Subject: New issue: Bioinformatics, Volume 41, Issue 9, September 2025

Bioinformatics

Bioinformatics

Volume 41, Issue 9, September 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

CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning

Asato Yoshinaga and Osamu Maruyama

NanoFilter: enhancing phasing performance by utilizing highly consistent INDELs and SNVs in nanopore sequencing

Shanming Chen and others

DiCARN-DNase: enhancing cell-to-cell Hi-C resolution using dilated cascading ResNet with self-attention and DNase-seq chromatin accessibility data

Samuel Olowofila and Oluwatosin Oluwadare

The impact of tokenizer selection in genomic language models

LeAnn M Lindsey and others

AQuA Tools: clear and reliable BEDPE operations for 3D genomics

Maharshi Chakraborty and others

Flashzoi: an enhanced Borzoi for accelerated genomic analysis

Johannes C Hingerl and others

Autocycler: long-read consensus assembly for bacterial genomes

Ryan R Wick and others

MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples

Tianci Wang and others

Sequence analysis

Evaluation of sequencing reads at scale using rdeval

Giulio Formenti and others

deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning

Homa MohammadiPeyhani and others

PF-AGCN: an adaptive graph convolutional network for protein'protein interaction-based function prediction

Shumin Yang and others

Panaln: indexing pangenome for read alignment

Lilu Guo and others

TransFactor'prediction of pro-viral SARS-CoV-2 host factors using a protein language model

Yang An and others

Accurate prediction of toxicity peptide and its function using multi-view tensor learning and latent semantic learning framework

Ke Yan and others

MVSO-PPIS: a structured objective learning model for protein'protein interaction sites prediction via multi-view graph information integration

Shuang Wang and others

Structural bioinformatics

RNA language model and graph attention network for RNA and small molecule binding sites prediction

Saisai Sun and others

MolPrompt: improving multi-modal molecular pre-training with knowledge prompts

Yang Li and others

MDGraphEmb: a toolkit for graph embedding and classification of protein conformational ensembles

Ferdoos Hossein Nezhad and others

ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins

Helena GarcÃa-Cebollada and others

Graph neural network and diffusion model for modeling RNA interatomic interactions

Marek Justyna and others

Structure-guided sequence representation learning for generalizable protein function prediction

SeokJun On and others

gapTrick'structural characterization of protein'protein interactions using AlphaFold

Grzegorz Chojnowski

Gene expression

HallmarkGraph: a cancer hallmark informed graph neural network for classifying hierarchical tumor subtypes

Qingsong Zhang and others

A semi-supervised Bayesian approach for marker gene trajectory inference from single-cell RNA-seq data

Junchao Wang and others

Mitigation of multi-scale biases in cell-type deconvolution for spatially resolved transcriptomics using HarmoDecon

Zirui Wang and others

Less is more: improving cell-type identification with augmentation-free single-cell RNA-Seq contrastive learning

Ibrahim Alsaggaf and others

Harp: data harmonization for computational tissue deconvolution across diverse transcriptomics platforms

Zahra Nozari and others

scPOEM: robust co-embedding of peaks and genes revealing peak'gene regulation

Yan Zhong and others

GE-IA-NAM: gene'environment interaction analysis via imaging-assisted neural additive model

Jingmao Li and others

getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection

Tong Wang and Zhi-Ping Liu

BISON: bi-clustering of spatial omics data with feature selection

Bencong Zhu and others

Robust multivariate regression controlling false discoveries for microbiome data

Gianna Serafina Monti and others

Systems biology

KGCLMDA: a computational model for predicting latent associations of microbial drugs using knowledge graphs and contrastive learning

Meiling Liu and others

GNNenrich: a novel method for pathway enrichment analysis based on graph neural network

Mallek Mziou-Sallami and others

PLSKO: a robust knockoff generator to control false discovery rate in omics variable selection

Guannan Yang and others

SPACE: STRING proteins as complementary embeddings

Dewei Hu and others

Discovering subnetworks in SBML models

Joseph L Hellerstein, PhD and others

Applications Note

Genome analysis

PyVADesign: a python-based cloning tool for one-step generation of large mutant libraries

R C M Kuin and others

scnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing

Austyn Trull and others

qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics

Xiang Liu and others

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

Carl M Kobel and others

Decipher RNA isoform combinations from minigene splicing assays and massive parallel sequencing with MAGIC

Camille Aucouturier and others

Sequence analysis

scafari: exploring scDNA-seq data

Sophie-Marie Wind and others

UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification

Jixin Deng and others

Structural bioinformatics

MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update)

TomÃ¡Å¡ RaÄek and others

FIBOS: R and python packages for analyzing protein packing and structure

Herson H M Soares and others

ChemBounce: a computational framework for scaffold hopping in drug discovery

Woo Dae Jang and others

Systems biology

NetMedPy: a Python package for large-scale network medicine screening

Andres Aldana and others

MultiNMRFit: a software to fit 1D and pseudo-2D NMR spectra

Pierre Millard and others

FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets

Jeffrey J Czajka and others

PEtab.jl: advancing the efficiency and utility of dynamic modelling

Sebastian Persson and others

SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences

Leonie J Lorenz and others

Correction

Correction to: OLTA: Optimizing bait seLection for TArgeted sequencing

International Society for Computational Biology

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