Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression
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DOI: 10.1371/journal.pone.0102451
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- Peter J. Turnbaugh & Ruth E. Ley & Micah Hamady & Claire M. Fraser-Liggett & Rob Knight & Jeffrey I. Gordon, 2007. "The Human Microbiome Project," Nature, Nature, vol. 449(7164), pages 804-810, October.
- Peter Chesson & Jessica J. Kuang, 2008. "The interaction between predation and competition," Nature, Nature, vol. 456(7219), pages 235-238, November.
- Tanya Yatsunenko & Federico E. Rey & Mark J. Manary & Indi Trehan & Maria Gloria Dominguez-Bello & Monica Contreras & Magda Magris & Glida Hidalgo & Robert N. Baldassano & Andrey P. Anokhin & Andrew C, 2012. "Human gut microbiome viewed across age and geography," Nature, Nature, vol. 486(7402), pages 222-227, June.
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- Iris Chen & Yogeshwar D Kelkar & Yu Gu & Jie Zhou & Xing Qiu & Hulin Wu, 2017. "High-dimensional linear state space models for dynamic microbial interaction networks," PLOS ONE, Public Library of Science, vol. 12(11), pages 1-20, November.
- Hannaford, Naomi E. & Heaps, Sarah E. & Nye, Tom M.W. & Curtis, Thomas P. & Allen, Ben & Golightly, Andrew & Wilkinson, Darren J., 2023. "A sparse Bayesian hierarchical vector autoregressive model for microbial dynamics in a wastewater treatment plant," Computational Statistics & Data Analysis, Elsevier, vol. 179(C).
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- Guy Amit & Amir Bashan, 2023. "Top-down identification of keystone taxa in the microbiome," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Abbas Kazerouni & Lawrence M Wein, 2017. "Exploring the Efficacy of Pooled Stools in Fecal Microbiota Transplantation for Microbiota-Associated Chronic Diseases," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-13, January.
- Xu, Libai & Kong, Dehan & Wang, Lidan & Gu, Hong & Kenney, Toby & Xu, Ximing, 2023. "Proportional stochastic generalized Lotka–Volterra model with an application to learning microbial community structures," Applied Mathematics and Computation, Elsevier, vol. 448(C).
- Sean M Gibbons & Sean M Kearney & Chris S Smillie & Eric J Alm, 2017. "Two dynamic regimes in the human gut microbiome," PLOS Computational Biology, Public Library of Science, vol. 13(2), pages 1-20, February.
- Xiaokan Guo & James Q Boedicker, 2016. "The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community," PLOS Computational Biology, Public Library of Science, vol. 12(9), pages 1-13, September.
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- Kumar P Mainali & Sharon Bewick & Peter Thielen & Thomas Mehoke & Florian P Breitwieser & Shishir Paudel & Arjun Adhikari & Joshua Wolfe & Eric V Slud & David Karig & William F Fagan, 2017. "Statistical analysis of co-occurrence patterns in microbial presence-absence datasets," PLOS ONE, Public Library of Science, vol. 12(11), pages 1-21, November.
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