Subject: New issue: Briefings in Bioinformatics, Volume 26, Issue 4, July 2025

Volume 26, Issue 4, July 2025

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Call for Proposals: 25th Anniversary Collection

Briefings in Bioinformatics is inviting proposals for a special collection celebrating its 25th anniversary. This curated collection of Review and Perspective Articles will examine the evolution of bioinformatics and explore future directions in the field. Topics of interest include bibliometric analyses, foundational methods, AI in bioinformatics, and translational applications.

Submit your proposal by 30 August 2025.

Papers

Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification

Genereux Akotenou and Achraf El Allali

Iterative clustering algorithm G-DESC-E and pan-cancer key gene analysis based on single-cell sequencing data

Ke Wu and others

Inference of gene coexpression networks from single-cell transcriptome data based on variance decomposition analysis

Bin Lian and others

Gene regulatory network integration with multi-omics data enhances survival predictions in cancer

Romana T Pop and others

pMHChat, characterizing the interactions between major histocompatibility complex class II molecules and peptides with large language models and deep hypergraph learning

Jiani Ma and others

Intelligent Batch Epitope Identification and Partitioning: an intelligent tool for the identification of B cell dominant epitopes

Yun-Fei Ma and Ye Liu

Deep learning'enhanced clustering and classification of protein molecule tertiary structures using weighted distance matrices

Junlong Liu and others

AFToolkit: a framework for molecular modeling of proteins with AlphaFold-derived representations

Maria Sindeeva and others

Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations

Youshu Cheng and others

Multi-level association rule mining and network pharmacology to identify the polypharmacological effects of herbal materials and compounds in traditional medicine

Hyejin Yu and others

DrugProtAI: A machine learning'driven approach for predicting protein druggability through feature engineering and robust partition-based ensemble methods

Ankit Halder and others

An artificial intelligence-based approach for identifying the proteins regulating liquid'liquid phase separation

Zahoor Ahmed and others

Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas

Zhi Ran and others

Multimodal zero-shot learning of previously unseen epitranscriptomes from RNA-seq data

Yiyou Song and others

A free energy perturbation-assisted machine learning strategy for mimotope screening in neoantigen-based vaccine design

Qinglu Zhong and others

AEPMA: peptide'microbe association prediction based on autoevolutionary heterogeneous graph learning

Zhiyang Hu and others

CMOMO: a deep multi-objective optimization framework for constrained molecular multi-property optimization

Xin Xia and others

AttenRNA: multi-scale deep attentive model with RNA feature variability analysis

Jing Li and others

A data-intelligence-intensive bioinformatics copilot system for large-scale omics research and scientific insights

Yang Liu and others

Assessing Random Forest self-reproducibility for optimal short biomarker signature discovery

Ahmed Debit and others

Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence

Zhiwei Nie and others

CAT: a conditional association test for microbiome data using a permutation approach

Yushu Shi and others

Kinase'inhibitor binding affinity prediction with pretrained graph encoder and language model

Xudong Guo and others

A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors

Anjie Qiao and others

HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data

Bishal Shrestha and Zheng Wang

NASNet-DTI: accurate drug'target interaction prediction using heterogeneous graphs and node adaptation

Ningyu Zhong and Zhihua Du

AI-guided discovery and optimization of antimicrobial peptides through species-aware language model

Daehun Bae and others

MetaGeno: a chromosome-wise multi-task genomic framework for ischaemic stroke risk prediction

Yue Yang and others

MDNN: memetic deep neural network for genomic prediction

Yijun Mao and others

IMOP-Cancer: identifying mutation order pairs impacting cancer phenotypes

Yijing Zhang and others

Path-MGCN: a pathway activity-based multi-view graph convolutional network for determining spatial domains

Qirui Zhou and others

PepTCR-Net: prediction of multi-class antigen peptides by T-cell receptor sequences with deep learning

Phi Le and others

Inferring cell-type-specific gene regulatory network from cellular transcriptomics data with GeneLink+

Wei Zhang and others

Benchmarking of computational demultiplexing methods for single-nucleus RNA sequencing data

Yile Fu and others

GRANet: a graph residual attention network for gene regulatory network inference

Junliang Zhou and others

Deep graph convolutional network-based multi-omics integration for cancer driver gene identification

Yingzhuo Wu and others

MambaCpG: an accurate model for single-cell DNA methylation status imputation using mamba

Qi Zhao and others

Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression

Chenyu Liu and others

RGCN-BA: relational graph convolutional network with batch awareness for single-cell RNA sequencing clustering

Yueyue Wang and others

A comprehensive benchmark of tools for efficient genomic interval querying

Richard A SchÃ¤fer and Rendong Yang

MAPTrans: mutual attention transformer with dynamic meta-path pruning for drug repositioning

Shanyang Ding and others

HybridKla: a hybrid deep learning framework for lactylation site prediction

Wanshan Ning and others

PLMFit: benchmarking transfer learning with protein language models for protein engineering

Thomas Bikias and others

Artifacts in spatial transcriptomics data: their detection, importance, prevalence, and prevention

Erich Kummerfeld and others

Formal verification of bioinformatics software using model checking and theorem proving

Hansika Weerasena and others

Dual balanced augmented topological noncoding RNA disease triplet association in heterogeneous graphs

Laiyi Fu and others

A robust and interpretable graph neural network-based protocol for predicting p-glycoprotein substrates

Kuang-Cheng Hsu and others

Deep reinforcement learning as an interaction agent to steer fragment-based 3D molecular generation for protein pockets

Xudong Zhang and others

Genetic/epigenetic DNA markers for linking suspects and tissues in complex crime scenes

Roy Mizrachi and others

Prediction of liquid-phase separation proteins using Siamese network with feature fusion

Ye-Hong Yang and others

On the impact of local protein structure features on prediction of major histocompatibility complex class I and II antigen presentation

Yat-tsai Richie Wan and Morten Nielsen

Identifying novel therapeutic targets of natural compounds in traditional Chinese medicine herbs with hypergraph representation learning

Yantong Qiao and others

BPA: a BERT-based priority annotation strategy for assessing the rationality of aquatic algal protein sequences

Rui-Hua Huang and others

Prioritizing pathway signature using deep learning approach: a novel strategy for traditional Chinese medicine formula generation and optimization

Zheng Wu and others

Decoding longitudinal microbiome trajectories: an interpretable machine learning approach for biomarker discovery and prediction

Yifan Dai and others

PanThera: predictive analysis of higher-order combination therapies using deep neural networks

Pedro A Campana and others

A comparative evaluation of computational models for RNA modification detection using nanopore sequencing with RNA004 chemistry

Yongji Zou and others

Pushing the boundaries of few-shot learning for low-data drug discovery with a Bayesian meta-learning hypernetwork framework

Jiacai Yi and others

DeepGraphMut: a graph-based deep learning method for cancer prognosis using somatic mutation profile

Aswin Jose and others

Graph-CRISPR: a gene editing efficiency prediction model based on graph neural network with integrated sequence and secondary structure feature extraction

Yaojia Jiang and others

DriverOmicsNet: an integrated graph convolutional network for multi-omics exploration of cancer driver genes

Yang-Hong Dai and others

RSCNN-PseU: random searching-based convolutional neural network model for identifying RNA pseudouridine

Jian Jin and Jie Feng

MKFGO: integrating multi-source knowledge fusion with pretrained language model for high-accuracy protein function prediction

Yi-Heng Zhu and others

AutoMethyc: an automated methylation analysis for massively parallel sequencing data

Fernando Ambriz-Barrera and others

Design of function-regulating RNA via deep learning and AlphaFold 3

Yan Xia and others

Reg2ST: recognizing potential patterns from gene expression for spatial transcriptomics prediction

Xu Wang and others

Indel calling from ONT sequencing data of family trios via sparse attention and 3D convolution

Ying Shi and others

DANet: spatial gene expression prediction from H&E histology images through dynamic alignment

Yulong Wu and others

HiCat: a semi-supervised approach for cell type annotation

Chang Bi and others

Deep clustering of single-cell RNA-seq using adversarial graph contrastive learning

Le Van Vinh and others

Guidance for the design and analysis of cell-type-specific DNA methylation epidemiology studies

Emma M Walker and others

LncPTPred: predicting lncRNA'protein interaction based on crosslinking and immunoprecipitation (CLIP-Seq) data

Gourab Das and others

Boosting data interpretation with GIBOOST to enhance visualization of complex high-dimensional data

Komlan Atitey and others

ProDualNet: dual-target protein sequence design method based on protein language model and structure model

Liu Cheng and others

Pore-C Pipeline-Toolbox: a comprehensive pipeline for Pore-C data analysis

Zhenji Wang and others

MULoc-target: Targeting peptide classification and detection using a protein language model

Yuexu Jiang and others

LOCAS: multilabel mRNA localization with supervised contrastive learning

Abrar Rahman Abir and others

MuST: multiple-modality structure transformation for single-cell spatial transcriptomics

Zelin Zang and others

ESM2_AMP: an interpretable framework for protein'protein interactions prediction and biological mechanism discovery

Yawen Sun and others

BBANsh: a deep learning architecture based on BERT and bilinear attention networks to identify potent shRNA

Yuanting Chen and others

Identifying potential miRNA'disease associations through an accurate matrix completion approach

Beier Li and others

Reviews

Advancing genome-based precision medicine: a review on machine learning applications for rare genetic disorders

Syed Raza Abbas and others

Paradigms, innovations, and biological applications of RNA velocity: a comprehensive review

Yajunzi Wang and others

An advanced network pharmacology investigation of Shufeng Jiedu formula in the treatment for respiratory tract infection based on LC'MS, data mining, molecular docking, and molecular dynamic simulation

Yan Zhang and others

A survey on deep learning for polygenic risk scores

Max Schuran and others

Cell type heterogeneity in gene co-expression networks: implications for toxicological research

Imke B Bruns and others

Case Studies

Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies

Federico GarcÃa-Criado and others

SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation

PREDAC-FluB: predicting antigenic clusters of seasonal influenza B viruses with protein language model embedding based convolutional neural network

Wenping Xie and others

Impact of halogenation on scaffold toxicity assessed using HD-GEM machine learning model

Bharath Reddy Boya and others

SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples

Xue Liu and others

BloodProST: prediction of blood-secretory proteins through self-training

Xuechen Mu and others

DiffusionST: a deep generative diffusion model-based framework for enhancing spatial transcriptomics data quality and identifying spatial domains

Yaxuan Cui and others

DensePPI-2: a bio-inspired update for sequence-based PPI prediction leveraging mutation rates

Tapas Chakraborty and others

Differential causal networks highlight sex-based differences in human tissues

Annamaria Defilippo and others

Towards machine learning fairness in classifying multicategory causes of deaths in colorectal or lung cancer patients

Catherine H Feng and others

Expediting the discovery of promising photothermal cyanine molecules through a transfer learning approach

Zhiwen Zhang and others

EXGEP: a framework for predicting genotype-by-environment interactions using ensembles of explainable machine-learning models

Tingxi Yu and others

Protein language model pseudolikelihoods capture features of in vivo B cell selection and evolution

Daphne van Ginneken and others

Investigating the shared genetic architecture between adiposity measures and obesity-related cancers

Siyue Wang and others

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