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Learning predictive signatures of HLA type from T-cell repertoires

María Ruiz Ortega, Mikhail V. Pogorelyy, Anastasia A. Minervina, Paul G. Thomas, Thierry Mora, Aleksandra M. Walczak

Research Article | published 06 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012724

Views: 366Citations: 0Saves: 0 • Shares: 0

Orchard: Building large cancer phylogenies using stochastic combinatorial search

Ethan Kulman, Rui Kuang, Quaid Morris

Methods | published 30 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012653

Views: 314Citations: 0Saves: 0 • Shares: 0

Multicellular model of neuroblastoma proposes unconventional therapy based on multiple roles of p53

Kenneth Y. Wertheim, Robert Chisholm, Paul Richmond, Dawn Walker

Research Article | published 23 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012648

Views: 491Citations: 0Saves: 1 • Shares: 1

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors

Henri Schmidt, Benjamin J. Raphael

Research Article | published 04 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012631

Views: 469Citations: 0Saves: 1 • Shares: 2

scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum

Yuqian Liu, Yan Chen, Huanwen Wu, Xuanping Zhang, Yuqi Wang, Xin Yi, Zhiyong Liang, Jiayin Wang

Research Article | published 02 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012608

Views: 408Citations: 0Saves: 0 • Shares: 0

Non-genetic differences underlie variability in proliferation among esophageal epithelial clones

Raúl A. Reyes Hueros, Rodrigo A. Gier, Sydney M. Shaffer

Research Article | published 28 Oct 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012360

Views: 449Citations: 1Saves: 0 • Shares: 0

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole G. Jensen, David Ladd, Mark Polster, Friederike Hanssen, Simon Heumos, nf-core community , Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein

Software | published 26 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012265

Views: 1651Citations: 3Saves: 19 • Shares: 2

Scuphr: A probabilistic framework for cell lineage tree reconstruction

Hazal Koptagel, Seong-Hwan Jun, Joanna Hård, Jens Lagergren

Research Article | published 09 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012094

Views: 730Citations: 1Saves: 0 • Shares: 0

Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory

Takahiro Kohsokabe, Shigeru Kuratanai, Kunihiko Kaneko

Research Article | published 29 Feb 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011867

Views: 1273Citations: 3Saves: 5 • Shares: 6

A zero-agnostic model for copy number evolution in cancer

Henri Schmidt, Palash Sashittal, Benjamin J. Raphael

Research Article | published 09 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011590

Views: 1274Citations: 4Saves: 7 • Shares: 4

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing

Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto D’Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna

Research Article | published 02 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011557

Views: 2677Citations: 2Saves: 7 • Shares: 34

Assessing the performance of methods for cell clustering from single-cell DNA sequencing data

Rituparna Khan, Xian Mallory

Research Article | published 12 Oct 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010480

Views: 1171Citations: 1Saves: 9 • Shares: 5

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors

Leah L. Weber, Chuanyi Zhang, Idoia Ochoa, Mohammed El-Kebir

Research Article | published 11 Oct 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011544

Views: 1249Citations: 8Saves: 9 • Shares: 3

LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity

Juan Xie, Hyeongseon Jeon, Gang Xin, Qin Ma, Dongjun Chung

Research Article | published 10 Jul 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011300

Views: 3102Citations: 5Saves: 8 • Shares: 9

Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression

Kexin Huang, Yun Zhang, Haoran Gong, Zhengzheng Qiao, Tiangang Wang, Weiling Zhao, Liyu Huang, Xiaobo Zhou

Research Article | published 25 May 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011122

Views: 1213Citations: 5Saves: 4 • Shares: 5

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