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OmnibusX: A unified platform for accessible multi-omics analysis.

• Authors : Truong, Linh¹ (AUTHOR); Truong, Thao¹ (AUTHOR); Nguyen, Huy¹ (AUTHOR)

• Source: PLoS Computational Biology. 9/8/2025, Vol. 21 Issue 9, p1-15. 15p.

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Neural network approaches, including use of topological data analysis, enhance classification of human induced pluripotent stem cell colonies by treatment condition.

• Authors : de Perez AR; Mathematics Department, Bailey College of Science and Mathematics, California Polytechnic State University - San Luis Obispo, San Luis Obispo, California, United States of America.; School of Mathematics, Georgia Institute of Technology, Atlanta, Georgia, United States of America.

Subjects: Neural Networks, Computer* ; Induced Pluripotent Stem Cells*/Induced Pluripotent Stem Cells*/Induced Pluripotent Stem Cells*/cytology ; Induced Pluripotent Stem Cells*/Induced Pluripotent Stem Cells*/Induced Pluripotent Stem Cells*/classification

• Source: PLoS computational biology [PLoS Comput Biol] 2025 Jul 11; Vol. 21 (7), pp. e1012801. Date of Electronic Publication: 2025 Jul 11 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines.

• Authors : Berke SR; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America.; Kanchan K

Subjects: Cloud Computing* ; Computational Biology*/Computational Biology*/Computational Biology*/methods ; Biomedical Research*/Biomedical Research*/Biomedical Research*/methods

• Source: PLoS computational biology [PLoS Comput Biol] 2025 Jul 02; Vol. 21 (7), pp. e1013215. Date of Electronic Publication: 2025 Jul 02 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology.

• Authors : Benkirane H; Université Paris-Saclay, CentraleSupélec, Laboratory of Mathematics and Computer Science (MICS), Gif-sur-Yvette, France.; IHU PRISM, National PRecISion Medicine Center in Oncology, Gustave Roussy, Villejuif, France.

Subjects: Deep Learning* ; Neoplasms*/Neoplasms*/Neoplasms*/genetics ; Neoplasms*/Neoplasms*/Neoplasms*/pathology

• Source: PLoS computational biology [PLoS Comput Biol] 2025 Jun 17; Vol. 21 (6), pp. e1013012. Date of Electronic Publication: 2025 Jun 17 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Learning and teaching biological data science in the Bioconductor community.

• Authors : Drnevich, Jenny¹ (AUTHOR); Tan, Frederick J.² (AUTHOR); Almeida-Silva, Fabricio^3,4 (AUTHOR)

• Source: PLoS Computational Biology. 4/22/2025, Vol. 21 Issue 4, p1-13. 13p.

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The specious art of single-cell genomics.

• Authors : Chari T; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America.; Pachter L

Subjects: Data Analysis* ; Genomics*; Humans

• Source: PLoS computational biology [PLoS Comput Biol] 2023 Aug 17; Vol. 19 (8), pp. e1011288. Date of Electronic Publication: 2023 Aug 17 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform.

• Authors : Escriba-Montagut X; Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.

Subjects: Software* ; Computational Biology*/Computational Biology*/Computational Biology*/methods; Humans

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Dec 09; Vol. 20 (12), pp. e1012626. Date of Electronic Publication: 2024 Dec 09 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR.

• Authors : Blimkie, Travis M.¹ (AUTHOR); An, Andy¹ (AUTHOR); Hancock, Robert E. W.¹ (AUTHOR)

• Source: PLoS Computational Biology. 9/16/2024, Vol. 20 Issue 9, p1-6. 6p.

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CHOIRBM: An R package for exploratory data analysis and interactive visualization of pain patient body map data.

• Authors : Cramer E; Division of Pain Medicine, Stanford University School of Medicine, Palo Alto, California, United States of America.; Ziadni M

Subjects: Data Analysis* ; Software*; Humans

• Source: PLoS computational biology [PLoS Comput Biol] 2022 Oct 27; Vol. 18 (10), pp. e1010496. Date of Electronic Publication: 2022 Oct 27 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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An optimal normalization method for high sparse compositional microbiome data.

• Authors : Sohn, Michael B.¹ (AUTHOR) ; Monaco, Cynthia^2,3 (AUTHOR); Gill, Steven R.³ (AUTHOR)

• Source: PLoS Computational Biology. 8/5/2024, Vol. 20 Issue 8, p1-19. 19p.

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