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For: Pandey V, Hadadi N, Hatzimanikatis V. Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models. PLoS Comput Biol 2019;15:e1007036. [PMID: 31083653 PMCID: PMC6532942 DOI: 10.1371/journal.pcbi.1007036] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/23/2019] [Accepted: 04/19/2019] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
1
Sun Q, An P, Li P, Wang H, Tao S, Liu Y. Unraveling Time-Resolved Transcriptional and Metabolic Shifts in the Mixed Fermentation of Saccharomyces cerevisiae and Hanseniaspora uvarum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025;73:12418-12432. [PMID: 40310988 DOI: 10.1021/acs.jafc.5c00722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2025]
2
Cheng Y, Yu W, Bi X, Liu Y, Li J, Du G, Chen J, Lv X, Liu L. CarveAdornCurate: a versatile cloud-based platform for constructing multiscale metabolic models. Trends Biotechnol 2025;43:1234-1259. [PMID: 40044549 DOI: 10.1016/j.tibtech.2025.01.011] [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: 08/04/2024] [Revised: 01/27/2025] [Accepted: 01/29/2025] [Indexed: 05/10/2025]
3
Li X, Walhout AJM, Yilmaz LS. Enhanced flux potential analysis links changes in enzyme expression to metabolic flux. Mol Syst Biol 2025;21:413-445. [PMID: 39962320 PMCID: PMC11965317 DOI: 10.1038/s44320-025-00090-9] [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: 08/28/2023] [Revised: 01/29/2025] [Accepted: 02/07/2025] [Indexed: 03/28/2025]  Open
4
Pandey V. MiNEApy: enhancing enrichment network analysis in metabolic networks. Bioinformatics 2025;41:btaf077. [PMID: 39985451 PMCID: PMC11889450 DOI: 10.1093/bioinformatics/btaf077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 02/01/2025] [Accepted: 02/20/2025] [Indexed: 02/24/2025]  Open
5
Scott H, Segrè D. Metabolic Flux Modeling in Marine Ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2025;17:593-620. [PMID: 39259978 DOI: 10.1146/annurev-marine-032123-033718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
6
Carter EL, Waterfield NR, Constantinidou C, Alam MT. A temperature-induced metabolic shift in the emerging human pathogen Photorhabdus asymbiotica. mSystems 2024;9:e0097023. [PMID: 39445821 PMCID: PMC11575385 DOI: 10.1128/msystems.00970-23] [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: 09/19/2023] [Accepted: 11/29/2023] [Indexed: 10/25/2024]  Open
7
Narasimha SM, Malpani T, Mohite OS, Nath JS, Raman K. Understanding flux switching in metabolic networks through an analysis of synthetic lethals. NPJ Syst Biol Appl 2024;10:104. [PMID: 39289347 PMCID: PMC11408705 DOI: 10.1038/s41540-024-00426-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 08/17/2024] [Indexed: 09/19/2024]  Open
8
Choudhury S, Narayanan B, Moret M, Hatzimanikatis V, Miskovic L. Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states. Nat Catal 2024;7:1086-1098. [PMID: 39463726 PMCID: PMC11499278 DOI: 10.1038/s41929-024-01220-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/06/2024] [Indexed: 10/29/2024]
9
Curvello R, Berndt N, Hauser S, Loessner D. Recreating metabolic interactions of the tumour microenvironment. Trends Endocrinol Metab 2024;35:518-532. [PMID: 38212233 DOI: 10.1016/j.tem.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
10
Morotti M, Grimm AJ, Hope HC, Arnaud M, Desbuisson M, Rayroux N, Barras D, Masid M, Murgues B, Chap BS, Ongaro M, Rota IA, Ronet C, Minasyan A, Chiffelle J, Lacher SB, Bobisse S, Murgues C, Ghisoni E, Ouchen K, Bou Mjahed R, Benedetti F, Abdellaoui N, Turrini R, Gannon PO, Zaman K, Mathevet P, Lelievre L, Crespo I, Conrad M, Verdeil G, Kandalaft LE, Dagher J, Corria-Osorio J, Doucey MA, Ho PC, Harari A, Vannini N, Böttcher JP, Dangaj Laniti D, Coukos G. PGE2 inhibits TIL expansion by disrupting IL-2 signalling and mitochondrial function. Nature 2024;629:426-434. [PMID: 38658764 PMCID: PMC11078736 DOI: 10.1038/s41586-024-07352-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
11
Hou C, Song X, Xiong Z, Wang G, Xia Y, Ai L. Investigating the Role of β-Disodium Glycerophosphate and Urea in Promoting Growth of Streptococcus thermophilus from Omics-Integrated Genome-Scale Models. Foods 2024;13:1006. [PMID: 38611312 PMCID: PMC11011449 DOI: 10.3390/foods13071006] [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: 02/29/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024]  Open
12
Tsouka S, Kumar P, Seubnooch P, Freiburghaus K, St-Pierre M, Dufour JF, Masoodi M. Transcriptomics-driven metabolic pathway analysis reveals similar alterations in lipid metabolism in mouse MASH model and human. COMMUNICATIONS MEDICINE 2024;4:39. [PMID: 38443644 PMCID: PMC10914730 DOI: 10.1038/s43856-024-00465-3] [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: 09/18/2023] [Accepted: 02/22/2024] [Indexed: 03/07/2024]  Open
13
Kaste JA, Shachar-Hill Y. Model validation and selection in metabolic flux analysis and flux balance analysis. Biotechnol Prog 2024;40:e3413. [PMID: 37997613 PMCID: PMC10922127 DOI: 10.1002/btpr.3413] [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: 09/21/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
14
Paklao T, Suratanee A, Plaimas K. ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology. BMC Bioinformatics 2023;24:492. [PMID: 38129786 PMCID: PMC10740312 DOI: 10.1186/s12859-023-05599-0] [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: 08/28/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]  Open
15
Carter EL, Constantinidou C, Alam MT. Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations. Brief Bioinform 2023;25:bbad439. [PMID: 38048080 PMCID: PMC10694557 DOI: 10.1093/bib/bbad439] [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: 07/24/2023] [Revised: 09/21/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023]  Open
16
Wendering P, Nikoloski Z. Model-driven insights into the effects of temperature on metabolism. Biotechnol Adv 2023;67:108203. [PMID: 37348662 DOI: 10.1016/j.biotechadv.2023.108203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/22/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023]
17
Bessell B, Loecker J, Zhao Z, Aghamiri SS, Mohanty S, Amin R, Helikar T, Puniya BL. COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery. Brief Bioinform 2023;24:bbad387. [PMID: 37930022 PMCID: PMC10627799 DOI: 10.1093/bib/bbad387] [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] [Revised: 09/04/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]  Open
18
Li G, Liu L, Du W, Cao H. Local flux coordination and global gene expression regulation in metabolic modeling. Nat Commun 2023;14:5700. [PMID: 37709734 PMCID: PMC10502109 DOI: 10.1038/s41467-023-41392-6] [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: 11/05/2020] [Accepted: 09/04/2023] [Indexed: 09/16/2023]  Open
19
Kaste JAM, Shachar-Hill Y. Model Validation and Selection in Metabolic Flux Analysis and Flux Balance Analysis. ARXIV 2023:arXiv:2303.12651v1. [PMID: 36994165 PMCID: PMC10055486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
20
Metabolic Robustness to Growth Temperature of a Cold- Adapted Marine Bacterium. mSystems 2023;8:e0112422. [PMID: 36847563 PMCID: PMC10134870 DOI: 10.1128/msystems.01124-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]  Open
21
Metabolomic and transcriptomic response to imatinib treatment of gastrointestinal stromal tumour in xenograft-bearing mice. Transl Oncol 2023;30:101632. [PMID: 36774883 PMCID: PMC9945753 DOI: 10.1016/j.tranon.2023.101632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/09/2023] [Accepted: 02/01/2023] [Indexed: 02/12/2023]  Open
22
Aminian-Dehkordi J, Valiei A, Mofrad MRK. Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases. Front Cardiovasc Med 2022;9:987104. [PMID: 36299869 PMCID: PMC9589059 DOI: 10.3389/fcvm.2022.987104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022]  Open
23
Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data. mSystems 2022;7:e0134721. [PMID: 35695574 PMCID: PMC9239220 DOI: 10.1128/msystems.01347-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
24
Zhu Y, Zhao J, Li J. Genome-scale metabolic modeling in antimicrobial pharmacology. ENGINEERING MICROBIOLOGY 2022;2:100021. [PMID: 39628842 PMCID: PMC11610950 DOI: 10.1016/j.engmic.2022.100021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/06/2024]
25
Wang P, Schumacher AM, Shiu SH. Computational prediction of plant metabolic pathways. CURRENT OPINION IN PLANT BIOLOGY 2022;66:102171. [PMID: 35078130 DOI: 10.1016/j.pbi.2021.102171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
26
Galvão Ferrarini M, Ziska I, Andrade R, Julien-Laferrière A, Duchemin L, César RM, Mary A, Vinga S, Sagot MF. Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations. Front Genet 2022;13:815476. [PMID: 35281848 PMCID: PMC8905348 DOI: 10.3389/fgene.2022.815476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/24/2022] [Indexed: 11/16/2022]  Open
27
Li X, Yilmaz LS, Walhout AJ. Compartmentalization of metabolism between cell types in multicellular organisms: a computational perspective. CURRENT OPINION IN SYSTEMS BIOLOGY 2022;29:100407. [PMID: 35224313 PMCID: PMC8865431 DOI: 10.1016/j.coisb.2021.100407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
28
Di Filippo M, Pescini D, Galuzzi BG, Bonanomi M, Gaglio D, Mangano E, Consolandi C, Alberghina L, Vanoni M, Damiani C. INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. PLoS Comput Biol 2022;18:e1009337. [PMID: 35130273 PMCID: PMC8853556 DOI: 10.1371/journal.pcbi.1009337] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 02/17/2022] [Accepted: 01/13/2022] [Indexed: 12/12/2022]  Open
29
Narad P, Naresh G, Sengupta A. Metabolomics and flux balance analysis. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00008-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
30
Pathania R, Srivastava A, Srivastava S, Shukla P. Metabolic systems biology and multi-omics of cyanobacteria: Perspectives and future directions. BIORESOURCE TECHNOLOGY 2022;343:126007. [PMID: 34634665 DOI: 10.1016/j.biortech.2021.126007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
31
Shichkova P, Coggan JS, Markram H, Keller D. A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. Front Mol Neurosci 2021;14:604559. [PMID: 34858137 PMCID: PMC8631404 DOI: 10.3389/fnmol.2021.604559] [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: 09/09/2020] [Accepted: 10/05/2021] [Indexed: 12/12/2022]  Open
32
Ravi S, Gunawan R. ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data. PLoS Comput Biol 2021;17:e1009589. [PMID: 34758020 PMCID: PMC8608322 DOI: 10.1371/journal.pcbi.1009589] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 11/22/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022]  Open
33
Frades I, Foguet C, Cascante M, Araúzo-Bravo MJ. Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment. Cancers (Basel) 2021;13:4609. [PMID: 34572839 PMCID: PMC8470216 DOI: 10.3390/cancers13184609] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/31/2022]  Open
34
Herrmann HA, Rusz M, Baier D, Jakupec MA, Keppler BK, Berger W, Koellensperger G, Zanghellini J. Thermodynamic Genome-Scale Metabolic Modeling of Metallodrug Resistance in Colorectal Cancer. Cancers (Basel) 2021;13:4130. [PMID: 34439283 PMCID: PMC8391396 DOI: 10.3390/cancers13164130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022]  Open
35
Leggieri PA, Liu Y, Hayes M, Connors B, Seppälä S, O'Malley MA, Venturelli OS. Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng 2021;23:169-201. [PMID: 33781078 PMCID: PMC8277735 DOI: 10.1146/annurev-bioeng-082120-022836] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
36
Seep L, Razaghi-Moghadam Z, Nikoloski Z. Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis. Sci Rep 2021;11:8544. [PMID: 33879809 PMCID: PMC8058346 DOI: 10.1038/s41598-021-87643-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/26/2021] [Indexed: 11/13/2022]  Open
37
Nanda P, Ghosh A. Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection. PLoS Comput Biol 2021;17:e1008860. [PMID: 33835998 PMCID: PMC8034727 DOI: 10.1371/journal.pcbi.1008860] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/09/2021] [Indexed: 12/27/2022]  Open
38
Qi Y, Wang H, Chen X, Wei G, Tao S, Fan M. Altered Metabolic Strategies: Elaborate Mechanisms Adopted by Oenococcus oeni in Response to Acid Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021;69:2906-2918. [PMID: 33587641 DOI: 10.1021/acs.jafc.0c07599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
39
Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism. Sci Rep 2021;11:4787. [PMID: 33637852 PMCID: PMC7910480 DOI: 10.1038/s41598-021-84114-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023]  Open
40
Weglarz-Tomczak E, Rijlaarsdam DJ, Tomczak JM, Brul S. GEM-Based Metabolic Profiling for Human Bone Osteosarcoma under Different Glucose and Glutamine Availability. Int J Mol Sci 2021;22:1470. [PMID: 33540580 PMCID: PMC7867237 DOI: 10.3390/ijms22031470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 12/31/2022]  Open
41
Weglarz-Tomczak E, Tomczak JM, Brul S. M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models. Bioinformatics 2021;37:2785-2786. [PMID: 33523116 PMCID: PMC8428599 DOI: 10.1093/bioinformatics/btab060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/31/2020] [Accepted: 01/26/2021] [Indexed: 11/16/2022]  Open
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Tomi-Andrino C, Norman R, Millat T, Soucaille P, Winzer K, Barrett DA, King J, Kim DH. Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions. PLoS Comput Biol 2021;17:e1007694. [PMID: 33493151 PMCID: PMC7861524 DOI: 10.1371/journal.pcbi.1007694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/04/2021] [Accepted: 12/28/2020] [Indexed: 12/11/2022]  Open
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van Rosmalen RP, Smith RW, Martins Dos Santos VAP, Fleck C, Suarez-Diez M. Model reduction of genome-scale metabolic models as a basis for targeted kinetic models. Metab Eng 2021;64:74-84. [PMID: 33486094 DOI: 10.1016/j.ymben.2021.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/05/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
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Zielinski DC, Patel A, Palsson BO. The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. Microorganisms 2020;8:E2050. [PMID: 33371386 PMCID: PMC7767376 DOI: 10.3390/microorganisms8122050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023]  Open
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Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020;19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023]  Open
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Kessell AK, McCullough HC, Auchtung JM, Bernstein HC, Song HS. Predictive interactome modeling for precision microbiome engineering. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2020.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Yilmaz LS, Li X, Nanda S, Fox B, Schroeder F, Walhout AJ. Modeling tissue-relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels. Mol Syst Biol 2020;16:e9649. [PMID: 33022146 PMCID: PMC7537831 DOI: 10.15252/msb.20209649] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 01/04/2023]  Open
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Dahal S, Yurkovich JT, Xu H, Palsson BO, Yang L. Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models. Proteomics 2020;20:e1900282. [PMID: 32579720 PMCID: PMC7501203 DOI: 10.1002/pmic.201900282] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/13/2020] [Indexed: 12/18/2022]
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Obata T. Toward an evaluation of metabolite channeling in vivo. Curr Opin Biotechnol 2020;64:55-61. [DOI: 10.1016/j.copbio.2019.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 12/25/2022]
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Halling PJ. Thermodynamic Favorability of End Products of Anaerobic Glucose Metabolism. ACS OMEGA 2020;5:15843-15849. [PMID: 32656405 PMCID: PMC7345408 DOI: 10.1021/acsomega.0c00790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
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