Journal Issue: Bioinformatics Volume 40(8);  2024 Aug

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Journal List

Volume 40(8);  2024 Aug

Applications Note

Genome Analysis

Genome-wide analysis and visualization of copy number with CNVpytor in igv.js
Arijit Panda, Milovan Suvakov, Helga Thorvaldsdottir, Jill P Mesirov, James T Robinson, Alexej Abyzov
Bioinformatics. 2024 Aug; 40(8): btae453. Published online 2024 Jul 17. doi: 10.1093/bioinformatics/btae453
PMCID:
PMC11303504
Abstract Article PDF–1.5M

Structural Bioinformatics

HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen–Deuterium Exchange Mass-Spectrometry datasets of different protein states
Maria K Janowska, Katherine Reiter, Pearl Magala, Miklos Guttman, Rachel E Klevit
Bioinformatics. 2024 Aug; 40(8): btae479. Published online 2024 Jul 30. doi: 10.1093/bioinformatics/btae479
PMCID:
PMC11310453
Abstract Article PDF–1.2M

Systems Biology

PhysioFit: a software to quantify cell growth parameters and extracellular fluxes
Loïc Le Grégam, Yann Guitton, Floriant Bellvert, Stéphanie Heux, Fabien Jourdan, Jean-Charles Portais, Pierre Millard
Bioinformatics. 2024 Aug; 40(8): btae488. Published online 2024 Jul 29. doi: 10.1093/bioinformatics/btae488
PMCID:
PMC11303505
Abstract Article PDF–1.2M

Original Papers

Data and Text Mining

Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks
Jiahao Gao, Mark Gerstein
Bioinformatics. 2024 Aug; 40(8): btae463. Published online 2024 Jul 25. doi: 10.1093/bioinformatics/btae463
PMCID:
PMC11316617
Abstract Article PDF–4.3M
Best practices to evaluate the impact of biomedical research software—metric collection beyond citations
Awan Afiaz, Andrey A Ivanov, John Chamberlin, David Hanauer, Candace L Savonen, Mary J Goldman, Martin Morgan, Michael Reich, Alexander Getka, Aaron Holmes, Sarthak Pati, Dan Knight, Paul C Boutros, Spyridon Bakas, J Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D Schloss, James A Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M Hoffman, Richard L Bradshaw, Jeffrey T Leek, Carrie Wright
Bioinformatics. 2024 Aug; 40(8): btae469. Published online 2024 Jul 27. doi: 10.1093/bioinformatics/btae469
PMCID:
PMC11297485
Abstract Article PDF–1.5M
BELHD: improving biomedical entity linking with homonym disambiguation
Samuele Garda, Ulf Leser
Bioinformatics. 2024 Aug; 40(8): btae474. Published online 2024 Jul 27. doi: 10.1093/bioinformatics/btae474
PMCID:
PMC11310454
Abstract Article PDF–1.9M

Gene Expression

Cellular proliferation biases clonal lineage tracing and trajectory inference
Becca Bonham-Carter, Geoffrey Schiebinger
Bioinformatics. 2024 Aug; 40(8): btae483. Published online 2024 Aug 5. doi: 10.1093/bioinformatics/btae483
PMCID:
PMC11316616
Abstract Article PDF–1.7M

Genome Analysis

BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model
Hanyu Luo, Li Tang, Min Zeng, Rui Yin, Pingjian Ding, Lingyun Luo, Min Li
Bioinformatics. 2024 Aug; 40(8): btae461. Published online 2024 Aug 6. doi: 10.1093/bioinformatics/btae461
PMCID:
PMC11310455
Abstract Article PDF–4.0M

Sequence Analysis

Fine-tuning protein embeddings for functional similarity evaluation
Andrew Dickson, Mohammad R K Mofrad
Bioinformatics. 2024 Aug; 40(8): btae445. Published online 2024 Jul 10. doi: 10.1093/bioinformatics/btae445
PMCID:
PMC11299545
Abstract Article PDF–3.7M
TSpred: a robust prediction framework for TCR–epitope interactions using paired chain TCR sequence data
Ha Young Kim, Sungsik Kim, Woong-Yang Park, Dongsup Kim
Bioinformatics. 2024 Aug; 40(8): btae472. Published online 2024 Jul 25. doi: 10.1093/bioinformatics/btae472
PMCID:
PMC11297499
Abstract Article PDF–4.0M

Structural Bioinformatics

MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability
Yunxiang Yu, Mengyun Gu, Hai Guo, Yabo Deng, Danna Chen, Jianwei Wang, Caixia Wang, Xia Liu, Wenjin Yan, Jinqi Huang
Bioinformatics. 2024 Aug; 40(8): btae473. Published online 2024 Jul 27. doi: 10.1093/bioinformatics/btae473
PMCID:
PMC11315609
Abstract Article PDF–3.5M

Systems Biology

Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems
Mauro Silberberg, Henning Hermjakob, Rahuman S Malik-Sheriff, Hernán E Grecco
Bioinformatics. 2024 Aug; 40(8): btae465. Published online 2024 Jul 30. doi: 10.1093/bioinformatics/btae465
PMCID:
PMC11303501
Abstract Article PDF–1.2M
New GO-based measures in multiple network alignment
Kimia Yazdani, Reza Mousapour, Wayne B Hayes
Bioinformatics. 2024 Aug; 40(8): btae476. Published online 2024 Jul 31. doi: 10.1093/bioinformatics/btae476
PMCID:
PMC11310457
Abstract Article PDF–1.4M
Articles from Bioinformatics are provided here courtesy of Oxford University Press