Subject: New issue: Bioinformatics, Volume 42, Issue 3, March 2026

Bioinformatics

Bioinformatics

Volume 42, Issue 3, March 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.

SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements

Functional lipid analysis via index-based lipidomics profile: a new computational module in LipidOne

Husam B R Alabed and others

FFC: a scalable FASTA compressor

Original Paper

Gene expression

stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images

scMix: learning temporal dynamics of gene expression under irregular time intervals

SeOMLR: one-step multi-view latent representation with self-weighted ensemble learning for multi-omics cancer subtyping

scDBic: a novel deep learning-based biclustering algorithm for analyzing scRNA-seq data

A hybrid neighborhood enhanced contrastive learning and self-knowledge distillation method for scRNA-seq data clustering analysis

Sequence analysis

Mamba6mA: a Mamba-based DNA N6-methyladenine site prediction model

Prediction of bacterial protein'compound interactions with only positive samples

Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism

RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction

Finding low-complexity DNA sequences with longdust

CoMBCR: Co-Learning Multi-Modalities of BCRs and gene expressions

Identification of autosomal and sex chromosome aneuploidies using next generation sequencing

Uniform design-embedded predictions of (tetra-)peptide physicochemical properties

Zhihui Zhu and others

UPDhmm: detecting uniparental disomy from NGS trio data

Genome analysis

CEMUSA: a graph-based integrative metric for evaluating clusters in spatial transcriptomics

STABIX: summary-statistic-based GWAS indexing and compression

PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework

TerminatorNet: comprehensive identification of intrinsic transcription terminators in bacteria

Brian Tjaden

Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches

Competing subclones and fitness diversity shape tumor evolution across cancer types

Structural bioinformatics

pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources

Multi-scale structural similarity embedding search across entire proteomes

Yana Rose and others

A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins

IgPose: a generative data-augmented pipeline for robust immunoglobulin'antigen binding prediction

Systems biology

moiraine: an R package to construct reproducible pipelines for the application and comparison of multi-omics integration methods

Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal

Topological model selection: a case-study in tumour-induced angiogenesis

Heather A Harrington and others

BrainConnect: processing brain connectivity and spatial transcriptomics data for integrative analysis

Data and Text Mining

Using semantic search to find publicly available gene-expression datasets

A dual diffusion model-based representation learning framework for antimicrobial peptides classification

Weizhong Zhao

Knowledge-based citation reasoning for biomedical domain

Joint modeling of longitudinal biomarker and survival outcomes with the presence of competing risk in the nested case'control studies with application to the TEDDY microbiome dataset

One-hot news: drug synergy models shortcut molecular features

Emine Beyza Ã‡andÄ±r

Statistical methods to harmonize electronic health record data across healthcare systems: case study and lessons learned

Brian D Williamson and others

Databases and ontologies

SummArIzeR: simplifying cross-database enrichment result clustering and annotation via large language models

Bioimage informatics

Scalable analysis of whole slide spatial proteomics with Harpy

Applications Notes

Sequence analysis

PyEvoMotion: a Python tool for population-based time-course analysis of genome evolution

Accelerating minimap2 for whole-genome alignment

PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data

Managing workflow executions with WESkit

Gene expression

ORFannotate: reproducible coding sequence annotation of transcriptome assemblies

Dogme: a nextflow pipeline for reprocessing nanopore RNA and DNA modifications

GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis

CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data

InSituPy: a framework for histology-guided, multi-sample analysis of single-cell spatial omics data

umite: fast quantification of Smart-seq3 libraries with improved UMI retrieval

CERTOMICS: trusted single-cell multiomics pipeline for high-resolution profiling of adoptive cellular immunotherapies

Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets

Genome analysis

Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis

Genetics and population analysis

SAIGE-GPU: accelerating genome- and phenome-wide association studies using GPUs

From genes to trajectories: mapping genetic influences on Huntington's disease progression

ReverseGWAS identifies combined phenotypes associated with a genotype in GWA studies

Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f-statistics

Structural bioinformatics

HaDeX2: multi-dimensional analysis of hydrogen'deuterium exchange mass spectrometry data

Systems biology

scDock: streamlining drug discovery targeting cell'cell communication via scRNA-seq analysis and molecular docking

PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems

Data and text mining

Aggregation of gene regulatory information and knowledge on FAIR principles enables discovery of pathogenic gene regulatory variants

Aleksandar MihajloviÄ‡

CCC-GPU: a graphics processing unit (GPU)-accelerated nonlinear correlation coefficient for large-scale transcriptomic analyses

Bioimage informatics

AutoFlow: an interactive Shiny app for supervised and unsupervised flow cytometry analysis

FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues

Letter to the Editor

Sequence analysis

Response to: "best practices when benchmarking CATCH for the design of genome enrichment probes"

International Society for Computational Biology

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