Bioinformatics

Bioinformatics

Volume 42, Issue 2, February 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.

Original Paper

Gene expression

ASTRO: Automated Spatial-Transcriptome whole RNA Output

CeLLTra: aligning cell names with gene expression via a pathway-informed transformer

Inference of marker genes of subtle cell state changes via iLR: iterative logistic regression

A spectral dimension reduction technique that improves pattern detection in multivariate spatial data

Sequence analysis

GAMMA: gap-aware motif mining under incomplete labeling with applications to MHC motifs

STransfer: a transfer learning-enhanced graph convolutional network for clustering spatial transcriptomics data

Chaojie Wang and Xin Yu

How negative sampling shapes the performance of transcription factor binding site prediction models

LtransHeteroGGM: local transfer learning for Gaussian graphical model-based heterogeneity analysis

Phylogenetics

Bit-reproducible parallel phylogenetic tree inference

Genome analysis

MetaFX: feature extraction from whole-genome metagenomic sequencing data

Learning a pairwise epigenomic and transcription factor binding association score across the human genome

Comprehensive evaluation of ACMG/AMP-based variant classification tools

PETScan: score-based genome-wide association analysis of RNA-Seq and ATAC-Seq data

Genome- and peak-informed two-stage framework for scATAC-seq cell type identification

Structural bioinformatics

Unsupervised synchronization of molecular dynamics trajectories via graph embedding and time warping

MMPCS: multi-view molecular pretraining based on consistency information and specific information

GeoGAD: geometry-aware antibody design framework for complementarity-determining region precision engineering

De novo protein'ligand design including protein flexibility and conformational adaptation

Systems biology

Semantic-enhanced heterogeneous graph learning for identifying ncRNAs associated with drug resistance

ChemGenXplore: an interactive tool for exploring and analysing chemical genomic data

MCOAN: multimodal contrastive representation learning for cross-omics adaptive disease regulatory network prediction

VUScope: a mathematical model for evaluating image-based drug response measurements and predicting long-term incubation outcomes

transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics

Databases and ontologies

CMAtlas: a comprehensive DNA methylation atlas for exploring epigenetic alterations in 34 human cancer types

A case-based explainable graph neural network framework for mechanistic drug repositioning

Bioimage Informatics

3D dendritic spines shape descriptors for efficient classification and morphology analysis in control and Alzheimer's disease modeling neurons

Data and Text Mining

Characterizing clinical toxicity in cancer combination therapies

Improving biomedical entity linking with generative relevance feedback

BioTriplex: a full-text annotated corpus for fine-tuning language models in gene-disease relation extraction tasks

Applications Notes

Genome analysis

Malaria-GENOMAP: a web-based tool for exploring genomic variation of malaria parasites

diffMONT: predicting methylation-specific PCR biomarkers based on nanopore sequencing data for clinical application

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

MethylModes: computationally efficient detection of multimodal distributions in DNA methylation data

Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks

Sequence analysis

sedimix: a workflow for the analysis of hominin nuclear DNA sequences from sediments

esloco: simulation-based estimation of local coverage in long-read DNA sequencing

scSNViz: visualization and analysis of cell-specific expressed SNVs

mimicDetector: a pipeline for protein motif mimicry detection in host-pathogen interactions

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences

PyTEA-O: a Python implementation of Two-Entropies Analysis for protein sequence variation analysis

Application of qualifying variants for genomic analysis

Sabine Ã sterle

Gene expression

FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data

UCell and pyUCell: single-cell gene signature scoring for R and Python

Systems biology

DicePlot: a package for high-dimensional categorical data visualization

sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit perturbation

ProteoGyver: a fast, user-friendly tool for routine QC and analysis of MS-based proteomics data

X-intNMF: a cross- and intra-omics regularized NMF framework for multi-omics integration

iModMix: integrative module analysis for multi-omics data

Isis NarvÃ¡ez-Bandera

COBRAxy: constraint-based metabolic modeling in Galaxy

Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell'cell communication

Data and text mining

DNAvi: integration, statistics, and visualization of cell-free DNA fragment traces

textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in Cytoscape

Databases and ontologies

The Lipid Interactome: an interactive and open access platform for exploring cellular lipid'protein interactions

Genetics and population analysis

Othram maps: a graph-powered platform for pedigree visualization and forensic intelligence

PYRAMA: an open-source tool for advanced meta-analysis of genome wide association studies

Structural bioinformatics

TrIPP: a trajectory iterative pK_a predictor

Review

Structural bioinformatics

Unavailability of experimental 3D structural data on protein folding dynamics and necessity for a new generation of structure prediction methods in this context

International Society for Computational Biology

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