Subject: New issue: Bioinformatics, Volume 42, Issue 5, May 2026

Volume 42, Issue 5, May 2026

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Latest impact metrics for Bioinformatics

We are pleased to share the latest impact metrics for Bioinformatics. The journal was recently awarded a CiteScoreâ"¢ (Scopus) of 9.6, a new Impact Factor of 5.4 (Journal Citation Reportsâ"¢), and received 6,750,412 total Full-text downloads in 2024.

We invite you to explore the latest breakthroughs published in Bioinformatics and consider the journal as the next outlet for your work.

A causal inference framework for identifying essential genes to enhance drug synergy prediction

Huaiwu Zhang and others

Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2

Alfred Ferrer Florensa and others

REACTOR: REgulon Activity analysis and Comparison Tool for single-cell transcriptOmics Research

Markus LindÃ©n and others

FuFiHLA: a tool for full-field HLA typing from long-read data

Jingqing Hu and others

Original Paper

Sequence analysis

BABAPPAlign: a multiple sequence alignment engine with a learned residue-level scoring function

Krishnendu Sinha

MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing

Ahmad Lutfi and others

Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment

LoriÃ©n LÃ³pez-Villellas and others

Much ado about nothing: modeling amino acid replacement with predicted protein structures

Lukas Buschmann and others

Refining sequence-to-expression modelling with chromatin accessibility

Orsolya Lapohos and others

Learning protein representations with conformational dynamics

Dan Kalifa and others

Protein language model embeddings improve HIV drug resistance prediction: a comprehensive benchmark with attention-based interpretability

Hayden Farquhar

Sassy: fuzzy searching DNA sequences using SIMD

Rick Beeloo and Ragnar Groot Koerkamp

TSEDTA: a transformer-based neural network with SMILES transformer and ESM2 embeddings for drug-target binding affinity prediction

Xu Sun and others

Genome analysis

MS-ConTab: multi-scale contrastive learning of mutation signatures for Pan-Cancer representation and stratification

Yifan Dou and others

Accelerated long-read variant calling with Clair3 for whole-genome sequencing

Zhenxian Zheng and others

Diagnosing scientific replicability through probabilistic distinguishability

Peng Wang and others

A framework to infer de novo exonic variants when parental genotypes are missing enhances association studies of autism

Haeun Moon and others

DTH: a nonparametric test for homogeneity of multivariate dispersions

Asmita Roy and others

Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity

Haotian Zhuang and others

A novel method for across-chromosome phasing without relative data

Emmanuel Sapin and others

SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators

Luka Maisuradze and others

Utilization of long-read sequencing for the detection of structural rearrangements with AgileStructure

Carolina Lascelles and others

Data and Text Mining

MZSGO: multimodal zero-shot protein function annotation via evolutionary signals and textual semantics

Boyue Cui and others

Metappuccino: large language model-driven reconstruction of sequence read archive metadata for cancer research

Fiona Hak and others

A large-scale neutral comparison study of survival models on low-dimensional data

Lukas Burk and others

Secure bioinformatics: privacy-preserving federated analytics using homomorphic encryption

Weizhuang Zhou and others

GR2ST: spatial transcriptomics prediction based on graph-enhanced multimodal contrastive learning

Jingli Zhou and others

KG-bench: benchmarking graph neural network algorithms for drug repurposing

Siqi Wei and others

A cross-attentive multi-task graph learning framework for chemical reaction modeling

Maryam Astero and others

IDAP: an integrated literature- and knowledge-graph-driven evidence prioritization pipeline for precision oncology

Yebin Ryu and others

Cell-o1: training LLMs to solve single-cell reasoning puzzles with reinforcement learning

Yin Fang and others

Genetics and population analysis

Tractor workflow: a scalable Nextflow framework for local ancestry-aware genome-wide association studies

Nirav N Shah and others

ChASM: a statistically rigorous method for the detection of chromosomal aneuploidies in ancient DNA studies

Adam B Rohrlach and others

Databases and ontologies

Accurate SPARQL generation via in-context learning and schema-based query construction

Hikaru Nagazumi and others

CancerOmicsStudio (CoS): a web server for integrative and interpretable analysis of multi-omics cancer data

Chenqi Liao and others

Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation

Matthijs Brouwer and others

Bioimage informatics

Bidirectional Mamba-2 boosts EEG super-resolution via regression and diffusion

Ugo Lomoio and others

Structural bioinformatics

Molecular fingerprints are strong models for peptide function prediction

Jakub Adamczyk and others

From atoms to fragments: a coarse representation for efficient and functional protein design

Leonardo V Castorina and others

HybridMolGen: a unified framework for goal-directed molecular generation via multi-objective reinforcement learning

Masoud Amiri and Zahra Nasirinia

Spark: sparse hierarchical energy minimization for scalable prediction of RNA pseudoknots

Mateo Gray and others

MuFaDDG: a sequence-based multiscale feature fusion framework for protein stability changes prediction

Jianting Gong and others

Inferring the qualities of protein'RNA models with graph transformers

Andrew Jordan Siciliano and others

Gene expression

Local transcriptional covariation produces accurate estimates of cell phenotype

Sinan Ozbay and others

Nested co-expression network analysis identifies compact gene clusters in a black box

I A Dyugay and others

Reconstructing cell-cell interaction network in single-cell spatial transcriptomics via directed heterogeneous graph autoencoder

Jin-Xian Hu and others

AXOLOTL: an accurate method for detecting aberrant gene expression in rare diseases using coexpression constraints

Wenjian Xu and others

Systems biology

HybridGNN: a graph neural network approach for human miRNA'disease association prediction

Basharat Ahmad and others

Supervised fine-tuning enhances unsupervised learning from 45 million amino acids in TCR and peptide sequences

Kewei Zhou and others

NAViFluX: a visualization'centric platform for interactive analysis, refinement and design of genome'scale metabolic networks

Manjunatha Beduru Krishnamurthy and others

Learning drug synergy through environment-conditioned feature modulation

Shuting Jin and others

MetaCCI: meta cell'cell interaction inference and its application to CCIs characteristics of MDS

Heewon Park and others

Applications Notes

Sequence analysis

FALCON2: compression-based metagenomic classification of ancient viruses

LuÃs L Marques and others

QCatch: a framework for quality control assessment and analysis of single-cell sequencing data

Yuan Gao and others

FUSE: data-driven functional segmentation of DNA methylation data

Susanna HolmstrÃ¶m and others

StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution

Baptiste Hennecart and others

Phylogenetics

treestructure: an R package to detect population structure in phylogenetic trees

FabrÃcia F Nascimento and others

Treemble: a graphical tool to generate Newick strings from phylogenetic tree images

John B Allard and Sudhir Kumar

Genome analysis

CpGene: a web application for epigenetic signature identification from DNA methylation arrays

Konstantinos Lazaros and others

nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction

Joon Klaps and others

Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data

Guanlan Dong and others

Segzoo: a turnkey system that summarizes genome annotations

MickaÃ«l Mendez and others

Yomix: an interactive tool for the exploration of low-dimensional embeddings in omics data

Nicolas Perrin-Gilbert and others

Gene expression

EMTscore infers divergent EMT pathways from omics data and enables rapid screening for EMT-associated gene sets

Haimei Wen and others

Identification of high-risk cells in single-cell spatially resolved transcriptomics data using Diagnostic Evidence GAuge of Single-cells with spatial smoothing

Debolina Chatterjee and others

PyFgsea: a Rust-powered, fgseaMultilevel-aligned GSEA framework with rolling-window enrichment along single-cell trajectories

Kuanghao Wang and Hong Shi

Systems biology

HySimODE: a hybrid stochastic-deterministic simulation framework for multiscale models of biological systems

Criseida G Zamora-Chimal and Alexander P S Darlington

dAMN: a genome-scale neural-mechanistic hybrid model to predict bacterial growth dynamics

Jean-Loup Faulon and others

Data and Text Mining

StrucPTM: a database of structurally validated protein modifications and their conformational variation

Seong-gwang Jeon and others

Genetics and population analysis

NCBoost v2: a classifier for non-coding single-nucleotide variants in Mendelian diseases

RAREsim2: flexible simulation of rare variant genetic data using real haplotypes

Jessica I Murphy and others

Structural bioinformatics

EMERALD-UI: an interactive web application to unveil novel protein biology hidden in the alternative alignment space

Andrei Preoteasa and others

Letter to the Editor

Genome Analysis

Best practices when benchmarking CATCH for the design of genome enrichment probes

Hayden C Metsky and others

Correction

Correction to: Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker

International Society for Computational Biology

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