TRIMER: Transcription Regulation Integrated with Metabolic Regulation

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

doi:10.1016/j.isci.2021.103218

TRIMER: Transcription Regulation Integrated with Metabolic Regulation

Journal Article · Mon Nov 01 00:00:00 EDT 2021 · iScience

DOI:https://doi.org/10.1016/j.isci.2021.103218· OSTI ID:1824873

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

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Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

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

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

OSTI ID:: 1824873

Alternate ID(s):: OSTI ID: 1839206
OSTI ID: 1896670

Report Number(s):: BNL--222578-2022-JAAM; S258900422101186X; 103218; PII: S258900422101186X

Journal Information:: iScience, Journal Name: iScience Journal Issue: 11 Vol. 24; ISSN 2589-0042

Publisher:: ElsevierCopyright Statement

Country of Publication:: Netherlands

Language:: English

References (37)

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Burgard, Anthony P.; Pharkya, Priti; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 84, Issue 6 https://doi.org/10.1002/bit.10803	journal	October 2003
Constraints-based models: Regulation of Gene Expression Reduces the Steady-state Solution Space Covert, Markus W.; Palsson, Bernhard O. Journal of Theoretical Biology, Vol. 221, Issue 3 https://doi.org/10.1006/jtbi.2003.3071	journal	April 2003
Identifying significant edges in graphical models of molecular networks Scutari, Marco; Nagarajan, Radhakrishnan Artificial Intelligence in Medicine, Vol. 57, Issue 3 https://doi.org/10.1016/j.artmed.2012.12.006	journal	March 2013
Systems biology as a foundation for genome-scale synthetic biology Barrett, Christian L.; Kim, Tae Yong; Kim, Hyun Uk Current Opinion in Biotechnology, Vol. 17, Issue 5 https://doi.org/10.1016/j.copbio.2006.08.001	journal	October 2006
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
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models Lewis, Nathan E.; Hixson, Kim K.; Conrad, Tom M. Molecular Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1038/msb.2010.47	journal	January 2010
Unraveling condition‐dependent networks of transcription factors that control metabolic pathway activity in yeast Fendt, Sarah‐Maria; Oliveira, Ana Paula; Christen, Stefan Molecular Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1038/msb.2010.91	journal	January 2010
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki Molecular Systems Biology, Vol. 2, Article No. 2006.0008 https://doi.org/10.1038/msb4100050	journal	February 2006
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
Network-based prediction of human tissue-specific metabolism Shlomi, Tomer; Cabili, Moran N.; Herrgård, Markus J. Nature Biotechnology, Vol. 26, Issue 9 https://doi.org/10.1038/nbt.1487	journal	August 2008
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use Varma, Amit; Palsson, Bernhard O. Bio/Technology, Vol. 12, Issue 10 https://doi.org/10.1038/nbt1094-994	journal	October 1994
Regulatory on/off minimization of metabolic flux changes after genetic perturbations Shlomi, T.; Berkman, O.; Ruppin, E. Proceedings of the National Academy of Sciences, Vol. 102, Issue 21 https://doi.org/10.1073/pnas.0406346102	journal	May 2005
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
Analysis of optimality in natural and perturbed metabolic networks Segre, D.; Vitkup, D.; Church, G. M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 23 https://doi.org/10.1073/pnas.232349399	journal	November 2002
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities Edwards, J. S.; Palsson, B. O. Proceedings of the National Academy of Sciences, Vol. 97, Issue 10 https://doi.org/10.1073/pnas.97.10.5528	journal	May 2000
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
cMonkey ₂ : Automated, systematic, integrated detection of co-regulated gene modules for any organism Reiss, David J.; Plaisier, Christopher L.; Wu, Wei-Ju Nucleic Acids Research, Vol. 43, Issue 13 https://doi.org/10.1093/nar/gkv300	journal	April 2015
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12 Santos-Zavaleta, Alberto; Salgado, Heladia; Gama-Castro, Socorro Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1077	journal	November 2018
Approximating discrete probability distributions with dependence trees Chow, C.; Liu, C. IEEE Transactions on Information Theory, Vol. 14, Issue 3 https://doi.org/10.1109/TIT.1968.1054142	journal	May 1968
Indole signalling contributes to the stable maintenance of Escherichia coli multicopy plasmids Chant, Eleanor L.; Summers, David K. Molecular Microbiology, Vol. 63, Issue 1 https://doi.org/10.1111/j.1365-2958.2006.05481.x	journal	January 2007
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Varma, A.; Palsson, B. O. Applied and Environmental Microbiology, Vol. 60, Issue 10 https://doi.org/10.1128/aem.60.10.3724-3731.1994	journal	January 1994
Pedigrees of some mutant strains of Escherichia coli K-12 Bachmann, B. J. Bacteriological Reviews, Vol. 36, Issue 4 https://doi.org/10.1128/br.36.4.525-557.1972	journal	December 1972
Proof without prejudice: use of the Kolmogorov-Smirnov test for the analysis of histograms from flow systems and other sources. Young, I. T. Journal of Histochemistry & Cytochemistry, Vol. 25, Issue 7 https://doi.org/10.1177/25.7.894009	journal	July 1977
Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints Ren, Shaogang; Zeng, Bo; Qian, Xiaoning BMC Bioinformatics, Vol. 14, Issue S2 https://doi.org/10.1186/1471-2105-14-S2-S17	journal	January 2013
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
Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer’s disease Yu, Han; Blair, Rachael Hageman BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-2872-8	journal	July 2019
Robust mutant strain design by pessimistic optimization Apaydin, Meltem; Xu, Liang; Zeng, Bo BMC Genomics, Vol. 18, Issue S6 https://doi.org/10.1186/s12864-017-4025-7	journal	October 2017
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
Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism Machado, Daniel; Herrgård, Markus PLoS Computational Biology, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pcbi.1003580	journal	April 2014
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
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling Shen, Fangzhou; Sun, Renliang; Yao, Jie PLOS Computational Biology, Vol. 15, Issue 3 https://doi.org/10.1371/journal.pcbi.1006835	journal	March 2019
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
An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of E scherichia coli Carrera, Javier; Estrela, Raissa; Luo, Jing Molecular Systems Biology, Vol. 10, Issue 7 https://doi.org/10.15252/msb.20145108	journal	July 2014
A system‐level model for the microbial regulatory genome Brooks, Aaron N.; Reiss, David J.; Allard, Antoine Molecular Systems Biology, Vol. 10, Issue 7 https://doi.org/10.15252/msb.20145160	journal	July 2014

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