Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline

Niu, Puhua; Soto, Maria J.; Yoon, Byung-Jun; Dougherty, Edward R.; Alexander, Francis J.; Blaby, Ian; Qian, Xiaoning

doi:10.1016/j.xpro.2022.101184

Title: Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline

Journal Article · 01 March 2022 · Star Protocols

DOI: https://doi.org/10.1016/j.xpro.2022.101184 · OSTI ID:1846823

Niu, Puhua; Soto, Maria J.; Yoon, Byung-Jun; Dougherty, Edward R.; Alexander, Francis J.; Blaby, Ian; Qian, Xiaoning

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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0012704; AC02-05CH11231

OSTI ID:: 1846823

Journal Information:: Star Protocols, Journal Name: Star Protocols Journal Issue: 1 Vol. 3; ISSN 2666-1667

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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TRIMER: Transcription Regulation Integrated with Metabolic Regulation Niu, Puhua; Soto, Maria J.; Yoon, Byung-Jun iScience, Vol. 24, Issue 11 https://doi.org/10.1016/j.isci.2021.103218	journal	November 2021
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models Mahadevan, R.; Schilling, C. H. Metabolic Engineering, Vol. 5, Issue 4 https://doi.org/10.1016/j.ymben.2003.09.002	journal	October 2003
A genome‐scale computational study of the interplay between transcriptional regulation and metabolism Shlomi, Tomer; Eisenberg, Yariv; Sharan, Roded Molecular Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1038/msb4100141	journal	January 2007
Integrating high-throughput and computational data elucidates bacterial networks Covert, Markus W.; Knight, Eric M.; Reed, Jennifer L. Nature, Vol. 429, Issue 6987 https://doi.org/10.1038/nature02456	journal	May 2004
Constraint-based models predict metabolic and associated cellular functions Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A. Nature Reviews Genetics, Vol. 15, Issue 2 https://doi.org/10.1038/nrg3643	journal	January 2014
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas Nature Protocols, Vol. 14, Issue 3 https://doi.org/10.1038/s41596-018-0098-2	journal	February 2019
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis Chandrasekaran, Sriram; Price, Nathan D. Proceedings of the National Academy of Sciences, Vol. 107, Issue 41 https://doi.org/10.1073/pnas.1005139107	journal	September 2010
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli Covert, Markus W.; Xiao, Nan; Chen, Tiffany J. Bioinformatics, Vol. 24, Issue 18 https://doi.org/10.1093/bioinformatics/btn352	journal	July 2008
Solving Puzzles With Missing Pieces: The Power of Systems Biology Yurkovich, James T.; Palsson, Bernhard O. Proceedings of the IEEE, Vol. 104, Issue 1 https://doi.org/10.1109/JPROC.2015.2505338	journal	January 2016
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks Jensen, Paul A.; Lutz, Kyla A.; Papin, Jason A. BMC Systems Biology, Vol. 5, Issue 1 https://doi.org/10.1186/1752-0509-5-147	journal	January 2011
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection Haury, Anne-Claire; Mordelet, Fantine; Vera-Licona, Paola BMC Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1186/1752-0509-6-145	journal	January 2012
Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks Chandrasekaran, Sriram; Price, Nathan D. PLoS Computational Biology, Vol. 9, Issue 12 https://doi.org/10.1371/journal.pcbi.1003370	journal	December 2013
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast Wang, Zhuo; Danziger, Samuel A.; Heavner, Benjamin D. PLOS Computational Biology, Vol. 13, Issue 5 https://doi.org/10.1371/journal.pcbi.1005489	journal	May 2017
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods Huynh-Thu, Vân Anh; Irrthum, Alexandre; Wehenkel, Louis PLoS ONE, Vol. 5, Issue 9 https://doi.org/10.1371/journal.pone.0012776	journal	September 2010
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