Subject: New issue: Bioinformatics, Volume 41, Issue 8, August 2025

Bioinformatics

Bioinformatics

Volume 41, Issue 8, August 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.

GS-DTI: a graph-structure-aware framework leveraging large language models for drug'target interaction prediction

Qinze Yu and others

HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures

Louis ParÃ© and others

Original Paper

Genome analysis

Spatial mutual nearest neighbors for spatial transcriptomics data

Haowen Zhou and others

Efficient gene set analysis for DNA methylation addressing probe dependency and bias

Zongli Xu and others

Pedigree Painter (pepa): a tool for the visualization of genetic inheritance in chromosomal context

Andrea Pozzi and Yann Ponty

Identifying DNA methylation types and methylated base positions from bacteria using nanopore sequencing with multi-scale neural network

Zheng Chen and others

Sequence analysis

Efficient seeding for error-prone sequences with SubseqHash2

Xiang Li and others

AdDeam: a fast and scalable tool for estimating and clustering reference-level damage profiles

Louis Kraft and others

2OMe-LM: predicting 2²-O-methylation sites in human RNA using a pre-trained RNA language model

Qianpei Liu and others

Deep generative model of RNAs based on variational autoencoder with context-free grammar

Goro Terai and others

ReAlign-P: a vertical iterative realignment method for protein multiple sequence alignment

Yixiao Zhai and others

Beyond the leaderboard: leveraging predictive modeling for protein'ligand insights and discovery

Dan Kalifa and others

Sequence-only prediction of binding affinity changes: a robust and interpretable model for antibody engineering

Chen Liu and others

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities

Kerim Heber and others

Structural bioinformatics

Prot2Chat: protein large language model with early fusion of text, sequence, and structure

Zhicong Wang and others

MO-GCAN: multi-omics integration based on graph convolutional and attention networks

Yifan Dou and others

SOLeNNoID: a deep learning pipeline for solenoid residue detection in protein structures

Georgi I Nikov and others

ActSeek: fast and accurate search algorithm of active sites in alphafold database

Sandra Castillo and others

ASCE-PPIS: a protein'protein interaction sites predictor based on equivariant graph neural network with fusion of structure-aware pooling and graph collapse

Guanghao Shen and others

Geometry-complete latent diffusion model for 3D molecule generation

Qunhao Zhang and others

AF3Complex yields improved structural predictions of protein complexes

Jonathan Feldman and others

Spatio-temporal learning from molecular dynamics simulations for protein'ligand binding affinity prediction

Pierre-Yves Libouban and others

Hybrid protein'ligand binding residue prediction with protein language models: does the structure matter?

Hamza Gamouh and others

Gene expression

Spatial mutual nearest neighbors for spatial transcriptomics data

Haowen Zhou and others

SCassist: an AI based workflow assistant for single-cell analysis

Vijayaraj Nagarajan and others

Double optimal transport for differential gene regulatory network inference with unpaired samples

Mengyu Li and others

IGCLAPS: an interpretable graph contrastive learning method with adaptive positive sampling for scRNA-seq data analysis

Weihua Zheng and others

Simulating paired and longitudinal single-cell RNA sequencing data with rescueSim

Elizabeth A Wynn and others

Multi-omics single-cell data alignment and integration with enhanced contrastive learning and differential attention mechanism

Tianjiao Zhang and others

IsoBayes: a Bayesian approach for single-isoform proteomics inference

Jordy Bollon and others

Systems biology

Dynamic gene regulatory network inference from single-cell data using optimal transport

FranÃ§ois Lamoline and others

Data and text mining

CoxKAN: Kolmogorov-Arnold networks for interpretable, high-performance survival analysis

William Knottenbelt and others

Enhancing and accelerating cell type deconvolution of large-scale spatial transcriptomics slices with dual network model

Yuhong Zha and others

Leveraging large language models for literature-driven prioritization of protein binding pockets

Roman Stratiichuk and others

Bioimage informatics

SpatioMark: quantifying the impact of spatial proximity on cell phenotype

Sourish S Iyengar and others

Applications Note

Genome analysis

nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets

Candace Guzman-Cole, Ph.D and others

Gene expression

PEELing: an integrated and user-centric platform for spatially resolved proteomics data analysis

Xi Peng and others

Genetics and population analysis

Tsbrowse: an interactive browser for ancestral recombination graphs

Savita Karthikeyan and others

Systems biology

Coordinated Meta-Storms enables comparison of million-level microbiomes

Minan Wang and others

Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package

Daniel J Mullen and others

Bioimage informatics

bia-binder: a web-native cloud compute service for the bioimage analysis community

Craig T Russell and others

Quantile index predictors using R package hyper.gam

Tingting Zhan and others

International Society for Computational Biology

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