Subject: New issue: Bioinformatics, Volume 41, Issue 6, June 2025

Bioinformatics

Bioinformatics

Volume 41, Issue 6, June 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.

Original Paper

Genome analysis

GCfix: a fast and accurate fragment length-specific method for correcting GC bias in cell-free DNA

Chowdhury Rafeed Rahman and others

Beacon Reconstruction Attack: Reconstruction of genomes in genomic data-sharing beacons using summary statistics

Kousar Saleem and others

scNucMap: mapping the nucleosome landscapes at single-cell resolution

Qianming Xiang and others

Securing diagonal integration of multimodal single-cell data against ambiguous mapping

Han Zhou and others

StripePy: fast and robust characterization of architectural stripes

Andrea Raffo and others

SNACS: a tool for demultiplexing single-cell DNA sequencing data

Vanessa E Kennedy and others

Sequence analysis

Pool PaRTI: a PageRank-based pooling method for identifying critical residues and enhancing protein sequence representations

Alp Tartici and others

Sequence analysis and decoding with extra low-quality reads for DNA data storage

Jiyeon Park and others

Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs

Siegfried Dubois and others

ProtMamba: a homology-aware but alignment-free protein state space model

Damiano Sgarbossa and others

Structural bioinformatics

epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum assignment problem formulation

Xuechen Zhang and others

Benchmarking the methods for predicting base pairs in RNA'RNA interactions

Mei Lang and others

DeepAllo: allosteric site prediction using protein language model (pLM) with multitask learning

Moaaz Khokhar and others

ColBuilder: flexible structure generation of crosslinked collagen fibrils

Debora Monego and others

Mapping the space of protein binding sites with sequence-based protein language models

TuÄŸÃ§e OruÃ§ and others

GOBoost: leveraging long-tail gene ontology terms for accurate protein function prediction

Lei Zhang and others

Gene expression

TRENDY: gene regulatory network inference enhanced by transformer

Xueying Tian and others

CrossAttOmics: multiomics data integration with cross-attention

AurÃ©lien Beaude and others

Relation equivariant graph neural networks to explore the mosaic-like tissue architecture of kidney diseases on spatially resolved transcriptomics

Mauminah Raina and others

Simple controls exceed best deep learning algorithms and reveal foundation model effectiveness for predicting genetic perturbations

Daniel R Wong and others

DiSC: a statistical tool for fast differential expression analysis of individual-level single-cell RNA-seq data

Lujun Zhang and others

diffGEK: differential gene expression kinetics

Melania Barile and others

HABiC: an algorithm based on the exact computation of the Kantorovich-Rubinstein optimizer for binary classification in transcriptomics

Chiara Cordier and others

Gene spatial integration: enhancing spatial transcriptomics analysis via deep learning and batch effect mitigation

Rian Pratama and others

Genetics and population analysis

Debiased machine learning for ultra-high dimensional mediation analysis

Kecheng Wei and others

The sequence kernel association test for the proportional odds model

Jingxin Yan and others

Systems biology

Algebraic differentiation for fast sensitivity analysis of optimal flux modes in metabolic models

Hester Chapman and others

CAFE: an integrated web app for high-dimensional analysis and visualization in spectral flow cytometry

Md Hasanul Banna Siam and others

BiGSM: Bayesian inference of gene regulatory network via sparse modelling

Hang Qin and others

MADSP: predicting anti-cancer drug synergy through multi-source integration and attention-based representation learning

Yuqi Hong and others

IGCN: integrative graph convolution networks for patient level insights and biomarker discovery in multi-omics integration

Cagri Ozdemir and others

Data and Text Mining

The signed two-space proximity model for learning representations in protein'protein interaction networks

Nikolaos Nakis and others

A deep learning-based method for predicting the frequency classes of drug side effects based on multi-source similarity fusion

Haochen Zhao and others

Brownian motion data augmentation: a method to push neural network performance on nanopore sensors

Javier Kipen and others

Databases and ontologies

dsOMOP: bridging OMOP CDM and DataSHIELD for secure federated analysis of standardized clinical data

David Sarrat-GonzÃ¡lez and others

Bioimage informatics

Predicting ustekinumab treatment response in Crohn's disease using pre-treatment biopsy images

Chengfei Cai and others

Synergizing multimodal data and fingerprint space exploration for mechanism of action prediction

Kaimiao Hu and others

Knowledge-enhanced protein subcellular localization prediction from 3D fluorescence microscope images

Guo-Hua Zeng and others

Measurement and classification of bold'shy behaviours in medaka fish

Saul Pierotti and others

Applications Note

Genome analysis

SVbyEye: a visual tool to characterize structural variation among whole-genome assemblies

David Porubsky and others

HSDSnake: a user-friendly SnakeMake pipeline for analysis of duplicate genes in eukaryotic genomes

Xi Zhang and others

Sequence analysis

Mapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads

Nicolas Maurice and others

Structural bioinformatics

ASMC: investigating the amino acid diversity of enzyme active sites

Thomas Bailly and others

Residue conservation and solvent accessibility are (almost) all you need for predicting mutational effects in proteins

Matsvei Tsishyn and others

VTX: real-time high-performance molecular structure and dynamics visualization software

Maxime Maria and others

SOMMD: an R package for the analysis of molecular dynamics simulations using self-organizing map

Stefano Motta and others

Gene expression

OrthologAL: a Shiny application for quality-aware humanization of non-human pre-clinical high-dimensional gene expression data

Rishika Chowdary and others

SeuratIntegrate: an R package to facilitate the use of integration methods with Seurat

Florian Specque and others

Genetics and population analysis

Bayesian estimation of allele-specific expression in the presence of phasing uncertainty

Xue Zou and others

Pedixplorer: a Bioconductor package to streamline pedigree design and visualization

Louis Le NÃ©zet and others

Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations

Alessandro Lisi and others

HAP-SAMPLE2: data-based resampling for association studies with admixture

George Sun and others

Systems biology

esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis

Jiaqi Li and others

Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization

Joanna Lenkiewicz and others

Eclipse: a Python package for alignment of two or more nontargeted LC-MS metabolomics datasets

Daniel S Hitchcock and others

NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein'protein interactions

Schuyler D Smith and others

Data and text mining

BAYAS: simplifying access to Bayesian analysis for biologists

Christoph Waterkamp and others

EDAmame: interactive exploratory data analyses with explainable models

Aaron Chuah and others

Letter to the Editor

Structural bioinformatics

Comment on "Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction" by Sun and Gao

Sowmya Ramaswamy Krishnan and others

Correction

Correction to: Coding genomes with gapped pattern graph convolutional network

Correction to: Finding antibodies in cryo-EM maps with CrAI

International Society for Computational Biology

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