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Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning

Mohammad Neamul Kabir, Li Rong Wang, Wilson Wen Bin Goh

Education | published 24 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012716

Views: 109Citations: 0Saves: 0 • Shares: 0

BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk

Natalie R. Davidson, Fan Zhang, Casey S. Greene

Methods | published 17 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012742

Views: 204Citations: 0Saves: 0 • Shares: 0

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data

Evan Gorstein, Rosa Aghdam, Claudia Solís-Lemus

Research Article | published 13 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012143

Views: 289Citations: 0Saves: 0 • Shares: 0

The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models

Ahmed Daoud, Asa Ben-Hur

Research Article | published 10 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012755

Views: 330Citations: 0Saves: 0 • Shares: 0

A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data

Lulu Pan, Qian Gao, Kecheng Wei, Yongfu Yu, Guoyou Qin, Tong Wang

Research Article | published 10 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012739

Views: 288Citations: 0Saves: 0 • Shares: 1

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci

Zeinab Mousavi, Marios Arvanitis, ThuyVy Duong, Jennifer A. Brody, Alexis Battle, Nona Sotoodehnia, Ali Shojaie, Dan E. Arking, Joel S. Bader

Research Article | published 07 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012725

Views: 257Citations: 0Saves: 0 • Shares: 0

Ensemble learning-based predictor for driver synonymous mutation with sequence representation

Chuanmei Bi, Yong Shi, Junfeng Xia, Zhen Liang, Zhiqiang Wu, Kai Xu, Na Cheng

Research Article | published 06 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012744

Views: 929Citations: 0Saves: 0 • Shares: 0

Integrative analysis of ATAC-seq and RNA-seq for cells infected by human T-cell leukemia virus type 1

Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Norihiro Takenouchi, Masanori Nakagawa, Ki-Ryang Koh, Chiho Onishi, Hiromitsu Tanaka, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka

Research Article | published 02 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012690

Views: 489Citations: 0Saves: 9 • Shares: 3

Predicting lung aging using scRNA-Seq data

Qi Song, Alex Singh, John E. McDonough, Taylor S. Adams, Robin Vos, Ruben De Man, Greg Myers, Laurens J. Ceulemans, Bart M. Vanaudenaerde, Wim A. Wuyts, Xiting Yan, Jonas Schupp, James S. Hagood, Naftali Kaminski, Ziv Bar-Joseph

Research Article | published 19 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012632

Views: 1032Citations: 0Saves: 1 • Shares: 19

Hierarchical marker genes selection in scRNA-seq analysis

Yutong Sun, Peng Qiu

Research Article | published 12 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012643

Views: 453Citations: 0Saves: 3 • Shares: 0

Differential quantification of alternative splicing events on spliced pangenome graphs

Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Stephen Njuguna Kuria, Paola Bonizzoni, Luca Denti

Methods | published 09 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012665

Views: 533Citations: 0Saves: 0 • Shares: 5

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

Xavier Escriba-Montagut, Yannick Marcon, Augusto Anguita-Ruiz, Demetris Avraam, Jose Urquiza, Andrei S. Morgan, Rebecca C. Wilson, Paul Burton, Juan R. Gonzalez

Research Article | published 09 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012626

Views: 478Citations: 0Saves: 0 • Shares: 0

Large scale paired antibody language models

Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane

Research Article | published 06 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012646

Views: 1370Citations: 3Saves: 0 • Shares: 0

OneNet—One network to rule them all: Consensus network inference from microbiome data

Camille Champion, Raphaëlle Momal, Emmanuelle Le Chatelier, Mathilde Sola, Mahendra Mariadassou, Magali Berland

Research Article | published 06 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012627

Views: 487Citations: 0Saves: 0 • Shares: 2

Mapping genes for human face shape: Exploration of univariate phenotyping strategies

Meng Yuan, Seppe Goovaerts, Michiel Vanneste, Harold Matthews, Hanne Hoskens, Stephen Richmond, Ophir D. Klein, Richard A. Spritz, Benedikt Hallgrimsson, Susan Walsh, Mark D. Shriver, John R. Shaffer, Seth M. Weinberg, Hilde Peeters, Peter Claes

Research Article | published 02 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012617

Views: 589Citations: 0Saves: 0 • Shares: 0

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