Subject: New issue: Bioinformatics, Volume 42, Issue 1, January 2026

Bioinformatics

Bioinformatics

Volume 42, Issue 1, January 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.

PICNIC web server for predicting proteins involved in biomolecular condensates

Anna Hadarovich and others

OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data

Huidong Su and others

mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing

Hajime Suzuki and others

Benchmarking large language models for identifying transcription factor regulatory interactions

Lake Noel and others

EXPLANA: a user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies

Jennifer Fouquier and others

RISK: a next-generation tool for biological network annotation and visualization

Ira Horecka and Hannes RÃ¶st

CellCraft: an extensible visual programming application for gene regulatory network inference

Dongmin Shin and others

Original Paper

Genome analysis

ImmunoPepper: extracting personalized peptides from complex splicing graphs

Laurie PrÃ©lot and others

MegaPlantTF: a machine learning framework for comprehensive identification and classification of plant transcription factors

Genereux Akotenou and others

PanForest: predicting genes in genomes using random forests

Alan J S Beavan and others

Sequence analysis

Hi-Enhancer: a two-stage framework for prediction and localization of enhancers based on Blending-KAN and Stacking-Auto models

Aimin Li and others

Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index

Jens Zentgraf and others

NanoSSL: attention mechanism-based self-supervised learning method for protein identification using nanopores

Yong Xie and others

Phylogenetics

Efficient algorithms for simulating sequences along a phylogenetic tree

Elya Wygoda and others

Structural bioinformatics

Molecular-level protein semantic learning via structure-aware coarse-grained language modeling

Jun Zhang and others

PLM-eXplain: divide and conquer the protein embedding space

Jan van Eck and others

Building multiscale Markov state models by systematic mapping of temporal communities

Nir Nitskansky and others

RoBep: a region-oriented deep learning model for B-cell epitope prediction

Yitao Xu and others

Gene expression

isoSeQL: comparing long-read isoforms across multiple datasets

Christine S Liu and Jerold Chun

Spider: a flexible and unified framework for simulating spatial transcriptomics data

Jiyuan Yang and others

Analyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing

Hu Chen and others

Systems biology

Profiler: an open web platform for multi-omics analysis

Yanis Zirem and others

Signing protein'protein interaction networks

Lorenzo Federico Signorini and others

scSurv: a deep generative model for single-cell survival analysis

Chikara Mizukoshi and others

Reconstructing and comparing signal transduction networks from single-cell protein quantification data

Tim Stohn and others

Assessing differential cell composition in single-cell studies using voomCLR

Alemu Takele Assefa and others

Data and text mining

STAHD: a scalable and accurate method to detect spatial domains in high-resolution spatial transcriptomics data

Zhihua Du and others

Joint representation learning for oncology applications

Tanya Nandan and others

GOFlowLLM'curating miRNA literature with large language models and flowcharts

Andrew Green and others

Integrating curation into scientific publishing to train AI models

Jorge Abreu-Vicente and others

A hybrid unsupervised methodology on artificial intelligence filtering for automatically processing cellular DNA-encoded library (DEL) datasets

Yiran Huang and others

SurfFold: a unified model for protein inverse folding by integrating surface and structural information

Darong Li and others

RP3Net: a deep learning model for predicting recombinant protein production in Escherichia coli

Evgeny Tankhilevich and others

From articles to code: on-demand generation of core algorithms from scientific publications

Cameron S Movassaghi and others

Databases and ontologies

Causal knowledge graph analysis identifies adverse drug effects

Sumyyah Toonsi and others

dGAMLSS: an exact, distributed algorithm to fit Generalized Additive Models for Location, Scale, and Shape for privacy-preserving population reference charts

Fengling Hu and others

Bioimage informatics

Mutual learning for joint disease detection and severity prediction reveals multimodal pathogenesis for neurodegenerative disorders

Jin Zhang and others

Applications Notes

Genome analysis

CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation

Massimiliano S Tagliamonte and others

Genetics and population analysis

Pv3Rs: Plasmodium vivax relapse, recrudescence, and reinfection statistical genetic inference

Yong See Foo and others

Gene expression

OmicsQ: a user-friendly platform for interactive quantitative omics data analysis

Xuan-Tung Trinh and others

SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset

Ruqian Lyu and others

Capturing gene'cell duality in a cat's cradle

Anna Laddach and others

Sequence analysis

Alignoth: portable and interactive visualization of read alignments

Felix Wiegand and others

cuteSV-OL: a real-time structural variation detection framework for nanopore sequencing devices

Weimin Guo and others

MHASS: Microbiome HiFi Amplicon Sequencing Simulator

Rye Howard-Stone and Ion I MÄƒndoiu

BPSS: a Nextflow pipeline for Bacterial Peptide Sequence Selection to detect protein diversity

SylvÃ¨re Bastien and others

ViMOP: a user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing

Nils Peter Petersen and others

International Society for Computational Biology

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