Subject: New issue: Bioinformatics, Volume 41, Issue 7, July 2025

Bioinformatics

Bioinformatics

Volume 41, Issue 7, July 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.

Review

Genome analysis

Whole-genome phenotype prediction with machine learning: open problems in bacterial genomics

Tamsin James and others

Original Paper

Genome analysis

Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture

Jamil Gafur and others

DGHNN: a deep graph and hypergraph neural network for pan-cancer related gene prediction

Bing Li and others

Benchmarking peak calling methods for CUT&RUN

Amin Nooranikhojasteh and others

Annotation matters: the effect of structural gene annotation on orthology inference

Silvia Prieto-BaÃ±os and others

Composition-on-composition regression analysis for multi-omics integration of metagenomic data

Nicholas Rios and others

Sequence analysis

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing

David W Ludwig, II and others

Leveraging protein language models for cross-variant CRISPR/Cas9 sgRNA activity prediction

Yalin Hou and others

AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees

Jiaqi Luo and others

Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction

Meiling Liu and others

Phylogenetics

New heuristics for phylogeny estimation under the balanced minimum evolution criterion

Daniele Catanzaro and others

PhyClone: accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing

Emilia Hurtado and others

Structural bioinformatics

FusionEncoder: identification of intrinsically disordered regions based on multi-feature fusion

Sicen Liu and others

Unsupervised learning reveals landscape of local structural motifs across protein classes

Alexander Derry and others

Enhancing privacy in biosecurity with watermarked protein design

Yanshuo Chen and others

Gene expression

scGT:integration algorithm for single-cell RNA-seq and ATAC-seq based on graph transformer

Yunjing Qi and others

cytoKernel: robust kernel embeddings for assessing differential expression of single-cell data

Tusharkanti Ghosh and others

Genetics and population analysis

AncestryGeni: a novel genetic ancestry classification pipeline for small and noisy sequence data

Eran Elhaik and others

Deconfounded and debiased estimation for high-dimensional linear regression under hidden confounding with application to omics data

Zhaoyang Li and others

Systems biology

JESTR: Joint Embedding Space Technique for Ranking candidate molecules for the annotation of untargeted metabolomics data

Apurva Kalia and others

Topolow: a mapping algorithm for antigenic cross-reactivity and binding affinity assays

Omid Arhami and others

Inference of differential kinase interaction networks with KINference

Nicolai MeyerhÃ¶fer and others

Gene behaviors-based network enrichment analysis and its application to reveal immune disease pathways enriched with COVID-19 severity-specific gene networks

Heewon Park and others

KGG: a fully automated workflow for creating disease-specific knowledge graphs

Reagon Karki and others

Integration of multi-source gene interaction networks and omics data with graph attention networks to identify novel disease genes

Kaiyuan Yang and others

Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach

Sepideh Mofidifar and others

DrugTar improves druggability prediction by integrating large language models and gene ontologies

Niloofar Borhani and others

Data and text mining

Differentiable graph clustering with structural grouping for single-cell RNA-seq data

Xiaoqiang Yan and others

CSGL: chemical synthesis graph learning for molecule representation

Anchen Li and others

SyRACT: zero-shot biomedical document-level relation extraction with synergistic RAG and CoT

Xin Dong and others

EM-PLA: environment-aware heterogeneous graph-based multimodal protein'ligand binding affinity prediction

Zhiqi Xie and others

AutoPM3: enhancing variant interpretation via LLM-driven PM3 evidence extraction from scientific literature

Shumin Li and others

ProtGO: universal protein function prediction utilizing multi-modal gene ontology knowledge

Boyan Wang and others

BioGraphFusion: graph knowledge embedding for biological completion and reasoning

Yitong Lin and others

Databases and ontologies

dbscATAC: a resource of single-cell super-enhancers/enhancers and gene markers derived from scATAC-seq data

Yingmei Li and others

Bioimage informatics

SpyDen: simplifying molecular and structural analysis across spines and dendrites

Maximilian F Eggl and others

HECLIP: histology-enhanced contrastive learning for imputation of transcriptomics profiles

Qing Wang and others

Applications Note

Genome analysis

AI-HOPE: an AI-driven conversational agent for enhanced clinical and genomic data integration in precision medicine research

Ei-Wen Yang and others

FuNTB: a functional network clustering tool for the analysis of genome-wide genetic variants in Mycobacterium tuberculosis

Axel A Ramos-GarcÃa and others

CCRR: a user-friendly platform for analyzing complex chromosomal rearrangements in tumors

Jinjiang Liu and others

CAGEcleaner: reducing genomic redundancy in gene cluster mining

Lucas De Vrieze and others

MiCoDe: a web tool for performing microbiome community detection using a Bayesian weighted stochastic block model

Kevin C Lutz and others

Agptools: a utility suite for editing genome assemblies

Edward S Ricemeyer and others

Sequence analysis

Fast and flexible minimizer digestion with digest

Alan Zheng and others

PepMapViz: a versatile toolkit for peptide mapping, visualization, and comparative exploration

Zhenru Zhou and others

LegionProfiler: a computational tool for the identification of virulence factors and classification of Legionella pneumophila serogroup 1 isolates

Oluwafemi A Sarumi and others

Phylogenetics

Prediction of local convergent shifts in evolutionary rates with phyloConverge

Elysia Saputra and others

Structural bioinformatics

Nearl: extracting dynamic features from molecular dynamics trajectories for machine learning tasks

Yang Zhang and others

GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins

Zarifa Osmanli and others

Gene expression

DOSE-L1000-Viz: an interactive Shiny application for dose'response transcriptomic analysis, target-centric exploration, and signature search

Junmin Wang and Anthony Mathelier

shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data

Seung J Kim and others

PEANUT: Pathway Enrichment Analysis through Network UTilization

Yair Pickholz Berliner and others

Systems biology

Pathway Volcano: an interactive tool for pathway guided visualization of differential expression data

Thomas M O'Connell and Jianlin Cheng

SPONGE: simple prior omics network GEnerator

Ladislav Hovan and others

Data and text mining

AOP-helpFinder 3.0: from text mining to network visualization of key event relationships, and knowledge integration from multiple sources

Thomas Jaylet and others

CSpace: a concept embedding space for biomedical applications

Danilo Tomasoni and others

scMGCL: accurate and efficient integration representation of single-cell multi-omics data

Zhenglong Cheng and others

Databases and ontologies

PloverDB: a high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs

Amy K Glen and others

Letter to the Editor

Structural bioinformatics

Rebuttal letter of the "comment on "contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction" by Sun and Gao"

Saisai Sun and Janet Kelso

Correction

Correction to: Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments

International Society for Computational Biology

This email is intended for bionet@evol.mcmaster.ca.