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Mathematical basis and toolchain for hierarchical optimization of biochemical networks

Nisha Ann Viswan, Alexandre Tribut, Manvel Gasparyan, Ovidiu Radulescu, Upinder S. Bhalla

Methods | published 02 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012624

Views: 675Citations: 0Saves: 1 • Shares: 1

Fixation times on directed graphs

David A. Brewster, Martin A. Nowak, Josef Tkadlec

Research Article | published 18 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012299

Views: 1018Citations: 2Saves: 2 • Shares: 11

Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces

Enrique R. Sebastian, Julio Esparza, Liset M. de la Prida

Research Article | published 04 Jan 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011768

Views: 2977Citations: 4Saves: 24 • Shares: 53

Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay

Christopher R. Keefe, Matthew R. Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V. Wood, Evan Bolyen, J. Gregory Caporaso

Software | published 27 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011676

Views: 2345Citations: 4Saves: 14 • Shares: 25

Functional and spatial rewiring principles jointly regulate context-sensitive computation

Jia Li, Ilias Rentzeperis, Cees van Leeuwen

Research Article | published 11 Aug 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011325

Views: 965Citations: 3Saves: 4 • Shares: 1

iPiDA-SWGCN: Identification of piRNA-disease associations based on Supplementarily Weighted Graph Convolutional Network

Jialu Hou, Hang Wei, Bin Liu

Research Article | published 20 Jun 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011242

Views: 1512Citations: 8Saves: 10 • Shares: 1

Sparse RNNs can support high-capacity classification

Denis Turcu, L. F. Abbott

Research Article | published 14 Dec 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010759

Views: 1587Citations: 2Saves: 8 • Shares: 4

Statistical perspective on functional and causal neural connectomics: The Time-Aware PC algorithm

Rahul Biswas, Eli Shlizerman

Research Article | published 14 Nov 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010653

Views: 2345Citations: 11Saves: 9 • Shares: 10

iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank

Wenxiang Zhang, Jialu Hou, Bin Liu

Research Article | published 15 Aug 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010404

Views: 1907Citations: 13Saves: 14 • Shares: 8

Global dynamics of microbial communities emerge from local interaction rules

Simon van Vliet, Christoph Hauert, Kyle Fridberg, Martin Ackermann, Alma Dal Co

Research Article | published 04 Mar 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009877

Views: 5841Citations: 23Saves: 80 • Shares: 32

Discovering adaptation-capable biological network structures using control-theoretic approaches

Priyan Bhattacharya, Karthik Raman, Arun K. Tangirala

Research Article | published 21 Jan 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009769

Views: 3327Citations: 19Saves: 15 • Shares: 23

SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization

Lei Li, Zhen Gao, Yu-Tian Wang, Ming-Wen Zhang, Jian-Cheng Ni, Chun-Hou Zheng, Yansen Su

Research Article | published 12 Jul 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009165

Views: 2732Citations: 43Saves: 6 • Shares: 7

What do Eulerian and Hamiltonian cycles have to do with genome assembly?

Paul Medvedev, Mihai Pop

Education | published 20 May 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008928

Views: 4725Citations: 7Saves: 21 • Shares: 49

Causal network inference from gene transcriptional time-series response to glucocorticoids

Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt

Research Article | published 29 Jan 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008223

Views: 7776Citations: 28Saves: 105 • Shares: 16

Flux-based hierarchical organization of Escherichia coli’s metabolic network

Semidán Robaina-Estévez, Zoran Nikoloski

Research Article | published 20 Apr 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007832

Views: 2767Citations: 3Saves: 39 • Shares: 5

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