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For: López-Agudelo VA, Mendum TA, Laing E, Wu H, Baena A, Barrera LF, Beste DJV, Rios-Estepa R. A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks. PLoS Comput Biol 2020;16:e1007533. [PMID: 32542021 PMCID: PMC7316355 DOI: 10.1371/journal.pcbi.1007533] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 06/25/2020] [Accepted: 05/08/2020] [Indexed: 01/06/2023]  Open
Number Cited by Other Article(s)
1
Xu Y, Banerjee R, Kasibhatla S, McFadden J, Joshi R, Borah Slater K. Differential producibility analysis reveals drug-associated carbon and nitrogen metabolite expressions in Mycobacterium tuberculosis. J Biol Chem 2025;301:108288. [PMID: 39929299 PMCID: PMC11986224 DOI: 10.1016/j.jbc.2025.108288] [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: 12/09/2024] [Revised: 01/21/2025] [Accepted: 02/04/2025] [Indexed: 03/28/2025]  Open
2
Mardinoglu A, Palsson BØ. Genome-scale models in human metabologenomics. Nat Rev Genet 2025;26:123-140. [PMID: 39300314 DOI: 10.1038/s41576-024-00768-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/22/2024]
3
Chowdhury NB, Pokorzynski N, Rucks EA, Ouellette SP, Carabeo RA, Saha R. Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in Chlamydia trachomatis persistence. mSystems 2024;9:e0071724. [PMID: 38940523 PMCID: PMC11323709 DOI: 10.1128/msystems.00717-24] [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: 05/24/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024]  Open
4
Chowdhury NB, Pokorzynski N, Rucks EA, Ouellette SP, Carabeo RA, Saha R. Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572198. [PMID: 38187683 PMCID: PMC10769294 DOI: 10.1101/2023.12.18.572198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
5
Borah Slater K, Beyß M, Xu Y, Barber J, Costa C, Newcombe J, Theorell A, Bailey MJ, Beste DJV, McFadden J, Nöh K. One-shot 13 C15 N-metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux. Mol Syst Biol 2023;19:e11099. [PMID: 36705093 PMCID: PMC9996240 DOI: 10.15252/msb.202211099] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023]  Open
6
Sarmah DT, Parveen R, Kundu J, Chatterjee S. Latent tuberculosis and computational biology: A less-talked affair. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023;178:17-31. [PMID: 36781150 DOI: 10.1016/j.pbiomolbio.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
7
Romano GE, Silva-Pereira TT, de Melo FM, Sisco MC, Banari AC, Zimpel CK, Soler-Camargo NC, Guimarães AMDS. Unraveling the metabolism of Mycobacterium caprae using comparative genomics. Tuberculosis (Edinb) 2022;136:102254. [PMID: 36126496 DOI: 10.1016/j.tube.2022.102254] [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: 02/27/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 11/19/2022]
8
Wang Y, Shi Q, Chen Q, Zhou X, Yuan H, Jia X, Liu S, Li Q, Ge L. Emerging advances in identifying signal transmission molecules involved in the interaction between Mycobacterium tuberculosis and the host. Front Cell Infect Microbiol 2022;12:956311. [PMID: 35959378 PMCID: PMC9359464 DOI: 10.3389/fcimb.2022.956311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 11/21/2022]  Open
9
Santamaria G, Ruiz-Rodriguez P, Renau-Mínguez C, Pinto FR, Coscollá M. In Silico Exploration of Mycobacterium tuberculosis Metabolic Networks Shows Host-Associated Convergent Fluxomic Phenotypes. Biomolecules 2022;12:376. [PMID: 35327567 PMCID: PMC8945471 DOI: 10.3390/biom12030376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/29/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023]  Open
10
López-Agudelo VA, Baena A, Barrera V, Cabarcas F, Alzate JF, Beste DJV, Ríos-Estepa R, Barrera LF. Dual RNA Sequencing of Mycobacterium tuberculosis-Infected Human Splenic Macrophages Reveals a Strain-Dependent Host-Pathogen Response to Infection. Int J Mol Sci 2022;23:ijms23031803. [PMID: 35163725 PMCID: PMC8836425 DOI: 10.3390/ijms23031803] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022]  Open
11
Borah K, Xu Y, McFadden J. Dissecting Host-Pathogen Interactions in TB Using Systems-Based Omic Approaches. Front Immunol 2021;12:762315. [PMID: 34795672 PMCID: PMC8593131 DOI: 10.3389/fimmu.2021.762315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/18/2021] [Indexed: 01/10/2023]  Open
12
Ramirez-Malule H, López-Agudelo VA, Gómez-Ríos D, Ochoa S, Ríos-Estepa R, Junne S, Neubauer P. TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale Metabolic Model of Streptomyces clavuligerus. Bioengineering (Basel) 2021;8:103. [PMID: 34436106 PMCID: PMC8389198 DOI: 10.3390/bioengineering8080103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/04/2021] [Accepted: 07/16/2021] [Indexed: 11/26/2022]  Open
13
Borah K, Mendum TA, Hawkins ND, Ward JL, Beale MH, Larrouy‐Maumus G, Bhatt A, Moulin M, Haertlein M, Strohmeier G, Pichler H, Forsyth VT, Noack S, Goulding CW, McFadden J, Beste DJV. Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis. Mol Syst Biol 2021;17:e10280. [PMID: 33943004 PMCID: PMC8094261 DOI: 10.15252/msb.202110280] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022]  Open
14
Jean-Pierre F, Henson MA, O’Toole GA. Metabolic Modeling to Interrogate Microbial Disease: A Tale for Experimentalists. Front Mol Biosci 2021;8:634479. [PMID: 33681294 PMCID: PMC7930556 DOI: 10.3389/fmolb.2021.634479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022]  Open
15
Sertbas M, Ulgen KO. Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. Front Cell Dev Biol 2020;8:566702. [PMID: 33251208 PMCID: PMC7673413 DOI: 10.3389/fcell.2020.566702] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]  Open
16
Kulyashov M, Peltek SE, Akberdin IR. A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus. Microorganisms 2020;8:E1002. [PMID: 32635563 PMCID: PMC7409357 DOI: 10.3390/microorganisms8071002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 11/16/2022]  Open
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