, Yadong Liu, Xian Yu, Hongzhe Guo, Tao Jiang ...
 
 
 
 
DGCL: dual-graph neural networks contrastive learning for molecular property prediction border= 
 
Xiuyu Jiang, Liqin Tan, Qingsong Zou
 
 
 
HIP: a method for high-dimensional multi-view data integration and prediction accounting for subgroup heterogeneity border= 
 
Jessica Butts, Leif Verace, Christine Wendt, Russel P Bowler, Craig P Hersh ...
 
 
 
scEGG: an exogenous gene-guided clustering method for single-cell transcriptomic data border= 
 
Dayu Hu, Renxiang Guan, Ke Liang, Hao Yu, Hao Quan ...
 
 
 
DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes border= 
 
Tongqing Wei, Chenqi Lu, Hanxiao Du, Qianru Yang, Xin Qi ...
 
 
 
MLSNet: a deep learning model for predicting transcription factor binding sites border= 
 
Yuchuan Zhang, Zhikang Wang, Fang Ge, Xiaoyu Wang, Yiwen Zhang ...
 
 
 
DrugReSC: targeting disease-critical cell subpopulations with single-cell transcriptomic data for drug repurposing in cancer border= 
 
Chonghui Liu, Yan Zhang, Yingjian Liang, Tianjiao Zhang, Guohua Wang
 
 
 
Recover then aggregate: unified cross-modal deep clustering with global structural information for single-cell data border= 
 
Ziyi Wang, Peng Luo, Mingming Xiao, Boyang Wang, Tianyu Liu ...
 
 
 
Development and experimental validation of computational methods for human antibody affinity enhancement border= 
 
Junxin Li, Linbu Liao, Chao Zhang, Kaifang Huang, Pengfei Zhang ...
 
 
 
An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology border= 
 
Michael Y Fatemi, Yunrui Lu, Alos B Diallo, Gokul Srinivasan, Zarif L Azher ...
 
 
 
scDFN: enhancing single-cell RNA-seq clustering with deep fusion networks border=  
 
Tianxiang Liu, Cangzhi Jia, Yue Bi, Xudong Guo, Quan Zou ...
 
 
 
Detecting expressed genes in cell populations at the single-cell level with scGeneXpress border= 
 
Sascha Jung, Céline Barlier, Aitor Martinez Perez, Antonio del Sol
 
 
 
MultiSC: a deep learning pipeline for analyzing multiomics single-cell data border=  
 
Xiang Lin, Siqi Jiang, Le Gao, Zhi Wei, Junwen Wang
 
 
 
PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation border= 
 
Jiajing Xie, Yuhang Song, Hailong Zheng, Shijie Luo, Ying Chen ...
 
 
 
Pioneering bioinformatics with agent-based modelling: an innovative protocol to accurately forecast skin or respiratory allergic reactions to chemical sensitizers border= 
 
Giulia Russo, Elena Crispino, Silvia Casati, Emanuela Corsini, Andrew Worth ...
 
 
 
AntigenBoost: enhanced mRNA-based antigen expression through rational amino acid substitution border= 
 
Yumiao Gao, Siran Zhu, Huichun Li, Xueting Hao, Wen Chen ...
 
 
 
Digital PCR threshold robustness analysis and optimization using dipcensR border= 
 
Matthijs Vynck, Wim Trypsteen, Olivier Thas, Jo Vandesompele, Ward De Spiegelaere
 
 
 
Gene expression prediction from histology images via hypergraph neural networks border= 
 
Bo Li, Yong Zhang, Qing Wang, Chengyang Zhang, Mengran Li ...
 
 
 
MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization border= 
 
Yun Zuo, Bangyi Zhang, Wenying He, Yue Bi, Xiangrong Liu ...
 
 
 
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy border= 
 
Zhengzheng Lou, Xiaojiao Wei, Yuanhao Hu, Shizhe Hu, Yucong Wu ...
 
 
 
BANDRP: a bilinear attention network for anti-cancer drug response prediction based on fingerprint and multi-omics border= 
 
Cheng Cao, Haochen Zhao, Jianxin Wang
 
 
 
Mediation analysis in longitudinal study with high-dimensional methylation mediators border= 
 
Yidan Cui, Qingmin Lin, Xin Yuan, Fan Jiang, Shiyang Ma ...
 
 
 
MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides border= 
 
Chaorui Yan, Aoyun Geng, Zhuoyu Pan, Zilong Zhang, Feifei Cui
 
 
 
HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights border= 
 
Xinwan Su, Chengyu Shi, Fangzhou Liu, Manman Tan, Ying Wang ...
 
 
 
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping border= 
 
Zuqi Li, Sonja Katz, Edoardo Saccenti, David W Fardo, Peter Claes ...
 
 
 
Reconstructing tumor clonal heterogeneity and evolutionary relationships based on tumor DNA sequencing data border= 
 
Zhen Wang, Yanhua Fang, Ruoyu Wang, Liwen Kong, Shanshan Liang ...
 
 
 
Cancerous time estimation for interpreting the evolution of lung adenocarcinoma border= 
 
Yourui Han, Bolin Chen, Jun Bian, Ruiming Kang, Xuequn Shang
 
 
 
SELF-Former: multi-scale gene filtration transformer for single-cell spatial reconstruction border= 
 
Tianyi Chen, Xindian Wei, Lianxin Xie, Yunfei Zhang, Cheng Liu ...
 
 
 
scMGATGRN: a multiview graph attention network'based method for inferring gene regulatory networks from single-cell transcriptomic data border= 
 
Lin Yuan, Ling Zhao, Yufeng Jiang, Zhen Shen, Qinhu Zhang ...
 
 
 
Diagnostics of viral infections using high-throughput genome sequencing data border=  
 
Haochen Ning, Ian Boyes, Ibrahim Numanagić, Michael Rott, Li Xing ...
 
 
 
Building multiscale models with PhysiBoSS, an agent-based modeling tool border=  
 
Marco Ruscone, Andrea Checcoli, Randy Heiland, Emmanuel Barillot, Paul Macklin ...
 
 
 
Enhancing RNA-seq analysis by addressing all co-existing biases using a self-benchmarking approach with 2D structural insights border= 
 
Qiang Su, Yi Long, Deming Gou, Junmin Quan, Qizhou Lian
 
 
 
Statistical analysis of multiple regions-of-interest in multiplexed spatial proteomics data border= 
 
Sarah Samorodnitsky, Michael C Wu
 
 
 
AptaDiff: de novo design and optimization of aptamers based on diffusion models border= 
 
Zhen Wang, Ziqi Liu, Wei Zhang, Yanjun Li, Yizhen Feng ...
 
 
 
MetaDegron: multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons border= 
 
Mengqiu Zheng, Shaofeng Lin, Kunqi Chen, Ruifeng Hu, Liming Wang ...
 
 
 
A two-task predictor for discovering phase separation proteins and their undergoing mechanism border= 
 
Yetong Zhou, Shengming Zhou, Yue Bi, Quan Zou, Cangzhi Jia
 
 
 
m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data border= 
 
Boyi Yu, Genta Nagae, Yutaka Midorikawa, Kenji Tatsuno, Bhaskar Dasgupta ...
 
 
 
Therapeutic peptides identification via kernel risk sensitive loss-based k-nearest neighbor model and multi-Laplacian regularization border= 
 
Wenyu Zhang, Yijie Ding, Leyi Wei, Xiaoyi Guo, Fengming Ni
 
 
 
Predictability of antigen binding based on short motifs in the antibody CDRH3 border= 
 
Lonneke Scheffer, Eric Emanuel Reber, Brij Bhushan Mehta, Milena Pavlović, Maria Chernigovskaya ...
 
 
 
DeepCheck: multitask learning aids in assessing microbial genome quality border=  
 
Guo Wei, Nannan Wu, Kunyang Zhao, Sihai Yang, Long Wang ...
 
 
 
Single-cell mosaic integration and cell state transfer with auto-scaling self-attention mechanism border= 
 
Zhiwei Rong, Jiali Song, Yipei Yu, Lan Mi, ManTang Qiu ...
 
 
 
ACLNDA: an asymmetric graph contrastive learning framework for predicting noncoding RNA'disease associations in heterogeneous graphs border= 
 
Laiyi Fu, ZhiYuan Yao, Yangyi Zhou, Qinke Peng, Hongqiang Lyu
 
 
 
Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection border= 
 
Gulshan Kumar Sharma, Rakesh Sharma, Kavita Joshi, Sameer Qureshi, Shubhita Mathur ...
 
 
 
Cross-population enhancement of PrediXcan predictions with a gnomAD-based east Asian reference framework border= 
 
Han-Ching Chan, Amrita Chattopadhyay, Tzu-Pin Lu
 
 
 
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework border= 
 
Kai Shi, Qiaohui Liu, Qingrong Ji, Qisheng He, Xing-Ming Zhao
 
 
 
Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders border= 
 
Simone Rancati, Giovanna Nicora, Mattia Prosperi, Riccardo Bellazzi, Marco Salemi ...
 
 
 
Cell cycle expression heterogeneity predicts degree of differentiation border=  
 
Kathleen Noller, Patrick Cahan
 
 
 
Structure-preserved integration of scRNA-seq data using heterogeneous graph neural network border= 
 
Xun Zhang, Kun Qian, Hongwei Li
 
 
 
Constructing the dynamic transcriptional regulatory networks to identify phenotype-specific transcription regulators border= 
 
Yang Guo, Zhiqiang Xiao
 
 
 
A robust statistical approach for finding informative spatially associated pathways border= 
 
Leqi Tian, Jiashun Xiao, Tianwei Yu
 
 
 
Optimized patient-specific immune checkpoint inhibitor therapies for cancer treatment based on tumor immune microenvironment modeling border= 
 
Yao Yao, Youhua Frank Chen, Qingpeng Zhang
 
 
 
BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data border= 
 
Yanghong Guo, Bencong Zhu, Chen Tang, Ruichen Rong, Ying Ma ...
 
 
 
GexMolGen: cross-modal generation of hit-like molecules via large language model encoding of gene expression signatures border= 
 
Jiabei Cheng, Xiaoyong Pan, Yi Fang, Kaiyuan Yang, Yiming Xue ...
 
 
 
IPFMC: an iterative pathway fusion approach for enhanced multi-omics clustering in cancer research border= 
 
Haoyang Zhang, Sha Liu, Bingxin Li, Xionghui Zhou
 
 
 
Multi-view learning framework for predicting unknown types of cancer markers via directed graph neural networks fitting regulatory networks border= 
 
Xin-Fei Wang, Lan Huang, Yan Wang, Ren-Chu Guan, Zhu-Hong You ...
 
 
 
Deep contrastive learning for predicting cancer prognosis using gene expression values border= 
 
Anchen Sun, Elizabeth J Franzmann, Zhibin Chen, Xiaodong Cai
 
 
 
Multimodal contrastive learning for spatial gene expression prediction using histology images border= 
 
Wenwen Min, Zhiceng Shi, Jun Zhang, Jun Wan, Changmiao Wang
 
 
 
A consensus-based classification workflow to determine genetically inferred ancestry from comprehensive genomic profiling of patients with solid tumors border= 
 
Zachary D Wallen, Mary K Nesline, Sarabjot Pabla, Shuang Gao, Erik Vanroey ...
 
 
 
Predicting disease-associated microbes based on similarity fusion and deep learning border= 
 
Hailin Chen, Kuan Chen
 
 
 
IMGT/RobustpMHC: robust training for class-I MHC peptide binding prediction border=  
 
Anjana Kushwaha, Patrice Duroux, Véronique Giudicelli, Konstantin Todorov, Sofia Kossida
 
 
 
STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data border= 
 
Peng Ran, Yunzhi Wang, Kai Li, Shiman He, Subei Tan ...
 
 
 
scDTL: enhancing single-cell RNA-seq imputation through deep transfer learning with bulk cell information border= 
 
Liuyang Zhao, Landu Jiang, Yufeng Xie, JianHao Huang, Haoran Xie ...
 
 
 
Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis border= 
 
Zhenhao Zhang, Yuxi Liu, Meichen Xiao, Kun Wang, Yu Huang ...
 
 
 
GGN-GO: geometric graph networks for predicting protein function by multi-scale structure features border= 
 
Jia Mi, Han Wang, Jing Li, Jinghong Sun, Chang Li ...
 
 
 
DEWNA: dynamic entropy weight network analysis and its application to the DNA-binding proteome in A549 cells with cisplatin-induced damage border= 
 
Shisheng Wang, Wenjuan Zeng, Yin Yang, Jingqiu Cheng, Dan Liu ...
 
 
 
An unbiased comparison of immunoglobulin sequence aligners border=  
 
Thomas Konstantinovsky, Ayelet Peres, Pazit Polak, Gur Yaari
 
 
 
Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction border= 
 
Han Phan, Céline Brouard, Raphaël Mourad
 
 
 
Deep learning model for protein multi-label subcellular localization and function prediction based on multi-task collaborative training border= 
 
Peihao Bai, Guanghui Li, Jiawei Luo, Cheng Liang
 
 
 
Multi-level multi-view network based on structural contrastive learning for scRNA-seq data clustering border= 
 
Zhenqiu Shu, Min Xia, Kaiwen Tan, Yongbing Zhang, Zhengtao Yu
 
 
 
Prototype-based contrastive substructure identification for molecular property prediction border= 
 
Gaoqi He, Shun Liu, Zhuoran Liu, Changbo Wang, Kai Zhang ...
 
 
 
Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses border= 
 
Felipe Campelo, Ana Laura Grossi de Oliveira, João Reis-Cunha, Vanessa Gomes Fraga, Pedro Henrique Bastos ...
 
 
 
siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis border= 
 
Rongzhuo Long, Ziyu Guo, Da Han, Boxiang Liu, Xudong Yuan ...
 
 
 
SpaDiT: diffusion transformer for spatial gene expression prediction using scRNA-seq border= 
 
Xiaoyu Li, Fangfang Zhu, Wenwen Min
 
 
 
Graph domain adaptation'based framework for gene expression enhancement and cell type identification in large-scale spatially resolved transcriptomics border= 
 
Rongbo Shen, Meiling Cheng, Wencang Wang, Qi Fan, Huan Yan ...
 
 
 
A multi-task prediction method based on neighborhood structure embedding and signed graph representation learning to infer the relationship between circRNA, miRNA, and cancer border= 
 
Lan Huang, Xin-Fei Wang, Yan Wang, Ren-Chu Guan, Nan Sheng ...
 
 
 
A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers border= 
 
Xin-Fei Wang, Lan Huang, Yan Wang, Ren-Chu Guan, Zhu-Hong You ...
 
 
 
scTCA: a hybrid Transformer-CNN architecture for imputation and denoising of scDNA-seq data border= 
 
Zhenhua Yu, Furui Liu, Yang Li
 
 
 
Unlocking cross-modal interplay of single-cell joint profiling with CellMATE border=  
 
Qi Wang, Bolei Zhang, Yue Guo, Luyu Gong, Erguang Li ...
 
 
 
mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data border= 
 
Xiaoxiu Tan, Feng Xue, Chenhong Zhang, Tao Wang
 
 
 
ToxGIN: an In silico prediction model for peptide toxicity via graph isomorphism networks integrating peptide sequence and structure information border= 
 
Qiule Yu, Zhixing Zhang, Guixia Liu, Weihua Li, Yun Tang
 
 
 
Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP border= 
 
Chen Su, William A Pastor, Amin Emad
 
 
 
Identifying cell types by lasso-constraint regularized Gaussian graphical model based on weighted distance penalty border= 
 
Wei Zhang, Yaxin Xu, Xiaoying Zheng, Juan Shen, Yuanyuan Li
 
 
 
SpaGIC: graph-informed clustering in spatial transcriptomics via self-supervised contrastive learning border= 
 
Wei Liu, Bo Wang, Yuting Bai, Xiao Liang, Li Xue ...
 
 
 
Molecular group and correlation guided structural learning for multi-phenotype prediction border= 
 
Xueping Zhou, Manqi Cai, Molin Yue, Juan C Celedón, Jiebiao Wang ...
 
 
 
Deciphering gene expression patterns using large-scale transcriptomic data and its applications border= 
 
Shunjie Chen, Pei Wang, Haiping Guo, Yujie Zhang
 
 
 
Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network border= 
 
Qi Dai, Hu Chen, Wen-Jing Yi, Jia-Ning Zhao, Wei Zhang ...
 
 
 
AIGen: an artificial intelligence software for complex genetic data analysis border=  
 
Tingting Hou, Xiaoxi Shen, Shan Zhang, Muxuan Liang, Li Chen ...
 
 
 
Robust self-supervised learning strategy to tackle the inherent sparsity in single-cell RNA-seq data border= 
 
Sejin Park, Hyunju Lee
 
 
 
TIPS: a novel pathway-guided joint model for transcriptome-wide association studies border= 
 
Neng Wang, Zhenyao Ye, Tianzhou Ma
 
 
 
MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data border= 
 
Martin Bosilj, Alen SuljiÄ, Samo Zakotnik, Jan SluneÄko, Rok Kogoj ...
 
 
 
MPA-MutPred: a novel strategy for accurately predicting the binding affinity change upon mutation in membrane protein complexes border= 
 
Fathima Ridha, M Michael Gromiha
 
 
 
Nmix: a hybrid deep learning model for precise prediction of 2'-O-methylation sites based on multi-feature fusion and ensemble learning border= 
 
Yu-Qing Geng, Fei-Liao Lai, Hao Luo, Feng Gao
 
 
 
CMTT-JTracker: a fully test-time adaptive framework serving automated cell lineage construction border= 
 
Liuyin Chen, Sanyuan Fu, Zijun Zhang
 
 
 
BFAST: joint dimension reduction and spatial clustering with Bayesian factor analysis for zero-inflated spatial transcriptomics data border= 
 
Yang Xu, Dian Lv, Xuanxuan Zou, Liang Wu, Xun Xu ...
 
 
 
Digital annealing optimization for natural product structure elucidation border=  
 
Chien Lee, Pei-Hua Wang, Yufeng Jane Tseng
 
 
 
SIngle cell level Genotyping Using scRna Data (SIGURD) border=  
 
Martin Grasshoff, Milena Kalmer, Nicolas Chatain, Kim Kricheldorf, Angela Maurer ...
 
 
 
RiceSNP-BST: a deep learning framework for predicting biotic stress'associated SNPs in rice border= 
 
Jiajun Xu, Yujia Gao, Quan Lu, Renyi Zhang, Jianfeng Gui ...
 
 
 
The mathematical exploration for the mechanism of lung adenocarcinoma formation and progression border= 
 
Yourui Han, Bolin Chen, Zhongwen Bi, Jun Bian, Ruiming Kang ...
 
 
 
A metagene based similarity network fusion approach for multi-omics data integration identified novel subtypes in renal cell carcinoma border= 
 
Congcong Jia, Tong Wang, Dingtong Cui, Yaxin Tian, Gaiqin Liu ...
 
 
 
Review Article
 
 
 
 
DrugDoctor: enhancing drug recommendation in cold-start scenario via visit-level representation learning and training border= 
 
Yabin Kuang, Minzhu Xie
 
 
 
Current computational tools for protein lysine acylation site prediction 
 
Zhaohui Qin, Haoran Ren, Pei Zhao, Kaiyuan Wang, Huixia Liu ...
 
 
 
Knowledge Graphs for drug repurposing: a review of databases and methods border=  
 
Pablo Perdomo-Quinteiro, Alberto Belmonte-Hernández
 
 
 
Deep learning in template-free de novo biosynthetic pathway design of natural products border= 
 
Xueying Xie, Lin Gui, Baixue Qiao, Guohua Wang, Shan Huang ...
 
 
 
Bioinformatics approaches for studying molecular sex differences in complex diseases border= 
 
Rebecca Ting Jiin Loo, Mohamed Soudy, Francesco Nasta, Mirco Macchi, Enrico Glaab
 
 
 
Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review border= 
 
Quang-Huy Nguyen, Ha Nguyen, Edwin C Oh, Tin Nguyen
 
 
 
Thinking points for effective batch correction on biomedical data border=  
 
Harvard Wai Hann Hui, Weijia Kong, Wilson Wen Bin Goh
 

Author summary: Batch effects introduce heterogeneity into data and hinder accurate analysis. Despite advancements in biomedical technologies and analysis algorithms, addressing batch effects remains a significant challenge due to their complex nature, which requires diverse considerations. To facilitate better handling of batch effects, we offer a comprehensive set of thinking points designed to help researchers ensure more robust analysis.

 
 
 
Robust variable selection methods with Cox model'a selective practical benchmark study border= 
 
Yunwei Zhang, Samuel Muller
 
 
 
Bioinformatics in Russia: history and present-day landscape border=  
 
Muhammad A Nawaz, Igor E Pamirsky, Kirill S Golokhvast
 
 
 
Progress and opportunities of foundation models in bioinformatics border=  
 
Qing Li, Zhihang Hu, Yixuan Wang, Lei Li, Yimin Fan ...
 
 
 
Making PBPK models more reproducible in practice border=  
 
Elena Domínguez-Romero, Stanislav Mazurenko, Martin Scheringer, Vítor A P Martins dos Santos, Chris T Evelo ...
 
 
 
A review of feature selection strategies utilizing graph data structures and Knowledge Graphs border= 
 
Sisi Shao, Pedro Henrique Ribeiro, Christina M Ramirez, Jason H Moore
 
 
 
Adversarial regularized autoencoder graph neural network for microbe-disease associations prediction border= 
 
Limuxuan He, Quan Zou, Qi Dai, Shuang Cheng, Yansu Wang
 

  • The biological processes and interactions of microorganisms and diseases are studied.

  • An autoencoding graph neural network predicts associations between microorganisms and diseases.

  • Generative adversarial networks address the limitations of encoder capture and mitigate sampling sparsity.

 
 
 
A gentle introduction to pangenomics border= 
 
Chelsea A Matthews, Nathan S Watson-Haigh, Rachel A Burton, Anna E Sheppard
 
 
 
Graph databases in systems biology: a systematic review border=  
 
Ilya Mazein, Adrien Rougny, Alexander Mazein, Ron Henkel, Lea Gütebier ...
 
 
 
Case Study
 
 
 
 
Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1 border= 
 
Aliaa E Ali, Li-Li Li, Michael J Courtney, Olli T Pentikäinen, Pekka A Postila
 
 
 
CDHu40: a novel marker gene set of neuroendocrine prostate cancer border=  
 
Sheng Liu, Hye Seung Nam, Ziyu Zeng, Xuehong Deng, Elnaz Pashaei ...
 
 
 
AESurv: autoencoder survival analysis for accurate early prediction of coronary heart disease border= 
 
Yike Shen, Arce Domingo-Relloso, Allison Kupsco, Marianthi-Anna Kioumourtzoglou, Maria Tellez-Plaza ...
 
 
 
scPanel: a tool for automatic identification of sparse gene panels for generalizable patient classification using scRNA-seq datasets border= 
 
Yi Xie, Jianfei Yang, John F Ouyang, Enrico Petretto
 
 
 
Development and validation of an explainable machine learning model for predicting multidimensional frailty in hospitalized patients with cirrhosis border= 
 
Fang Yang, Chaoqun Li, Wanting Yang, Yumei He, Liping Wu ...
 
 
 
Predicting functional outcome in ischemic stroke patients using genetic, environmental, and clinical factors: a machine learning analysis of population-based prospective cohort study border= 
 
Siding Chen, Zhe Xu, Jinfeng Yin, Hongqiu Gu, Yanfeng Shi ...
 
 
 
Long-range alternative splicing contributes to neoantigen specificity in glioblastoma border= 
 
Mingjun Ji, Qing Yu, Xin-Zhuang Yang, Xianhong Yu, Jiaxin Wang ...
 
 
 
A multi-omics study of brain tissue transcription and DNA methylation revealing the genetic pathogenesis of ADHD border= 
 
Jingkai Wang, Qiu-Wen Zhu, Jia-Hao Mai, Shun Zhang, Yuqing Wang ...
 
 
 
Mut-Map: Comprehensive Computational Pipeline for Structural Mapping and Analysis of Cancer-Associated Mutations border= 
 
Ali F Alsulami
 
 
 
Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity border= 
 
Sébastien De Landtsheer, Apurva Badkas, Dagmar Kulms, Thomas Sauter
 
 
 
Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability border= 
 
André Borges Farias, Gustavo Sganzerla Martinez, Edgardo Galán-Vásquez, Marisa Fabiana Nicolás, Ernesto Pérez-Rueda
 
 
 
Generating pregnant patient biological profiles by deconvoluting clinical records with electronic health record foundation models border= 
 
David Seong, Samson Mataraso, Camilo Espinosa, Eloise Berson, S Momsen Reincke ...
 
 
 
Correction
 
 
 
 
Correction to: Structure prediction of linear and cyclic peptides using CABS-flex border= 
 
 
 
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