Volume 40(5); 2024 May

Applications Note

Data and Text Mining

NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph

Antonio Di Maria, Lorenzo Bellomo, Fabrizio Billeci, Alfio Cardillo, Salvatore Alaimo, Paolo Ferragina, Alfredo Ferro, Alfredo Pulvirenti

Bioinformatics. 2024 May; 40(5): btae194. Published online 2024 Apr 10. doi: 10.1093/bioinformatics/btae194

PMCID:: PMC11074003

Article PDF–1.8M

Genetics and Population Analysis

shinyseg: a web application for flexible cosegregation and sensitivity analysis

Christian Carrizosa, Dag E Undlien, Magnus D Vigeland

Bioinformatics. 2024 May; 40(5): btae201. Published online 2024 Apr 10. doi: 10.1093/bioinformatics/btae201

PMCID:: PMC11069105

Article PDF–749K

Phylogenetics

pipesnake: generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci

Ian G Brennan, Sonal Singhal, Ziad Al Bkhetan

Bioinformatics. 2024 May; 40(5): btae195. Published online 2024 Apr 10. doi: 10.1093/bioinformatics/btae195

PMCID:: PMC11082421

Article PDF–1011K

Sequence Analysis

SimReadUntil for benchmarking selective sequencing algorithms on ONT devices

Maximilian Mordig, Gunnar Rätsch, André Kahles

Bioinformatics. 2024 May; 40(5): btae199. Published online 2024 Apr 11. doi: 10.1093/bioinformatics/btae199

PMCID:: PMC11065473

Article PDF–627K

Structural Bioinformatics

CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences

Nikolaos Louros, Frederic Rousseau, Joost Schymkowitz

Bioinformatics. 2024 May; 40(5): btae279. Published online 2024 Apr 25. doi: 10.1093/bioinformatics/btae279

PMCID:: PMC11078773

Article PDF–4.2M

Original Papers

Data and Text Mining

TransGEM: a molecule generation model based on Transformer with gene expression data

Yanguang Liu, Hailong Yu, Xinya Duan, Xiaomin Zhang, Ting Cheng, Feng Jiang, Hao Tang, Yao Ruan, Miao Zhang, Hongyu Zhang, Qingye Zhang

Bioinformatics. 2024 May; 40(5): btae189. Published online 2024 Apr 17. doi: 10.1093/bioinformatics/btae189

PMCID:: PMC11078772

Article PDF–5.0M

Gene Expression

scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism

Qun Jiang, Shengquan Chen, Xiaoyang Chen, Rui Jiang

Bioinformatics. 2024 May; 40(5): btae265. Published online 2024 Apr 15. doi: 10.1093/bioinformatics/btae265

PMCID:: PMC11076148

Article PDF–5.4M

Peptide set test: a peptide-centric strategy to infer differentially expressed proteins

Junmin Wang, Steven Novick

Bioinformatics. 2024 May; 40(5): btae270. Published online 2024 Apr 17. doi: 10.1093/bioinformatics/btae270

PMCID:: PMC11074007

Article PDF–4.9M

Genome Analysis

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Hengchi Chen, Arthur Zwaenepoel, Yves Van de Peer

Bioinformatics. 2024 May; 40(5): btae272. Published online 2024 Apr 17. doi: 10.1093/bioinformatics/btae272

PMCID:: PMC11078771

Article PDF–6.5M

Sequence Analysis

Revisiting drug–protein interaction prediction: a novel global–local perspective

Zhecheng Zhou, Qingquan Liao, Jinhang Wei, Linlin Zhuo, Xiaonan Wu, Xiangzheng Fu, Quan Zou

Bioinformatics. 2024 May; 40(5): btae271. Published online 2024 Apr 22. doi: 10.1093/bioinformatics/btae271

PMCID:: PMC11087820

Article PDF–1.7M

CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics

Semih Kurt, Mandi Chen, Hosein Toosi, Xinsong Chen, Camilla Engblom, Jeff Mold, Johan Hartman, Jens Lagergren

Bioinformatics. 2024 May; 40(5): btae284. Published online 2024 Apr 27. doi: 10.1093/bioinformatics/btae284

PMCID:: PMC11087824

Article PDF–11M

LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model

Pawel Pratyush, Soufia Bahmani, Suresh Pokharel, Hamid D Ismail, Dukka B KC

Bioinformatics. 2024 May; 40(5): btae290. Published online 2024 Apr 25. doi: 10.1093/bioinformatics/btae290

PMCID:: PMC11088740

Article PDF–5.0M

Systems Biology

Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS

Remi Trimbour, Ina Maria Deutschmann, Laura Cantini

Bioinformatics. 2024 May; 40(5): btae143. Published online 2024 Mar 9. doi: 10.1093/bioinformatics/btae143

PMCID:: PMC11065476

Article PDF–6.2M

A supervised Bayesian factor model for the identification of multi-omics signatures

Jeremy P Gygi, Anna Konstorum, Shrikant Pawar, Edel Aron, Steven H Kleinstein, Leying Guan

Bioinformatics. 2024 May; 40(5): btae202. Published online 2024 Apr 11. doi: 10.1093/bioinformatics/btae202

PMCID:: PMC11078774

Article PDF–7.0M

NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population

Anja Mösch, Filippo Grazioli, Pierre Machart, Brandon Malone

Bioinformatics. 2024 May; 40(5): btae205. Published online 2024 Apr 13. doi: 10.1093/bioinformatics/btae205

PMCID:: PMC11076149

Article PDF–2.8M

BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities

Telmo Blasco, Francesco Balzerani, Luis V Valcárcel, Pedro Larrañaga, Concha Bielza, María Pilar Francino, José Ángel Rufián-Henares, Francisco J Planes, Sergio Pérez-Burillo

Bioinformatics. 2024 May; 40(5): btae266. Published online 2024 Apr 30. doi: 10.1093/bioinformatics/btae266

PMCID:: PMC11082422

Article PDF–3.7M

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