Minimizing the number of optimizations for efficient community dynamic flux balance analysis
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1007786
Download full text from publisher
References listed on IDEAS
- Katharine M. Ng & Jessica A. Ferreyra & Steven K. Higginbottom & Jonathan B. Lynch & Purna C. Kashyap & Smita Gopinath & Natasha Naidu & Biswa Choudhury & Bart C. Weimer & Denise M. Monack & Justin L., 2013. "Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens," Nature, Nature, vol. 502(7469), pages 96-99, October.
- Charles K Fisher & Pankaj Mehta, 2014. "Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression," PLOS ONE, Public Library of Science, vol. 9(7), pages 1-10, July.
- Arianna Calcinotto & Arianna Brevi & Marta Chesi & Roberto Ferrarese & Laura Garcia Perez & Matteo Grioni & Shaji Kumar & Victoria M. Garbitt & Meaghen E. Sharik & Kimberly J. Henderson & Giovanni Ton, 2018. "Microbiota-driven interleukin-17-producing cells and eosinophils synergize to accelerate multiple myeloma progression," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Ren Dodge & Eric W. Jones & Haolong Zhu & Benjamin Obadia & Daniel J. Martinez & Chenhui Wang & Andrés Aranda-Díaz & Kevin Aumiller & Zhexian Liu & Marco Voltolini & Eoin L. Brodie & Kerwyn Casey Huan, 2023. "A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Kenta Suzuki & Masato S. Abe & Daiki Kumakura & Shinji Nakaoka & Fuki Fujiwara & Hirokuni Miyamoto & Teruno Nakaguma & Mashiro Okada & Kengo Sakurai & Shohei Shimizu & Hiroyoshi Iwata & Hiroshi Masuya, 2022. "Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks," IJERPH, MDPI, vol. 19(3), pages 1-14, January.
- 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.
- Vinod Nikhra, 2019. "Therapeutic Potential of Gut Microbiome Manipulation: Concepts in Fecal Microbiota Transplantation," Current Research in Diabetes & Obesity Journal, Juniper Publishers Inc., vol. 11(1), pages 1-9, June.
- Jordy Evan Sulaiman & Jaron Thompson & Yili Qian & Eugenio I. Vivas & Christian Diener & Sean M. Gibbons & Nasia Safdar & Ophelia S. Venturelli, 2024. "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
- 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).
- 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).
- Naomi Ohta & Bo Norby & Guy H Loneragan & Javier Vinasco & Henk C den Bakker & Sara D Lawhon & Keri N Norman & Harvey M Scott, 2019. "Quantitative dynamics of Salmonella and E. coli in feces of feedlot cattle treated with ceftiofur and chlortetracycline," PLOS ONE, Public Library of Science, vol. 14(12), pages 1-17, December.
- Elvin Koh & In Young Hwang & Hui Ling Lee & Ryan De Sotto & Jonathan Wei Jie Lee & Yung Seng Lee & John C. March & Matthew Wook Chang, 2022. "Engineering probiotics to inhibit Clostridioides difficile infection by dynamic regulation of intestinal metabolism," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Guy Amit & Amir Bashan, 2023. "Top-down identification of keystone taxa in the microbiome," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Alexander Y. G. Yip & Olivia G. King & Oleksii Omelchenko & Sanjana Kurkimat & Victoria Horrocks & Phoebe Mostyn & Nathan Danckert & Rohma Ghani & Giovanni Satta & Elita Jauneikaite & Frances J. Davie, 2023. "Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
- 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.
- K. E. Huus & T. T. Hoang & A. Creus-Cuadros & M. Cirstea & S. L. Vogt & K. Knuff-Janzen & P. J. Sansonetti & P. Vonaesch & B. B. Finlay, 2021. "Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- Li, Jie & Shen, Xuzhu & Li, YaoTang, 2021. "Modeling the temporal dynamics of gut microbiota from a local community perspective," Ecological Modelling, Elsevier, vol. 460(C).
- Giuliano Bonanomi & Mohamed Idbella & Ahmed M. Abd-ElGawad, 2021. "Microbiota Management for Effective Disease Suppression: A Systematic Comparison between Soil and Mammals Gut," Sustainability, MDPI, vol. 13(14), pages 1-16, July.
- Randy Hamchand & Kevin Wang & Deguang Song & Noah W. Palm & Jason M. Crawford, 2024. "Mucosal sugars delineate pyrazine vs pyrazinone autoinducer signaling in Klebsiella oxytoca," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Vinod Nikhra, 2019. "Therapeutic Potential of Gut Microbiome Manipulation: Concepts in Fecal Microbiota Transplantation," Current Research in Diabetes & Obesity Journal, Juniper Publishers Inc., vol. 11(1), pages 9-17, June.
- 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.
- 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.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1007786. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.