Subject: New issue: Bioinformatics, Volume 41, Issue 5, May 2025

Bioinformatics

Bioinformatics

Volume 41, Issue 5, May 2025

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Thank you, Alfonso: An Impactful Bioinformatics Collection

Last year marked 20 years of Alfonso leading Bioinformatics. We are expressing our gratitude and celebrating his remarkable contributions by highlighting some of the 62,000 papers he handled.

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Original Paper

Genome analysis

Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly

Lia Obinu and others

High-dimensional biomarker identification for interpretable disease prediction via machine learning models

Yifan Dai and others

ROICellTrack: a deep learning framework for integrating cellular imaging modalities in subcellular spatial transcriptomic profiling of tumor tissues

Xiaofei Song and others

Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species

Maximillian G Marin and others

Sequence analysis

ProtNote: a multimodal method for protein'function annotation

Samir Char and others

De novo clustering of large long-read transcriptome datasets with isONclust3

Alexander J Petri and others

EPIPDLF: a pretrained deep learning framework for predicting enhancer'promoter interactions

Zhichao Xiao and others

scMUSCL: multi-source transfer learning for clustering scRNA-seq data

Arash Khoeini and others

MVSF-AB: accurate antibody'antigen binding affinity prediction via multi-view sequence feature learning

Minghui Li and others

Missense variants pathogenicity annotation from homologous proteins

Gabriel Ruiz-AlÃas and others

Structural bioinformatics

Finding antibodies in cryo-EM maps with CrAI

Vincent Mallet and others

In silico identification of archaeal DNA-binding proteins

Linus Donvil and others

Topology-driven negative sampling enhances generalizability in protein'protein interaction prediction

Ayan Chatterjee and others

ProBASS'a language model with sequence and structural features for predicting the effect of mutations on binding affinity

Sagara N S Gurusinghe and others

Charting the structure-sequence landscape of light chain amyloids

Gabriele Orlando and others

Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning

Shaun M Kandathil and others

SimSon: simple contrastive learning of SMILES for molecular property prediction

Chae Eun Lee and others

Gene expression

Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA

Mayank Mahajan and others

m2ST: dual multi-scale graph clustering for spatially resolved transcriptomics

Wei Zhang and others

Nonparametric IPSS: fast, flexible feature selection with false discovery control

Omar Melikechi and others

scACCorDiON: a clustering approach for explainable patient level cell'cell communication graph analysis

James S Nagai and others

Systems biology

Topology-based metrics for finding the optimal sparsity in gene regulatory network inference

Nils Lundqvist and others

Mapping the attractor landscape of Boolean networks with biobalm

Van-Giang Trinh and others

Data and text mining

Co-design protein sequence and structure in discrete space via generative flow

Sen Yang and others

MSNGO: multi-species protein function annotation based on 3D protein structure and network propagation

Beibei Wang and others

Bioimage informatics

Functional protein biomarkers based on distributions of expression levels in single-cell imaging data

Misung Yi and others

VSOT: volume-surface optimization for accurate ultrastructure analysis of dendritic spines

Boyu Lyu and others

A noise-robust classification method for cryo-ET subtomograms with out-of-distribution detection

Wenjia Meng and others

Applications Note

Genome analysis

Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors

Naama Wagner and others

Sequence analysis

RabbitSketch: a high-performance sketching library for genome analysis

Tong Zhang and others

Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes

Alison Kyrouz and others

Structural bioinformatics

CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features

Zhe Liu and others

Systems biology

JAX-RNAfold: scalable differentiable folding

Ryan K Krueger and others

MS1FA: Shiny app for the annotation of redundant features in untargeted metabolomics datasets

Ruibing Shi and others

MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics

Pedro Fontanarrosa and others

KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics

Javed M Aman and others

Data and text mining

Automatic biomarker discovery and enrichment with BRAD

Joshua Pickard and others

Databases and ontologies

argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)

Svetlana Ugarcina Perovic and others

PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2

Robyn J Wright and others

OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem

James McLaughlin and others

Bioimage informatics

Preserving full spectrum information in imaging mass spectrometry data reduction

Roger A R Moens and others

TissueViewer: a web-based multiplexed image viewer

David Gerardus Pieter van IJzendoorn and others

MobiDB-lite 4.0: faster prediction of intrinsic protein disorder and structural compactness

Mahta Mehdiabadi and others

Correction

Correction to: Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment

International Society for Computational Biology

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