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Select item 120809591.

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

Ayan Chatterjee, Babak Ravandi, Parham Haddadi, Naomi H Philip, Mario Abdelmessih, William R Mowrey, Piero Ricchiuto, Yupu Liang, Wei Ding, Juan Carlos Mobarec, Tina Eliassi-Rad

Bioinformatics. 2025 May; 41(5): btaf148. Published online 2025 Apr 7. doi: 10.1093/bioinformatics/btaf148

PMCID:: PMC12080959

Article PDF–8.8M

Select item 120703902.

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

Misung Yi, Tingting Zhan, Hallgeir Rui, Inna Chervoneva

Bioinformatics. 2025 May; 41(5): btaf182. Published online 2025 Apr 21. doi: 10.1093/bioinformatics/btaf182

PMCID:: PMC12070390

Article PDF–3.6M

Select item 120703803.

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

Bioinformatics. 2025 May; 41(5): btaf281. Published online 2025 May 10. doi: 10.1093/bioinformatics/btaf281

Corrects:: Bioinformatics. 2025 Feb; 41(2): btaf034.

PMCID:: PMC12070380

Correction PDF–179K

Select item 120656274.

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

Lia Obinu, Timothy Booth, Heleen De Weerd, Urmi Trivedi, Andrea Porceddu

Bioinformatics. 2025 May; 41(5): btaf175. Published online 2025 Apr 16. doi: 10.1093/bioinformatics/btaf175

PMCID:: PMC12065627

Article PDF–4.7M

Select item 120654305.

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

Arash Khoeini, Funda Sar, Yen-Yi Lin, Colin Collins, Martin Ester

Bioinformatics. 2025 May; 41(5): btaf137. Published online 2025 Mar 27. doi: 10.1093/bioinformatics/btaf137

PMCID:: PMC12065430

Article PDF–2.8M

Select item 120578126.

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

Mayank Mahajan, Martin Hemberg

Bioinformatics. 2025 May; 41(5): btaf138. Published online 2025 May 2. doi: 10.1093/bioinformatics/btaf138

PMCID:: PMC12057812

Article PDF–4.1M

Select item 120578117.

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

Nils Lundqvist, Mateusz Garbulowski, Thomas Hillerton, Erik L L Sonnhammer

Bioinformatics. 2025 May; 41(5): btaf120. Published online 2025 Mar 24. doi: 10.1093/bioinformatics/btaf120

PMCID:: PMC12057811

Article PDF–3.3M

Select item 120578098.

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

Zhichao Xiao, Yan Li, Yijie Ding, Liang Yu

Bioinformatics. 2025 May; 41(5): btae716. Published online 2025 Mar 1. doi: 10.1093/bioinformatics/btae716

PMCID:: PMC12057809

Article PDF–5.2M

Select item 120549759.

RabbitSketch: a high-performance sketching library for genome analysis

Tong Zhang, Zekun Yin, Xiaoming Xu, Lifeng Yan, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu

Bioinformatics. 2025 May; 41(5): btaf249. Published online 2025 Apr 26. doi: 10.1093/bioinformatics/btaf249

PMCID:: PMC12054975

Article PDF–1019K

Select item 1204141710.

AlertGS: determining alerts for gene sets

Franziska Kappenberg, Jörg Rahnenführer

Bioinformatics. 2025 Apr; 41(4): btaf133. Published online 2025 Apr 3. doi: 10.1093/bioinformatics/btaf133

PMCID:: PMC12041417

Article PDF–3.7M

Select item 1204141311.

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

Keun Hong Son, Je-Yoel Cho

Bioinformatics. 2025 Apr; 41(4): btaf128. Published online 2025 Apr 25. doi: 10.1093/bioinformatics/btaf128

PMCID:: PMC12041413

Article PDF–2.1M

Select item 1203437812.

Gradient matching accelerates mixed-effects inference for biochemical networks

Yulan B van Oppen, Andreas Milias-Argeitis

Bioinformatics. 2025 Apr; 41(4): btaf154. Published online 2025 Apr 8. doi: 10.1093/bioinformatics/btaf154

PMCID:: PMC12034378

Article PDF–3.9M

Select item 1202179413.

Refining Boolean models with the partial most permissive scheme

Nadine Ben Boina, Brigitte Mossé, Anaïs Baudot, Elisabeth Remy

Bioinformatics. 2025 Apr; 41(4): btaf123. Published online 2025 Mar 22. doi: 10.1093/bioinformatics/btaf123

PMCID:: PMC12021794

Article PDF–3.9M

Select item 1201409814.

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

Sachin Mathur, Mathieu Beauvais, Arnau Giribet, Nicolas Aragon Barrero, Chaorui-Tom Zhang, Towsif Rahman, Seqian Wang, Jeremy Huang, Nima Nouri, Andre Kurlovs, Ziv Bar-Joseph, Peyman Passban

Bioinformatics. 2025 Apr; 41(4): btaf158. Published online 2025 Apr 10. doi: 10.1093/bioinformatics/btaf158