Volume 27, Issue 1, January 2026

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Papers

A novel two-sample Mendelian randomization framework integrating common and rare variants: application to assess the effect of HDL-C on preeclampsia risk

Yu Zhang and others

GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data

Bingyan Wang and others

iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm

Ruhai Chen and others

Identification of cancer mini-drivers by deciphering selective landscape in the cancer genome

Xunuo Zhu and others

GRAFT: a graph-aware fusion transformer for cancer driver gene prediction

Sang-Pil Cho and Young-Rae Cho

UBD: incorporating uncertainty in cell type proportion estimates from bulk samples to infer cell-type-specific profiles

Youshu Cheng and others

CoBRA: compound binding site prediction using RNA language model

Wonkyeong Jang and Woong-Hee Shin

MACFIV: a novel framework for nonlinear causal inference in the body mass index'hypertension relationship with many weak and pleiotropic genetic instruments

Dong Chen and others

ProTCR: a protein language model-driven framework for decoding TCR-antigen recognition toward precision immunotherapies

Minrui Xu and others

Benchmarking community drug response prediction models: datasets, models, tools, and metrics for cross-dataset generalization analysis

Alexander Partin and others

Enhancing TFEA.ChIP with ENCODE regulatory maps for generalizable transcription factor enrichment

Yosra Berrouayel and Luis del Peso

Adaptive multi-view information bottleneck for multi-omics data clustering

Zhen Tian and others

CSRefiner: a lightweight framework for fine-tuning cell segmentation models with small datasets

Can Shi and others

EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites

Yonglin Peng and others

CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing

Jiayi Li and others

DeepRMSF: a deep learning-based automated approach for predicting atomic-level flexibility in RNA structure

Chenjie Feng and others

CNAttention: an attention-based deep multiple-instance method for uncovering copy number aberration signatures across cancers

Ziying Yang and Michael Baudis

GPCRact: a hierarchical framework for predicting ligand-induced GPCR activity via allosteric communication modeling

Hyojin Son and Gwan-Su Yi

CoxMDS: multiple data splitting for high-dimensional mediation analysis with survival outcomes in epigenome-wide studies

Minhao Yao and others

ASTWAS: modeling alternative polyadenylation and SNP effects in kernel-driven TWAS reveal novel genetic associations for complex traits

Yan Wang and others

An effective fragment-based dual conditional diffusion framework for molecular generation

Haotian Chen and others

Revealing hidden regulatory dependencies: multi-perspective graph learning for single-cell gene regulatory network inference

Wenying He and others

BHMnet: Bayesian high-dimensional mediation analysis with network information integration for correlated mediators

Yunju Im and Yuan Huang

MoAGNN: a multi-omics hierarchical graph neural network for subtype classification and prognosis prediction in lung adenocarcinoma

Cheng-Pei Lin and others

Turning heterogeneity of statistical epistasis networks to an advantage

Diane Duroux and others

Learning to explore tree neighbourhoods for phylogenetic inference

Federico Julian Camerota VerdÃ' and others

PHScaffolding: a hypergraph clustering and dual-weight integration strategy for scaffolding with Pore-C reads

Quan Su and others

GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis

Stefano Marangoni and others

BiChemoCLAM: a weakly supervised multimodal framework for chemotherapy response prediction

Jinglong Gui and others

DL-GapFilling: a novel deep learning framework for improved plant genome gap filling

Yu Chen and others

Clustering single-cell multi-omics data via multi-subspace contrastive learning with structural smoothness

Yun Ding and others

Decoding RNA triple helices: identification from sequence and secondary structure

Margherita A G Matarrese and others

Predicting protein'carbohydrate binding sites: a deep learning approach integrating protein language model embeddings and structural features

Md Muhaiminul Islam Nafi and M Saifur Rahman

Multi-platform integration of brain and CSF proteomes reveals biomarker panels for Alzheimer's disease

Wei-Yun Tsai and others

Task-specific pre-training for molecular property prediction

Wenbo Zhang and others

MPHGNN: metapath-guided heterogeneous graph neural network for miRNA-drug resistance association prediction

Guangsheng Huang and others

Scalable embedding fusion with protein language models: insights from benchmarking text-integrated representations

Young Su Ko and others

SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data

Tatsunori Osone and others

plmmr: an R package to fit penalized linear mixed models for genome-wide association data with complex correlation structure

Tabitha K Peter and others

S²potAE: multimodal spatial spot autoencoder integrating image and transcriptomic features for deconvolution

Tianyi Chen and others

Probing genomic language models: Nucleotide Generative Pretrained Transformer and the role of pretraining in learned representations

Shae M Mclaughlin and Daniel A Lim

scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation

Yanlin Jiang and others

BayesRare: Bayesian mixture model for population-level rare cell type detection in multi-subject single-cell RNA sequencing data

Yinqiao Yan and Hao Wu

PGVDA: a pathway-aggregated genetic dosage framework for interpretable disease classification using machine learning

Sanghyun Shon and others

Integrating multi-structure covalent docking with machine-learning consensus scoring enhances potency ranking of human acetylcholinesterase inhibitors

Chaitanya K Jaladanki and others

PathCLAST: pathway-augmented contrastive learning with attention for interpretable spatial transcriptomics

Minho Noh and others

PheCode-guided multi-modal topic modeling of electronic health records improves disease incidence prediction and GWAS discovery from UK Biobank

Ziqi Yang and others

Cross-dataset transcriptomic analyses identify a conserved ENPP2⁺ macrophage'fibroblast activation axis in hypertrophic cardiomyopathy

Fanyi Huang and others

Global and local integrated gradient-based diffusion model for de novo drug design

Sejin Park and others

TriDTI: tri-modal representation learning with cross-modal alignment for drug'target interaction prediction

Gwang-Hyeon Yun and others

Systematic evaluation of computational tools to predict the effects of mutations on protein-ligand binding affinity in the absence of experimental structures

Qisheng Pan and others

Transfer learning-based two-sample Mendelian randomization method for heterogeneous population

Yun Wei and others

SGAC: a graph neural network framework for imbalanced and structure-aware AMP classification

Yingxu Wang and others

Exploring potential transcription factors and their regulatory relationships based on asymmetric covariance natural vector encoding method and machine learning algorithms

Guoqing Hu and others

Multi-seed searching algorithm for integrated codon optimization of mRNA stability and translational efficiency in vaccine design

Yuhan Bo and others

CTAS: a network control theory-based approach to identify key regulatory TFs of AS events during epithelial'mesenchymal transition

Yan Gan and others

Signal-based spatial domain identification of spatially resolved transcriptomics with multigraph fusion

Yaxiong Ma and others

Enhancing protein structure prediction: evaluating the role of amino acid physicochemical features in homology search

Saeedeh Akbari Roknabadi and others

GATCL: graph attention network meets contrastive learning for spatial domain identification

Jichong Mu and others

Dynamic-GLEP: a dynamics-informed deep learning framework for ligand efficacy prediction in representative Class A GPCRs

Zhiyi Chen and others

iDLDDG: predicting protein stability changes from missense mutations in DNA-binding proteins using integrated deep learning features

Xuan Yu and others

3D reconstruction of spatial transcriptomics with spatial pattern enhanced graph convolutional neural network

Chen Tang and others

NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing

Chia-Chen Chu and others

Transformer-based graphs for drug'drug interaction with chemical knowledge embedding

Jinlu Zhang and others

EPINTLM: enhancer'promoter prediction with pretrained k-mer embeddings and residual cross-attention

Thi Lan Nguyen and others

Imputing missing values in single-cell RNA-sequencing data: a statistical and machine learning-based approach

A F M Shamsuzzaman and others

SHEST: single-cell-level artificial intelligence from haematoxylin and eosin morphology for cell-type prediction and spatial transcriptomics reconstruction

Hoyeon Jeong and others

PEPNet: a two-stage point cloud framework with hierarchical embedding and antigen'antibody interaction modeling for epitope prediction

Jiayi Chen and others

An unsupervised method for spatial transcriptomics analysis based on adversarial autoencoder

Wei Lan and others

A two-stage GAN-based instrumental variable method for causal analysis of omics data

Yuan Zhou and others

MCPmed: a call for Model Context Protocol-enabled bioinformatics web services for LLM-driven discovery

Matthias Flotho and others

Pangenome-guided sequence assembly via binary optimization

Josh Cudby and others

Phylogenomics to structure: evolutionary and clinical signals in the TP53 DNA-binding core through LOOCV-validated ensemble learning

Syed Raza Abbas and others

Reviews

A systematic review of molecular representation learning foundation models

Bosheng Song and others

A comprehensive survey of genome language models in bioinformatics

Liyuan Shu and others

Advances in scCUT&Tag and computational analysis for single-cell gene regulatory element mapping

Jun Wu and others

Personalized gene expression prediction in the era of deep learning: a review

Viksar Dubey and Li Shen

Advances and challenges in single-cell RNA sequencing data analysis: a comprehensive review

Ali Mohammad Nesari and others

Computational tools for tandem repeat detection using long-read sequencing

Qian Liu and Jincheng Li

A survey of contrastive learning methods in molecular representation

Ali Forooghi and others

Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa

Daudi Jjingo and others

Systematic evaluation of computational methods for cell segmentation

Rongrong Yang and others

Case Studies

Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification

Wenli Zhai and others

Detection of alternative splicing: deep sequencing or deep learning?

Lena Maria Hackl and others

Ab initio detection of multiple epitranscriptomic modifications from Oxford nanopore technology direct RNA sequencing data

Adriano Fonzino and others

BiGvCL: bipartite graph-based cross-domain contrastive learning model for the predicting drug-gene interactions

Shida He and others

ANIA: an inception-attention network for predicting minimum inhibitory concentration of antimicrobial peptides

Yen-Peng Chiu and others

Divergent Eurasian ancestry and local adaptation shape the genetic landscapes of the Yugur and Uyghur

Siyong Yu and others

Bayesian multi-cell type models for the analysis of complex immune cell populations with application to ovarian cancer

Chase J Sakitis and others

ChemEmbed: a deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings

Muhammad Faizan-Khan and others

A de novo assembly based fusion gene detection concept based on DNA-seq data of 100 Ewing sarcoma cases

Xinwei Zhao and others

Human messenger RNA harbors widespread noncoding splice isoforms

Qili Shi and others

DTAP: a unified graph transformer framework for joint prediction of drug'target affinity and docking pose

Junxi Liu and others

Revealing shared molecular markers and mechanisms in colorectal cancer and COVID-19 through bioinformatics and machine learning

Hairui Wang and others

MHAFR-DDI: a multimodal hierarchical attention fusion and relation-aware architecture for drug'drug interaction event prediction

Mengli Li and others

Letter to Editor

Re: Qi et al. "A roadmap for T cell receptor'peptide'MHC binding prediction by machine learning: glimpse and foresight" (Briefings in Bioinformatics, 2025)

Cedric Ly and others

Reply to: ˜testing the generalizability of DeepPlantAllergy on challenging allergen prediction scenarios'

Wala Dhouib and others

Corrections

Corrections to the following abstracts

Correction to: Consensus statement on the credibility assessment of machine learning predictors

Correction to: MetImputBERT: a pretrained BERT framework for missing value imputation in NMR metabolomics data

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