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For: Gerstl MP, Müller S, Regensburger G, Zanghellini J. Flux tope analysis: studying the coordination of reaction directions in metabolic networks. Bioinformatics 2019;35:266-273. [PMID: 30649351 PMCID: PMC6330010 DOI: 10.1093/bioinformatics/bty550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 05/30/2018] [Accepted: 06/29/2018] [Indexed: 01/06/2023]  Open
Number Cited by Other Article(s)
1
Kundu S. A mathematically rigorous algorithm to define, compute and assess relevance of the probable dissociation constants in characterizing a biochemical network. Sci Rep 2024;14:3507. [PMID: 38347039 PMCID: PMC10861591 DOI: 10.1038/s41598-024-53231-9] [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: 06/21/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024]  Open
2
Saa PA, Zapararte S, Drovandi CC, Nielsen LK. LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models. BMC Bioinformatics 2024;25:3. [PMID: 38166586 PMCID: PMC10763395 DOI: 10.1186/s12859-023-05616-2] [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: 12/13/2023] [Indexed: 01/04/2024]  Open
3
Kundu S. ReDirection: an R-package to compute the probable dissociation constant for every reaction of a user-defined biochemical network. Front Mol Biosci 2023;10:1206502. [PMID: 37942290 PMCID: PMC10628733 DOI: 10.3389/fmolb.2023.1206502] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/14/2023] [Indexed: 11/10/2023]  Open
4
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
5
The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility. PLoS Comput Biol 2022;18:e1010203. [PMID: 35759507 PMCID: PMC9269948 DOI: 10.1371/journal.pcbi.1010203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 07/08/2022] [Accepted: 05/14/2022] [Indexed: 11/30/2022]  Open
6
Thermodynamic Approaches in Flux Analysis. Methods Mol Biol 2020. [PMID: 31893383 DOI: 10.1007/978-1-0716-0159-4_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2025]
7
Ullah E, Yosafshahi M, Hassoun S. Towards scaling elementary flux mode computation. Brief Bioinform 2019;21:1875-1885. [PMID: 31745550 DOI: 10.1093/bib/bbz094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 01/05/2023]  Open
8
Fernandez-de-Cossio-Diaz J, Mulet R. Maximum entropy and population heterogeneity in continuous cell cultures. PLoS Comput Biol 2019;15:e1006823. [PMID: 30811392 PMCID: PMC6411232 DOI: 10.1371/journal.pcbi.1006823] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 03/11/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]  Open
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