Subject: New issue: Bioinformatics, Volume 41, Issue 10, October 2025

Bioinformatics

Bioinformatics

Volume 41, Issue 10, October 2025

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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.

Original Paper

Genome analysis

acmgscaler: an R package and Colab for standardized gene-level variant effect score calibration within the ACMG/AMP framework

Mihaly Badonyi and Joseph A Marsh

Privacy-preserving federated unsupervised domain adaptation with application to age prediction from DNA methylation data

Cem Ata Baykara and others

InterVelo: a mutually enhancing model for estimating pseudotime and RNA velocity in multi-omic single-cell data

Yurou Wang and others

Sequence analysis

SKiM: accurately classifying metagenomic ONT reads in limited memory

Trevor Schneggenburger and Jaroslaw Zola

An innovative peptide toxicity prediction model based on multi-scale convolutional neural network and residual connection

Shengli Zhang and others

Exploring homology detection via k-means clustering of proteins embedded with a large language model

Thomas Minotto and others

Phylogenetics

HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X

Guy Baele and others

Structural bioinformatics

An image-based protein'ligand binding representation learning framework via multi-level flexible dynamics trajectory pre-training

Hongxin Xiang and others

An interpretable alphabet for local protein structure search based on amino acid neighborhoods

Saba Zerefa and others

Gene expression

High-dimensional causal mediation analysis by partial sum statistic and sample splitting strategy in imaging genetics application

Hung-Ching Chang and others

FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs

Hukam C Rawal and others

DiSTect: a Bayesian model for disease-associated gene discovery and prediction in spatial transcriptomics

Qicheng Zhao and others

Conformal inference for reliable single cell RNA-seq annotation

Marcos LÃ³pez-De-Castro and others

CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data

Daniel Kim and others

ToxAssay: a hierarchical model-driven tool for advanced toxicogenomics biomarker discovery

Md Masud Rana and others

scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data

Jinpu Li and others

Genetics and population analysis

BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1000s of omics datasets

Pavel P Kuksa and others

Federated learning for the pathogenicity annotation of genetic variants in multi-site clinical settings

Nigreisy Montalvo and others

Systems biology

MPAC: a computational framework for inferring pathway activities from multi-omic data

Peng Liu and others

Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models

Alan Utsuni Sabino and others

KADAIF: an anomaly detection method for complex microbiome data

Omri Peleg and others

Cancer survival prediction based on soft-label guided contrastive learning and global feature fusion

Huiying Jiang and others

MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction

Yue Luo and Lei Deng

HyperPhS: a pharmacophore-guided multimodal representation framework for metabolic stability prediction through contrastive hypergraph learning

Xiaoyi Liu and others

Data and text mining

Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation

Armin Rauschenberger and others

Predicting the trend of SARS-CoV-2 mutation frequencies using historical data

Xinyu Zhou and others

Pre-Meta: priors-augmented retrieval for LLM-based metadata generation

Phil Tinn and others

aMLProt: an automated machine learning library for protein applications

Ruite Xiang and others

Automating candidate gene prioritization with large language models: from naive scoring to literature-grounded validation

Taushif Khan and others

DeepProtein: deep learning library and benchmark for protein sequence learning

Jiaqing Xie and others

The role of graph topology in the performance of biomedical Knowledge Graph Completion models

Alberto Cattaneo and others

Bioimage informatics

UAMRL: multi-granularity uncertainty-aware multimodal representation learning for drug-target affinity prediction

Wenzhe Xu and others

Applications Note

Genome analysis

Warp analysis research pipelines: cloud-optimized workflows for biological data processing and reproducible analysis

Kylee Degatano and others

PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences

Mariia Pospelova and Yana Safonova

DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation

Elias Dohmen and others

Enhancing genome recovery across metagenomic samples using MAGmax

Arangasamy Yazhini and Johannes SÃ¶ding

reDA: differential abundance testing on scATAC-seq data using random walk with restart

Zirui Chen and others

Sequence analysis

Î¨-co-mAFiA: concurrent detection of pseudouridine and m⁶A in single RNA molecules

Adrian Chan and others

Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE

Evan Komp and others

Easy and interactive taxonomic profiling with Metabuli App

SunJae Lee and others

Phylogenetics

Delineating inter- and intra-antibody repertoire evolution with AntibodyForests

Daphne van Ginneken and others

Structural bioinformatics

SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains

Alexandre Boulay and others

STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation

Nele P Quast and others

Genetics and population analysis

WinPCA: a package for windowed principal component analysis

L Moritz Blumer and others

PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption

GÃ¼liz Akkaya and others

Integrating population-level and cell-based signatures for drug repositioning

Chunfeng He and others

PTL-PRS: an R package for transfer learning of polygenic risk scores with pseudovalidation

Bokeum Cho and Seunggeun Lee

Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series

Melis Gencel and others

Systems biology

FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data

Guido Barzaghi and others

CANA v1.0.0: efficient quantification of canalization in automata networks

Austin M Marcus and others

GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk

Suleiman Aminu and others

Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT

Daniel E SchÃ¤ffer and others

Data and text mining

Parsing GTF and FASTA files using the eccLib Library

Tomasz Chady and Zuzanna Karolina Filutowska

Databases and Ontologies

Oncopacket: integration of cancer research data using GA4GH phenopackets

Michael Sierk and others

BAV-LLPS: a database of bacterial, archaea, and virus liquid'liquid phase separation proteins

Cecilia B Rodriguez and others

monarchr: an R package for querying biomedical knowledge graphs

Shawn T O'Neil and others

Bioimage informatics

AXZ viewer: a web application to visualize unprocessed AFM-IR data

Wouter Duverger and others

G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration

Donn Liew and others

Letter to the Editor

Sequence analysis

Balancing complexity and clarity'towards clinician-ready antibiotic resistance prediction models

Dickson Aruhomukama

Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows

Rok Kogoj and others

International Society for Computational Biology

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