Volume 41, Issue 4, April 2025

Review

Genetics and population analysis

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

Dennis J Hazelett

Bioinformatics, Volume 41, Issue 4, April 2025, btaf153, https://doi.org/10.1093/bioinformatics/btaf153

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Original Paper

Genome analysis

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

Brintha VP and Manikandan Narayanan

Bioinformatics, Volume 41, Issue 4, April 2025, btaf139, https://doi.org/10.1093/bioinformatics/btaf139

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Approximating edit distances between complex tandem repeats efficiently

Riki Kawahara and Shinichi Morishita

Bioinformatics, Volume 41, Issue 4, April 2025, btaf155, https://doi.org/10.1093/bioinformatics/btaf155

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Sequence analysis

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

Hiruna Samarakoon and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf111, https://doi.org/10.1093/bioinformatics/btaf111

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AVPpred-BWR: antiviral peptides prediction via biological words representation

Zhuoyu Wei and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf126, https://doi.org/10.1093/bioinformatics/btaf126

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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 and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf124, https://doi.org/10.1093/bioinformatics/btaf124

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

Min Zeng and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf127, https://doi.org/10.1093/bioinformatics/btaf127

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

Marcelo González and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf135, https://doi.org/10.1093/bioinformatics/btaf135

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OLTA: Optimizing bait seLection for TArgeted sequencing

Mete Orhun Minbay and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf146, https://doi.org/10.1093/bioinformatics/btaf146

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Phylogenetics

Marker selection strategies for circulating tumor DNA guided by phylogenetic inference

Xuecong Fu and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf145, https://doi.org/10.1093/bioinformatics/btaf145

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Structural bioinformatics

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

Francis Gaudreault and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf129, https://doi.org/10.1093/bioinformatics/btaf129

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

Brittany Lasher and David A Hendrix

Bioinformatics, Volume 41, Issue 4, April 2025, btaf108, https://doi.org/10.1093/bioinformatics/btaf108

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

Lucas Chivot and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf166, https://doi.org/10.1093/bioinformatics/btaf166

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Gene expression

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

Jessica Gliozzo and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf150, https://doi.org/10.1093/bioinformatics/btaf150

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

Ghislain Fievet and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf168, https://doi.org/10.1093/bioinformatics/btaf168

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Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics

Xuanwei Chen and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf131, https://doi.org/10.1093/bioinformatics/btaf131

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Systems biology

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

Steven Broll and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf099, https://doi.org/10.1093/bioinformatics/btaf099

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

Jyoti Jyoti and Marc-Thorsten Hütt

Bioinformatics, Volume 41, Issue 4, April 2025, btaf095, https://doi.org/10.1093/bioinformatics/btaf095

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

Yiyi Li and Mingzhou Song

Bioinformatics, Volume 41, Issue 4, April 2025, btaf121, https://doi.org/10.1093/bioinformatics/btaf121

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Seed2LP: seed inference in metabolic networks for reverse ecology applications

Chabname Ghassemi Nedjad and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf140, https://doi.org/10.1093/bioinformatics/btaf140

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Refining Boolean models with the partial most permissive scheme

Nadine Ben Boina and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf123, https://doi.org/10.1093/bioinformatics/btaf123

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

Zheng Deng and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf134, https://doi.org/10.1093/bioinformatics/btaf134

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Gradient matching accelerates mixed-effects inference for biochemical networks

Yulan B van Oppen and Andreas Milias-Argeitis

Bioinformatics, Volume 41, Issue 4, April 2025, btaf154, https://doi.org/10.1093/bioinformatics/btaf154

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Data and text mining

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

Yueying Jing and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf117, https://doi.org/10.1093/bioinformatics/btaf117

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LipidFun: a database of lipid functions

Wen-Jen Lin and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf110, https://doi.org/10.1093/bioinformatics/btaf110

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

Zuqi Li and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf122, https://doi.org/10.1093/bioinformatics/btaf122

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Predicting explainable dementia types with LLM-aided feature engineering

Aditya M Kashyap and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf156, https://doi.org/10.1093/bioinformatics/btaf156

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

Chang-Uk Jeong and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf160, https://doi.org/10.1093/bioinformatics/btaf160

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Databases and ontologies

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

Carlos Cruz-Castillo and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf070, https://doi.org/10.1093/bioinformatics/btaf070

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HISSTA: a human in situ single-cell transcriptome atlas

Jiwon Yu and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf142, https://doi.org/10.1093/bioinformatics/btaf142

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Bioimage informatics

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

Chensheng Zhang and others

Bioinformatics, Volume 41, Issue 4, April 2025, btae617, https://doi.org/10.1093/bioinformatics/btae617

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A framework for analyzing EEG data using high-dimensional tests

Qiuyan Zhang and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf109, https://doi.org/10.1093/bioinformatics/btaf109

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Applications Note

Genome analysis

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

Tanya Jain and Claire Clelland

Bioinformatics, Volume 41, Issue 4, April 2025, btaf116, https://doi.org/10.1093/bioinformatics/btaf116

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wgatools: an ultrafast toolkit for manipulating whole-genome alignments

Wenjie Wei and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf132, https://doi.org/10.1093/bioinformatics/btaf132

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MAFin: motif detection in multiple alignment files

Michail Patsakis and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf125, https://doi.org/10.1093/bioinformatics/btaf125

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Sequence analysis

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

Gabriele Leoni and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf102, https://doi.org/10.1093/bioinformatics/btaf102

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

Isin Altinkaya and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf098, https://doi.org/10.1093/bioinformatics/btaf098

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CoverM: read alignment statistics for metagenomics

Samuel T N Aroney and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf147, https://doi.org/10.1093/bioinformatics/btaf147

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

Christopher T Saunders and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf136, https://doi.org/10.1093/bioinformatics/btaf136

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Realfreq: real-time base modification analysis for nanopore sequencing

Suneth Samarasinghe and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf151, https://doi.org/10.1093/bioinformatics/btaf151

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Gene expression

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

Jialin Liu and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf119, https://doi.org/10.1093/bioinformatics/btaf119

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

Sachin Mathur and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf158, https://doi.org/10.1093/bioinformatics/btaf158

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Systems biology

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

Bitan Sarkar and Yang Ni

Bioinformatics, Volume 41, Issue 4, April 2025, btaf130, https://doi.org/10.1093/bioinformatics/btaf130

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Data and text mining

Lit-OTAR framework for extracting biological evidences from literature

Santosh Tirunagari and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf113, https://doi.org/10.1093/bioinformatics/btaf113

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

Padmapriya Swaminathan and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf144, https://doi.org/10.1093/bioinformatics/btaf144

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Databases and ontologies

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

Haiyang Bian and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf149, https://doi.org/10.1093/bioinformatics/btaf149

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Bioimage informatics

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

Alexander Vallmitjana and others

Bioinformatics, Volume 41, Issue 4, April 2025, btaf162, https://doi.org/10.1093/bioinformatics/btaf162

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