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For: Biggs MB, Papin JA. Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. PLoS Comput Biol 2017;13:e1005413. [PMID: 28263984 PMCID: PMC5358886 DOI: 10.1371/journal.pcbi.1005413] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/20/2017] [Accepted: 02/15/2017] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
1
Gelbach PE, Cetin H, Finley SD. Flux sampling in genome-scale metabolic modeling of microbial communities. BMC Bioinformatics 2024;25:45. [PMID: 38287239 PMCID: PMC10826046 DOI: 10.1186/s12859-024-05655-3] [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: 06/21/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024]  Open
2
Pan DT, Wang P, Wang XL, Sun YQ, Xiu ZL. Dynamic flux balance analysis of 1,3-propanediol production by clostridium butyricum fermentation. Biotechnol Prog 2024;40:e3411. [PMID: 37985220 DOI: 10.1002/btpr.3411] [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: 08/12/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023]
3
Bruggeman FJ, Teusink B, Steuer R. Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models. Bioessays 2023;45:e2300015. [PMID: 37559168 DOI: 10.1002/bies.202300015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023]
4
Gelbach PE, Finley SD. Genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer. iScience 2023;26:107569. [PMID: 37664588 PMCID: PMC10474475 DOI: 10.1016/j.isci.2023.107569] [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: 03/30/2023] [Revised: 05/24/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023]  Open
5
Molversmyr H, Øyås O, Rotnes F, Vik JO. Extracting functionally accurate context-specific models of Atlantic salmon metabolism. NPJ Syst Biol Appl 2023;9:19. [PMID: 37244928 DOI: 10.1038/s41540-023-00280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/05/2023] [Indexed: 05/29/2023]  Open
6
Gelbach PE, Finley SD. Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537368. [PMID: 37197028 PMCID: PMC10173371 DOI: 10.1101/2023.04.18.537368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
7
Cheng Y, Bi X, Xu Y, Liu Y, Li J, Du G, Lv X, Liu L. Machine learning for metabolic pathway optimization: A review. Comput Struct Biotechnol J 2023;21:2381-2393. [PMID: 38213889 PMCID: PMC10781721 DOI: 10.1016/j.csbj.2023.03.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023]  Open
8
Gelbach PE, Finley SD. Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.532000. [PMID: 36993493 PMCID: PMC10052244 DOI: 10.1101/2023.03.09.532000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
9
Wendering P, Nikoloski Z. COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PLoS Comput Biol 2022;18:e1009906. [PMID: 35320266 PMCID: PMC8942231 DOI: 10.1371/journal.pcbi.1009906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/09/2022] [Indexed: 11/18/2022]  Open
10
Carey MA, Medlock GL, Stolarczyk M, Petri WA, Guler JL, Papin JA. Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. PLoS Comput Biol 2022;18:e1009870. [PMID: 35196325 PMCID: PMC8901074 DOI: 10.1371/journal.pcbi.1009870] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/07/2022] [Accepted: 01/27/2022] [Indexed: 01/01/2023]  Open
11
Liang Y, Ma A, Zhuang G. Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles. Front Microbiol 2022;13:829717. [PMID: 35283862 PMCID: PMC8905317 DOI: 10.3389/fmicb.2022.829717] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 01/30/2023]  Open
12
Ankrah NYD, Bernstein DB, Biggs M, Carey M, Engevik M, García-Jiménez B, Lakshmanan M, Pacheco AR, Sulheim S, Medlock GL. Enhancing Microbiome Research through Genome-Scale Metabolic Modeling. mSystems 2021;6:e0059921. [PMID: 34904863 PMCID: PMC8670372 DOI: 10.1128/msystems.00599-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
13
Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis. mSystems 2021;6:e0091921. [PMID: 34609164 PMCID: PMC8547418 DOI: 10.1128/msystems.00919-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
14
Esvap E, Ulgen KO. Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome. ACS Synth Biol 2021;10:2121-2137. [PMID: 34402617 DOI: 10.1021/acssynbio.1c00140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
15
Bernstein DB, Sulheim S, Almaas E, Segrè D. Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. Genome Biol 2021;22:64. [PMID: 33602294 PMCID: PMC7890832 DOI: 10.1186/s13059-021-02289-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023]  Open
16
Rodríguez-Mier P, Poupin N, de Blasio C, Le Cam L, Jourdan F. DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks. PLoS Comput Biol 2021;17:e1008730. [PMID: 33571201 PMCID: PMC7904180 DOI: 10.1371/journal.pcbi.1008730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/24/2021] [Accepted: 01/21/2021] [Indexed: 11/18/2022]  Open
17
Zhang X, Zhang J, Yang J. Large-scale dynamic social data representation for structure feature learning. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2020. [DOI: 10.3233/jifs-189010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
18
Systematically gap-filling the genome-scale metabolic model of CHO cells. Biotechnol Lett 2020;43:73-87. [PMID: 33040240 DOI: 10.1007/s10529-020-03021-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
19
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions. PLoS Comput Biol 2020;16:e1007847. [PMID: 32348298 PMCID: PMC7213742 DOI: 10.1371/journal.pcbi.1007847] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 05/11/2020] [Accepted: 04/03/2020] [Indexed: 11/19/2022]  Open
20
Jacoby RP, Succurro A, Kopriva S. Nitrogen Substrate Utilization in Three Rhizosphere Bacterial Strains Investigated Using Proteomics. Front Microbiol 2020;11:784. [PMID: 32411116 PMCID: PMC7198800 DOI: 10.3389/fmicb.2020.00784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/01/2020] [Indexed: 12/25/2022]  Open
21
Medlock GL, Papin JA. Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning. Cell Syst 2020;10:109-119.e3. [PMID: 31926940 PMCID: PMC6975163 DOI: 10.1016/j.cels.2019.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/27/2019] [Accepted: 11/14/2019] [Indexed: 11/16/2022]
22
Bernstein DB, Dewhirst FE, Segrè D. Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. eLife 2019;8:39733. [PMID: 31194675 PMCID: PMC6609349 DOI: 10.7554/elife.39733] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 06/13/2019] [Indexed: 12/18/2022]  Open
23
Thommes M, Wang T, Zhao Q, Paschalidis IC, Segrè D. Designing Metabolic Division of Labor in Microbial Communities. mSystems 2019;4:e00263-18. [PMID: 30984871 PMCID: PMC6456671 DOI: 10.1128/msystems.00263-18] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/15/2019] [Indexed: 12/19/2022]  Open
24
Castillo S, Patil KR, Jouhten P. Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019;58:111-133. [PMID: 30911891 DOI: 10.1007/978-3-030-13035-0_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
25
Medlock GL, Carey MA, McDuffie DG, Mundy MB, Giallourou N, Swann JR, Kolling GL, Papin JA. Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota. Cell Syst 2018;7:245-257.e7. [PMID: 30195437 PMCID: PMC6166237 DOI: 10.1016/j.cels.2018.08.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/15/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022]
26
Machado D, Andrejev S, Tramontano M, Patil KR. Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. Nucleic Acids Res 2018;46:7542-7553. [PMID: 30192979 PMCID: PMC6125623 DOI: 10.1093/nar/gky537] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 12/26/2022]  Open
27
Zhang Z, Fang C, Wang Y, Zhang J, Yu J, Zhang Y, Wang X, Zhong J. COL1A1: A potential therapeutic target for colorectal cancer expressing wild-type or mutant KRAS. Int J Oncol 2018;53:1869-1880. [PMID: 30132520 PMCID: PMC6192778 DOI: 10.3892/ijo.2018.4536] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/08/2018] [Indexed: 12/13/2022]  Open
28
Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries. Curr Opin Biotechnol 2017;51:103-108. [PMID: 29278837 DOI: 10.1016/j.copbio.2017.12.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 12/18/2022]
29
Magnúsdóttir S, Thiele I. Modeling metabolism of the human gut microbiome. Curr Opin Biotechnol 2017;51:90-96. [PMID: 29258014 DOI: 10.1016/j.copbio.2017.12.005] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/15/2022]
30
On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore. mSystems 2017;2:mSystems00169-17. [PMID: 29238753 PMCID: PMC5715109 DOI: 10.1128/msystems.00169-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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