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For: de Jong H, Casagranda S, Giordano N, Cinquemani E, Ropers D, Geiselmann J, Gouzé JL. Mathematical modelling of microbes: metabolism, gene expression and growth. J R Soc Interface 2017;14:20170502. [PMID: 29187637 PMCID: PMC5721159 DOI: 10.1098/rsif.2017.0502] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/31/2017] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Liyanaarachchi VC, Nishshanka GKSH, Nimarshana PHV, Chang JS, Ariyadasa TU, Nagarajan D. Modeling of astaxanthin biosynthesis via machine learning, mathematical and metabolic network modeling. Crit Rev Biotechnol 2024;44:996-1017. [PMID: 37587012 DOI: 10.1080/07388551.2023.2237183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/04/2023] [Accepted: 06/17/2023] [Indexed: 08/18/2023]
2
Chodkowski JL, Shade A. Bioactive exometabolites drive maintenance competition in simple bacterial communities. mSystems 2024;9:e0006424. [PMID: 38470039 PMCID: PMC11019792 DOI: 10.1128/msystems.00064-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024]  Open
3
Marschmann GL, Tang J, Zhalnina K, Karaoz U, Cho H, Le B, Pett-Ridge J, Brodie EL. Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model. Nat Microbiol 2024;9:421-433. [PMID: 38316928 PMCID: PMC10847045 DOI: 10.1038/s41564-023-01582-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
4
Kleijn IT, Marguerat S, Shahrezaei V. A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes. J R Soc Interface 2023;20:20230206. [PMID: 37751876 PMCID: PMC10522411 DOI: 10.1098/rsif.2023.0206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023]  Open
5
He H, Li Y, Zhang L, Ding Z, Shi G. Understanding and application of Bacillus nitrogen regulation: A synthetic biology perspective. J Adv Res 2022:S2090-1232(22)00205-3. [PMID: 36103961 DOI: 10.1016/j.jare.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/22/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]  Open
6
Ghuneim LAJ, Raghuvanshi R, Neugebauer KA, Guzior DV, Christian MH, Schena B, Feiner JM, Castillo-Bahena A, Mielke J, McClelland M, Conrad D, Klapper I, Zhang T, Quinn RA. Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection. THE ISME JOURNAL 2022;16:2065-2075. [PMID: 35597889 PMCID: PMC9381758 DOI: 10.1038/s41396-022-01252-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022]
7
Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. PLoS Comput Biol 2022;18:e1009843. [PMID: 35104290 PMCID: PMC8853647 DOI: 10.1371/journal.pcbi.1009843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 02/17/2022] [Accepted: 01/18/2022] [Indexed: 11/19/2022]  Open
8
Holt BA, Tuttle M, Xu Y, Su M, Røise JJ, Wang X, Murthy N, Kwong GA. Dimensionless parameter predicts bacterial prodrug success. Mol Syst Biol 2022;18:e10495. [PMID: 35005851 PMCID: PMC8744131 DOI: 10.15252/msb.202110495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022]  Open
9
Panikov NS. Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges. Microorganisms 2021;9:2352. [PMID: 34835477 PMCID: PMC8621822 DOI: 10.3390/microorganisms9112352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/18/2021] [Accepted: 10/27/2021] [Indexed: 12/04/2022]  Open
10
The effect of natural selection on the propagation of protein expression noise to bacterial growth. PLoS Comput Biol 2021;17:e1009208. [PMID: 34280182 PMCID: PMC8321134 DOI: 10.1371/journal.pcbi.1009208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 07/29/2021] [Accepted: 06/22/2021] [Indexed: 11/19/2022]  Open
11
Smith TP, Clegg T, Bell T, Pawar S. Systematic variation in the temperature dependence of bacterial carbon use efficiency. Ecol Lett 2021;24:2123-2133. [PMID: 34240797 DOI: 10.1111/ele.13840] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/25/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022]
12
Gene Expression Space Shapes the Bioprocess Trade-Offs among Titer, Yield and Productivity. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11135859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
13
Zimmermann J, Kaleta C, Waschina S. gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol 2021;22:81. [PMID: 33691770 PMCID: PMC7949252 DOI: 10.1186/s13059-021-02295-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/10/2021] [Indexed: 12/21/2022]  Open
14
Bruggeman FJ, Planqué R, Molenaar D, Teusink B. Searching for principles of microbial physiology. FEMS Microbiol Rev 2021;44:821-844. [PMID: 33099619 PMCID: PMC7685786 DOI: 10.1093/femsre/fuaa034] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/02/2020] [Indexed: 12/27/2022]  Open
15
Yáñez Feliú G, Earle Gómez B, Codoceo Berrocal V, Muñoz Silva M, Nuñez IN, Matute TF, Arce Medina A, Vidal G, Vitalis C, Dahlin J, Federici F, Rudge TJ. Flapjack: Data Management and Analysis for Genetic Circuit Characterization. ACS Synth Biol 2021;10:183-191. [PMID: 33382586 DOI: 10.1021/acssynbio.0c00554] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
16
Otero-Muras I, Carbonell P. Automated engineering of synthetic metabolic pathways for efficient biomanufacturing. Metab Eng 2020;63:61-80. [PMID: 33316374 DOI: 10.1016/j.ymben.2020.11.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 12/19/2022]
17
Pelicaen R, Gonze D, De Vuyst L, Weckx S. Genome-scale metabolic modeling of Acetobacter pasteurianus 386B reveals its metabolic adaptation to cocoa fermentation conditions. Food Microbiol 2020;92:103597. [PMID: 32950138 DOI: 10.1016/j.fm.2020.103597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
18
A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth. Proc Natl Acad Sci U S A 2020;117:18869-18879. [PMID: 32675233 DOI: 10.1073/pnas.2002959117] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
19
Swayambhu G, Moscatello N, Atilla-Gokcumen GE, Pfeifer BA. Flux Balance Analysis for Media Optimization and Genetic Targets to Improve Heterologous Siderophore Production. iScience 2020;23:101016. [PMID: 32279062 PMCID: PMC7152677 DOI: 10.1016/j.isci.2020.101016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/15/2019] [Accepted: 03/23/2020] [Indexed: 01/02/2023]  Open
20
Dourado H, Lercher MJ. An analytical theory of balanced cellular growth. Nat Commun 2020;11:1226. [PMID: 32144263 PMCID: PMC7060212 DOI: 10.1038/s41467-020-14751-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 01/31/2020] [Indexed: 02/07/2023]  Open
21
de Groot DH, Hulshof J, Teusink B, Bruggeman FJ, Planqué R. Elementary Growth Modes provide a molecular description of cellular self-fabrication. PLoS Comput Biol 2020;16:e1007559. [PMID: 31986156 PMCID: PMC7004393 DOI: 10.1371/journal.pcbi.1007559] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 02/06/2020] [Accepted: 11/22/2019] [Indexed: 02/04/2023]  Open
22
Sharma S, Steuer R. Modelling microbial communities using biochemical resource allocation analysis. J R Soc Interface 2019;16:20190474. [PMID: 31690234 PMCID: PMC6893496 DOI: 10.1098/rsif.2019.0474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 10/15/2019] [Indexed: 01/08/2023]  Open
23
Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms 2019;7:microorganisms7110553. [PMID: 31718036 PMCID: PMC6921056 DOI: 10.3390/microorganisms7110553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022]  Open
24
Faizi M, Steuer R. Optimal proteome allocation strategies for phototrophic growth in a light-limited chemostat. Microb Cell Fact 2019;18:165. [PMID: 31601201 PMCID: PMC6785936 DOI: 10.1186/s12934-019-1209-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/06/2019] [Indexed: 12/20/2022]  Open
25
Optimal control of bacterial growth for the maximization of metabolite production. J Math Biol 2018;78:985-1032. [PMID: 30334073 DOI: 10.1007/s00285-018-1299-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/18/2018] [Indexed: 12/24/2022]
26
Kleijn IT, Krah LHJ, Hermsen R. Noise propagation in an integrated model of bacterial gene expression and growth. PLoS Comput Biol 2018;14:e1006386. [PMID: 30289879 PMCID: PMC6192656 DOI: 10.1371/journal.pcbi.1006386] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 10/17/2018] [Accepted: 07/20/2018] [Indexed: 12/17/2022]  Open
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