Subject: New issue: Bioinformatics, Volume 41, Issue 4, April 2025

Volume 41, Issue 4, April 2025

View issue


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.

Read more here

Review

Genetics and population analysis

Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms

Dennis J Hazelett,Jonathan Wren

Original Paper

Genome analysis

Demixer: a probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample

Brintha VP,Manikandan Narayanan and others

Approximating edit distances between complex tandem repeats efficiently

Riki Kawahara,Shinichi Morishita and others

Sequence analysis

Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis

Hiruna Samarakoon,Yuk Kei Wan and others

AVPpred-BWR: antiviral peptides prediction via biological words representation

Zhuoyu Wei,Yongqi Shen and others

CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov'Arnold network

Pawel Pratyush,Callen Carrier and others

RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language model

Min Zeng,Xinyu Zhang and others

Negative dataset selection impacts machine learning-based predictors for multiple bacterial species promoters

Marcelo GonzÃ¡lez,Roberto E DurÃ¡n and others

OLTA: Optimizing bait seLection for TArgeted sequencing

Mete Orhun Minbay,Richard Sun and others

Phylogenetics

Marker selection strategies for circulating tumor DNA guided by phylogenetic inference

Xuecong Fu,Zhicheng Luo and others

Structural bioinformatics

AI-augmented physics-based docking for antibody-antigen complex prediction

Francis Gaudreault,Traian Sulea and others

bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity

Brittany Lasher,David A Hendrix and others

CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure

Lucas Chivot,NoÃ© Mathieux and others

Gene expression

miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources

Jessica Gliozzo,Mauricio A Soto Gomez and others

adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks

Ghislain Fievet,Julien BrosÃ©us and others

Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics

Xuanwei Chen,Qinghua Ran and others

AlertGS: determining alerts for gene sets

Franziska Kappenberg,JÃ¶rg RahnenfÃ¼hrer and others

A multi-view graph convolutional network framework based on adaptive adjacency matrix and multi-strategy fusion mechanism for identifying spatial domains

Yuhan Fu,Mengdi Nan and others

Systems biology

PROLONG: penalized regression for outcome guided longitudinal omics analysis with network and group constraints

Steven Broll,Sumanta Basu and others

Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns

Jyoti Jyoti,Marc-Thorsten HÃ¼tt and others

Exact model-free function inference using uniform marginal counts for null population

Yiyi Li,Mingzhou Song and others

Seed2LP: seed inference in metabolic networks for reverse ecology applications

Chabname Ghassemi Nedjad,Mathieu Bolteau and others

Refining Boolean models with the partial most permissive scheme

Nadine Ben Boina,Brigitte MossÃ© and others

MNMO: discover driver genes from a multi-omics data based-multi-layer network

Zheng Deng,Jingli Wu and others

Gradient matching accelerates mixed-effects inference for biochemical networks

Yulan B van Oppen,Andreas Milias-Argeitis and others

Data and text mining

H²GnnDTI: hierarchical heterogeneous graph neural networks for drug'target interaction prediction

Yueying Jing,Dongxue Zhang and others

LipidFun: a database of lipid functions

Wen-Jen Lin,Chia-Hsin Liu and others

Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data

Zuqi Li,Sam F L Windels and others

Predicting explainable dementia types with LLM-aided feature engineering

Aditya M Kashyap,Delip Rao and others

GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes

Chang-Uk Jeong,Jaesik Kim and others

Databases and ontologies

Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence

Carlos Cruz-Castillo,Luca Fumis and others

HISSTA: a human in situ single-cell transcriptome atlas

Jiwon Yu,Jiwoo Moon and others

Bioimage informatics

Cleavage-stage embryo segmentation using SAM-based dual branch pipeline: development and evaluation with the CleavageEmbryo dataset

Chensheng Zhang,Xintong Shi and others

A framework for analyzing EEG data using high-dimensional tests

Qiuyan Zhang,Wenjing Xiang and others

Applications Note

Genome analysis

nf-core/pacvar: a pipeline for analyzing long-read PacBio whole genome and repeat expansion sequencing data

Tanya Jain,Claire Clelland and others

wgatools: an ultrafast toolkit for manipulating whole-genome alignments

Wenjie Wei,Songtao Gui and others

MAFin: motif detection in multiple alignment files

Michail Patsakis,Kimonas Provatas and others

Sequence analysis

PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance

Gabriele Leoni,Mauro Petrillo and others

vcfgl: a flexible genotype likelihood simulator for VCF/BCF files

Isin Altinkaya,Rasmus Nielsen and others

CoverM: read alignment statistics for metagenomics

Samuel T N Aroney,Rhys J P Newell and others

Sawfish: improving long-read structural variant discovery and genotyping with local haplotype modeling

Christopher T Saunders,James M Holt and others

Realfreq: real-time base modification analysis for nanopore sequencing

Suneth Samarasinghe,Ira Deveson and others

Gene expression

CytoSimplex: visualizing single-cell fates and transitions on a simplex

Jialin Liu,Yichen Wang and others

PyEvoCell: an LLM-augmented single-cell trajectory analysis dashboard

Sachin Mathur,Mathieu Beauvais and others

Genetics and population analysis

XPRS: a tool for interpretable and explainable polygenic risk score

Na Yeon Kim,Seunggeun Lee and others

Systems biology

MR.RGM: an R package for fitting Bayesian multivariate bidirectional Mendelian randomization networks

Bitan Sarkar,Yang Ni and others

Data and text mining

Lit-OTAR framework for extracting biological evidences from literature

Santosh Tirunagari,Shyamasree Saha and others

CancerTrialMatch: a computational resource for the management of biomarker-based clinical trials at a community cancer center

Padmapriya Swaminathan,Anu Amallraja and others

Databases and ontologies

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization

Haiyang Bian,Yinxin Chen and others

Gencube: centralized retrieval and integration of multi-omics resources from leading databases

Keun Hong Son,Je-Yoel Cho and others

Bioimage informatics

GSLab: open-source platform for advanced phasor analysis in fluorescence microscopy

International Society for Computational Biology

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