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A diel multi-tissue genome-scale metabolic model of Vitis vinifera

Marta Sampaio, Miguel Rocha, Oscar Dias

Research Article | published 10 Oct 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012506

Views: 1118Citations: 0Saves: 0 • Shares: 1

Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae)

Sarah Percival, Joyce G. Onyenedum, Daniel H. Chitwood, Aman Y. Husbands

Research Article | published 05 Feb 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011845

Views: 1098Citations: 1Saves: 0 • Shares: 0

A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization

Philip J. Tubergen, Greg Medlock, Anni Moore, Xiaomu Zhang, Jason A. Papin, Cristian H. Danna

Research Article | published 27 Dec 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011651

Views: 972Citations: 2Saves: 15 • Shares: 4

Imaging with spatio-temporal modelling to characterize the dynamics of plant-pathogen lesions

Melen Leclerc, Stéphane Jumel, Frédéric M. Hamelin, Rémi Treilhaud, Nicolas Parisey, Youcef Mammeri

Research Article | published 20 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011627

Views: 1105Citations: 3Saves: 0 • Shares: 0

A 2D model to study how secondary growth affects the self-supporting behaviour of climbing plants

Giacomo Vecchiato, Tom Hattermann, Michele Palladino, Fabio Tedone, Patrick Heuret, Nick P. Rowe, Pierangelo Marcati

Research Article | published 16 Oct 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011538

Views: 1140Citations: 3Saves: 0 • Shares: 0

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

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber

Emanuel Cunha, Miguel Silva, Inês Chaves, Huseyin Demirci, Davide Rafael Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Dias

Research Article | published 20 Sep 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011499

Views: 1502Citations: 9Saves: 0 • Shares: 0

Network feature-based phenotyping of leaf venation robustly reconstructs the latent space

Kohei Iwamasa, Koji Noshita

Research Article | published 20 Jul 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010581

Views: 2938Citations: 0Saves: 11 • Shares: 31

Latent Dirichlet Allocation modeling of environmental microbiomes

Anastasiia Kim, Sanna Sevanto, Eric R. Moore, Nicholas Lubbers

Research Article | published 08 Jun 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011075

Views: 1416Citations: 2Saves: 16 • Shares: 1

Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression

Sam De Meyer, Daniel Felipe Cruz, Tom De Swaef, Peter Lootens, Jolien De Block, Kevin Bird, Heike Sprenger, Michael Van de Voorde, Stijn Hawinkel, Tom Van Hautegem, Dirk Inzé, Hilde Nelissen, Isabel Roldán-Ruiz, Steven Maere

Research Article | published 30 May 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011161

Views: 2054Citations: 8Saves: 0 • Shares: 0

Constructive connectomics: How neuronal axons get from here to there using gene-expression maps derived from their family trees

Stan Kerstjens, Gabriela Michel, Rodney J. Douglas

Research Article | published 25 Aug 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010382

Views: 4201Citations: 11Saves: 27 • Shares: 23

TreeKnit: Inferring ancestral reassortment graphs of influenza viruses

Pierre Barrat-Charlaix, Timothy G. Vaughan, Richard A. Neher

Research Article | published 19 Aug 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010394

Views: 2417Citations: 13Saves: 14 • Shares: 8

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

Topological Sholl descriptors for neuronal clustering and classification

Reem Khalil, Sadok Kallel, Ahmad Farhat, Pawel Dlotko

Research Article | published 22 Jun 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010229

Views: 7019Citations: 12Saves: 0 • Shares: 0

Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach

Mahmudul Hasan Rifat, Jamil Ahmed, Milad Ahmed, Foeaz Ahmed, Airin Gulshan, Mahmudul Hasan

Research Article | published 16 Jun 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009539

Views: 2749Citations: 1Saves: 0 • Shares: 0

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