Subject: New issue: Bioinformatics, Volume 41, Issue 11, November 2025

Bioinformatics

Bioinformatics

Volume 41, Issue 11, November 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.

Distinguishing specific from broad genetic associations between external correlates and common factors

Javier de la Fuente and others

Original Paper

Genome analysis

Genome size estimation from long read overlaps

Michael B Hall and others

ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing

Zhengfa Xue and others

OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis

Qingxiang Guo and others

Sequence analysis

TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction

Yu Xu and others

ZeroGEN: leveraging language models for zero-shot ligand design from protein sequences

Yangyang Chen and others

Detection of PCR chimeras in adaptive immune receptor repertoire sequences

Mark Chernyshev and others

De-Bruijn graph partitioning for scalable and accurate DNA storage processing

Florestan De Moor and others

DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing

Liyuan Shu and others

Structural bioinformatics

DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models

Minsoo Kim and others

Endowing protein language models with structural knowledge

Philip Hartout and others

RNAtive to recognize native-like structure in a set of RNA 3D models

Jan Pielesiak and others

MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs

Yanli Wang and others

TVAE-RNA: ensemble-based RNA secondary structure prediction via transformer variational autoencoders

Xiyuan Mei and others

Gene expression

Topological and functional characterization of human translation efficiency covariation network

Kangsheng Qi and Can Cenik

Self-supervised representation learning on gene expression data

Kevin Dradjat and others

A powerful framework for differential co-expression analysis of general risk factors

Andrew J Bass and others

Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data

Junhao Gu and others

Genetics and population analysis

Sparse polygenic risk score inference with the spike-and-slab LASSO

Junyi Song and others

DiffBreed: automatic differentiation enables efficient gradient-based optimization of breeding strategies

Kosuke Hamazaki and others

TCVS: tree-guided compositional variable selection analysis of microbiome data

Yicong Mao and others

Systems biology

Reconstructing gene network structure and dynamics from single cell data

Feng Chen and Chunhe Li

Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms

Melissa Van Norden and others

Data and text mining

DARKIN: a zero-shot benchmark for phosphosite'dark kinase association using protein language models

Emine AyÅŸe Sunar and others

ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation

Amir Hassan Shariatmadari and others

Databases and ontologies

Assembly and reasoning over semantic mappings at scale for biomedical data integration

Charles Tapley Hoyt and others

Bioimage informatics

IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment

Leo Hermet and others

Applications Note

Genome analysis

Benchmarking drug'drug interaction prediction methods: a perspective of distribution changes

Zhenqian Shen and others

PDP-Miner: an AI/ML tool to detect prophage tail proteins with depolymerase domains across thousands of bacterial genomes

Jeff Gauthier and others

insilicoSV: a flexible grammar-based framework for structural variant simulation and placement

Enzo Battistella and others

Tomtom-lite: accelerating Tomtom enables large-scale and real-time motif similarity scoring

Jacob Schreiber

SPARKI: a tool for the statistical analysis of pathogen identification results

Jacqueline M Boccacino and others

OpTiles: an R package for adaptive tiling and methylation variability profiling

Giorgia Migliaccio and others

Gene expression

PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime

Yuheng Lai and others

Systems biology

PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework

Yinan Zheng and others

BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells

Daniel R Bergman and others

GBA Solver: a user-friendly web server for growth balance analysis

Sajjad Ghaffarinasab and Hugo Dourado

Phylogenetics

aPhyloGeo: a Python application for correlating genetic and climatic conditions

Ana Laura Chenoweth Galaz and Nadia Tahiri

Structural bioinformatics

AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures

Stefaan Verwimp and others

Systems biology

NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline

Tiberiu Totu and others

Data and text mining

ShortCake: an integrated platform for efficient and reproducible single-cell analysis

Ryuichiro Nakato and Luis Augusto Eijy Nagai

Databases and Ontologies

HoloFoodR: a statistical programming framework for holo-omics data integration workflows

Tuomas Borman and others

Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs

Oscar Rojas Labra and others

Review

Systems biology

The cell as a token: high-dimensional geometry in language models and cell embeddings

William Gilpin

Decoding cell fate: integrated experimental and computational analysis at the single-cell level

Yutong Zhou and others

Correction

Correction to: Learning meaningful representation of single-neuron morphology via large-scale pre-training

International Society for Computational Biology

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