Subject: New issue: Briefings in Bioinformatics, Volume 26, Issue 2, March 2025

Volume 26, Issue 2, March 2025

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Articles

Ensemble learning based on matrix completion improves microbe-disease association prediction

Hailin Chen,Kuan Chen

Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets

Minfang Song,Shuai Ma and others

HSSPPI: hierarchical and spatial-sequential modeling for PPIs prediction

Yuguang Li,Zhen Tian and others

GcDUO: an open-source software for GC‰×‰GC'MS data analysis

Maria Llambrich,Frans M van der Kloet and others

Unveiling a novel cancer hallmark by evaluation of neural infiltration in cancer

Qi Dong,Yingying Guo and others

MAEST: accurately spatial domain detection in spatial transcriptomics with graph masked autoencoder

Pengfei Zhu,Han Shu and others

TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment

Bingqing Han,Yipeng Zhang and others

Inferring gene regulatory networks from time-series scRNA-seq data via GRANGER causal recurrent autoencoders

Liang Chen,Madison Dautle and others

Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants

Meng Yuan,Seppe Goovaerts and others

DockEM: an enhanced method for atomic-scale protein'ligand docking refinement leveraging low-to-medium resolution cryo-EM density maps

Jing Zou,Wenyi Zhang and others

A comparison of random forest variable selection methods for regression modeling of continuous outcomes

Nathaniel S O'Connell,Byron C Jaeger and others

Testing and overcoming the limitations of modular response analysis

Jean-Pierre Borg,Jacques Colinge and others

Consensus statement on the credibility assessment of machine learning predictors

Alessandra Aldieri,Thiranja Prasad Babarenda Gamage and others

Dissecting genetic regulation of metabolic coordination

Emily C Hector,Daiwei Zhang and others

Exploring diverse approaches for predicting interferon-gamma release: utilizing MHC class II and peptide sequences

Abir Omran,Alexander Amberg and others

Regularly updated benchmark sets for statistically correct evaluations of AlphaFold applications

Laszlo Dobson,GÃ¡bor E TusnÃ¡dy and others

Cox-Sage: enhancing Cox proportional hazards model with interpretable graph neural networks for cancer prognosis

Ruijun Mao,Li Wan and others

Optimizing sample size for supervised machine learning with bulk transcriptomic sequencing: a learning curve approach

Yunhui Qi,Xinyi Wang and others

Cancer gene identification through integrating causal prompting large language model with omics data'driven causal inference

Haolong Zeng,Chaoyi Yin and others

Predicting differentially methylated cytosines in TET and DNMT3 knockout mutants via a large language model

Saleh Sereshki,Stefano Lonardi

Scaling up drug combination surface prediction

Riikka Huusari,Tianduanyi Wang and others

Evaluating long-read assemblers to assemble several aphididae genomes

Nicolaas F V Burger,Vittorio F Nicolis and others

DRAG: design RNAs as hierarchical graphs with reinforcement learning

Yichong Li,Xiaoyong Pan and others

Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature

Sizhe Qiu,Bozhen Hu and others

Pragmatic soft-decision data readout of encoded large DNA

Qi Ge,Rui Qin and others

MulNet: a scalable framework for reconstructing intra- and intercellular signaling networks from bulk and single-cell RNA-seq data

Mingfei Han,Xiaoqing Chen and others

GiGs: graph-based integrated Gaussian kernel similarity for virus'drug association prediction

Yixuan Jin,Juanjuan Huang and others

Dual-stream cross-modal fusion alignment network for survival analysis

Jinmiao Song,Yatong Hao and others

MOSim: bulk and single-cell multilayer regulatory network simulator

Carolina MonzÃ³,Maider Aguerralde-Martin and others

AttentionGRN: a functional and directed graph transformer for gene regulatory network reconstruction from scRNA-seq data

Zhen Gao,Yansen Su and others

Deep learning-driven survival prediction in pan-cancer studies by integrating multimodal histology-genomic data

Yongfei Hu,Xinyu Li and others

BAMBI integrates biostatistical and artificial intelligence methods to improve RNA biomarker discovery

Peng Zhou,Zixiu Li and others

DS-MVP: identifying disease-specific pathogenicity of missense variants by pre-training representation

Qiufeng Chen,Lijun Quan and others

Relational similarity-based graph contrastive learning for DTI prediction

Jilong Bian,Hao Lu and others

SC-VAR: a computational tool for interpreting polygenic disease risks using single-cell epigenomic data

Gefei Zhao,Binbin Lai

PCLSurv: a prototypical contrastive learning-based multi-omics data integration model for cancer survival prediction

Zhimin Li,Wenlan Chen and others

deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model

Xiaoyan Wang,Junwei Luo and others

scSAMAC: saliency-adjusted masking induced attention contrastive learning for single-cell clustering

Bo Li,Yongkang Zhao and others

MethPriorGCN: a deep learning tool for inferring DNA methylation prior knowledge and guiding personalized medicine

Jie Ni,Bin Li and others

MolEM: a unified generative framework for molecular graphs and sequential orders

Hanwen Zhang,Deng Xiong and others

|$\mathcal{S}$|able: bridging the gap in protein structure understanding with an empowering and versatile pre-training paradigm

Jiashan Li,Xi Chen and others

Kolmogorov'Arnold networks for genomic tasks

Oleksandr Cherednichenko,Maria Poptsova

EMcnv: enhancing CNV detection performance through ensemble strategies with heterogeneous meta-graph neural networks

Xuwen Wang,Zhili Chang and others

DOMSCNet: a deep learning model for the classification of stomach cancer using multi-layer omics data

Kasmika Borah,Himanish Shekhar Das and others

CoupleVAE: coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data

Yahao Wu,Jing Liu and others

scMUG: deep clustering analysis of single-cell RNA-seq data on multiple gene functional modules

De-Min Liang,Pu-Feng Du

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting

Oleksandr Narykov,Yitan Zhu and others

FusionPub, a therapeutic landscape of human fusion genes

Himansu Kumar,Abayomi Adegunlehin and others

MRAgent: an LLM-based automated agent for causal knowledge discovery in disease via Mendelian randomization

Wei Xu,Gang Luo and others

Interpretable high-order knowledge graph neural network for predicting synthetic lethality in human cancers

Xuexin Chen,Ruichu Cai and others

Inferring kinase'phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets

Haoyang Cheng,Zhuoran Liang and others

Inter-view contrastive learning and miRNA fusion for lncRNA-protein interaction prediction in heterogeneous graphs

Yijun Mao,Jiale Wu and others

SMAC: identifying DNA N⁶-methyladenine (6mA) at the single-molecule level using SMRT CCS data

Haicheng Li,Junhua Niu and others

HPV-KITE: sequence analysis software for rapid HPV genotype detection

Marek Nowicki,Magdalena Mroczek and others

ScFold: a GNN-based model for efficient inverse folding of short-chain proteins via spatial reduction

Jiancheng Zhong,Zhiwei Zou and others

FGeneBERT: function-driven pre-trained gene language model for metagenomics

Chenrui Duan,Zelin Zang and others

Deep generative model for protein subcellular localization prediction

Guo-Hua Yuan,Jinzhe Li and others

FactVAE: a factorized variational autoencoder for single-cell multi-omics data integration analysis

Linjie Wang,Huixia Zhang and others

Multi-Manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomics

Ying Li,Qifeng Hu and others

RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling

Chun Shen Lim,Alexandra K Gibbon and others

DeepHeteroCDA: circRNA'drug sensitivity associations prediction via multi-scale heterogeneous network and graph attention mechanism

Zhijian Huang,Kai Chen and others

A multi-step completion process model of cell plasticity

Chen M Chen,Rosemary Yu

Federated transfer learning with differential privacy for multi-omics survival analysis

Gang Wen,Limin Li

A novel Bayesian hierarchical model for detecting differential circadian pattern in transcriptomic applications

Yutao Zhang,Haocheng Ding and others

Integrating CORUM and co-fractionation mass spectrometry to create enhanced benchmarks for protein complex predictions

Pengcheng Yang,Youngwoo Lee and others

A systematic evaluation of cell-type-specific differential methylation analysis in bulk tissue

Shuo Li,Pei Fen Kuan

A graph neural network approach for accurate prediction of pathogenicity in multi-type variants

Hongtao Yu,Guojing He and others

DMGAT: predicting ncRNA-drug resistance associations based on diffusion map and heterogeneous graph attention network

Tingyu Liu,Qiuhao Chen and others

SCANER: robust and sensitive identification of malignant cells from the scRNA-seq profiled tumor ecosystem

Peng Xia,Wei Wu and others

Evaluation of imputation and imputation-free strategies for differential abundance analysis in metaproteomics data

Xinyi Mou,Haoyu Du and others

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases

Cong M Pham,Timothy J Rankin and others

STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics

Yuxuan Pang,Chunxuan Wang and others

Mutual-assistance learning for trustworthy biomarker discovery and disease prediction

Jin Zhang,Yan Yang and others

IDP-EDL: enhancing intrinsically disordered protein prediction by combining protein language model and ensemble deep learning

Junxi Xie,Xiaopeng Jin and others

Nonlinear embedding and integration of omics data: a fast and tuning-free approach

Shengjie Liu,Tianwei Yu

Self-awareness of retrosynthesis via chemically inspired contrastive learning for reinforced molecule generation

Yi Zhang,Jindi Huang and others

Shared-weight graph framework for comprehensive protein stability prediction across diverse mutation types

Gen Li,Sijie Yao and others

Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer

Fabio Cumbo,Simone Truglia and others

DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks

Yizhen Wang,Li Cheng and others

PathSynergy: a deep learning model for predicting drug synergy in liver cancer

Fengyue Zhang,Xuqi Zhao and others

MIRACN: a residual convolutional neural network for predicting cell line specific functional regulatory variants

Zeyin Li,Min Wang and others

Carmna: classification and regression models for nitrogenase activity based on a pretrained large protein language model

Anqiang Ye,Ji-Yun Zhang and others

WheatGP, a genomic prediction method based on CNN and LSTM

Chunying Wang,Di Zhang and others

Deep learning in GPCR drug discovery: benchmarking the path to accurate peptide binding

Luuk R Hoegen Dijkhof,Teemu K E RÃ¶nkkÃ¶ and others

MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human

Yun Zuo,Xingze Fang and others

GraphATC: advancing multilevel and multi-label anatomical therapeutic chemical classification via atom-level graph learning

Wengyu Zhang,Qi Tian and others

sTPLS: identifying common and specific correlated patterns under multiple biological conditions

Jinyu Chen,Wenwen Min

Reviews

A comprehensive review and benchmark of differential analysis tools for Hi-C data

Elise Jorge,Sylvain Foissac and others

Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey

Shifu Luo,Hui Peng and others

VITALdb: to select the best viroinformatics tools for a desired virus or application

Mira Koul,Shalini Kaushik and others

Graph neural networks for single-cell omics data: a review of approaches and applications

Sijie Li,Heyang Hua and others

Benchmarking ensemble machine learning algorithms for multi-class, multi-omics data integration in clinical outcome prediction

Annette Spooner,Mohammad Karimi Moridani and others

A review of neural networks for metagenomic binning

Jair Herazo-Ã lvarez,Marco Mora and others

Elementary methods provide more replicable results in microbial differential abundance analysis

Juho Pelto,Kari Auranen and others

Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective

Shuang Ge,Shuqing Sun and others

Comprehensive benchmarking of large language models for RNA secondary structure prediction

Luciano I Zablocki,Leandro A Bugnon and others

A comprehensive review and evaluation of species richness estimation

Johanna Elena Schmitz,Sven Rahmann

A comprehensive review of cancer survival prediction using multi-omics integration and clinical variables

Dao Tran,Ha Nguyen and others

MINE: a new way to design genetics experiments for discovery

Isaac Torres,Shufan Zhang and others

Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine

Steffen Klamt,JÃ¼rgen Zanghellini and others

Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives

Jammi Prasanthi Sirasani,Cory Gardner and others

Case Study

Learning directed acyclic graphs for ligands and receptors based on spatially resolved transcriptomic data of ovarian cancer

Shrabanti Chowdhury,Sammy Ferri-Borgogno and others

A novel integrative multimodal classifier to enhance the diagnosis of Parkinson's disease

Xiaoyan Zhou,Luca Parisi and others

GEMDiff: a diffusion workflow bridges between normal and tumor gene expression states: a breast cancer case study

Xusheng Ai,Melissa C Smith and others

Disrupted microbial cross-feeding and altered L-phenylalanine consumption in people living with HIV

Hai Duc Nguyen,Woong-Ki Kim

REDInet: a temporal convolutional network-based classifier for A-to-I RNA editing detection harnessing million known events

Adriano Fonzino,Pietro Luca Mazzacuva and others

MUTATE: a human genetic atlas of multiorgan artificial intelligence endophenotypes using genome-wide association summary statistics

Aleix Boquet-Pujadas,Jian Zeng and others

Elucidating the interactions between Kinesin-5/BimC and the microtubule: insights from TIRF microscopy and molecular dynamics simulations

Wenhan Guo,Yuan Gao and others

CoPPIs algorithm: a tool to unravel protein cooperative strategies in pathophysiological conditions

Andrea Lomagno,Ishak Yusuf and others

Consistent semantic representation learning for out-of-distribution molecular property prediction

Xinlong Wen,Hao Liu and others

Assessing the impact of batch effect associated missing values on downstream analysis in high-throughput biomedical data

Harvard Wai Hann Hui,Wei Xin Chan and others

Corrections

Correction to: STMGraph: spatial-context-aware of transcriptomes via a dual-remasked dynamic graph attention model

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