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For: Handorf T, Klipp E. Modeling mechanistic biological networks: an advanced Boolean approach. ACTA ACUST UNITED AC 2011;28:557-63. [PMID: 22199382 DOI: 10.1093/bioinformatics/btr697] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Singh A, Dwivedi A. Network dynamics investigation of omics-data-driven circadian-hypoxia crosstalk logical model in gallbladder cancer reveals key therapeutic target combinations. Integr Biol (Camb) 2024;16:zyae018. [PMID: 39499101 DOI: 10.1093/intbio/zyae018] [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: 04/03/2024] [Revised: 08/13/2024] [Accepted: 10/28/2024] [Indexed: 11/07/2024]
2
Romers J, Thieme S, Münzner U, Krantz M. A scalable method for parameter-free simulation and validation of mechanistic cellular signal transduction network models. NPJ Syst Biol Appl 2020;6:2. [PMID: 31934349 PMCID: PMC6954118 DOI: 10.1038/s41540-019-0120-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/20/2019] [Indexed: 11/09/2022]  Open
3
Deshpande A, Layek RK. Fault detection and therapeutic intervention in gene regulatory networks using SAT solvers. Biosystems 2019;179:55-62. [PMID: 30831179 DOI: 10.1016/j.biosystems.2019.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/04/2018] [Accepted: 02/28/2019] [Indexed: 11/19/2022]
4
Dinwoodie IH. COMPUTATIONAL METHODS FOR ASYNCHRONOUS BASINS. DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS. SERIES B 2016;21:3391-3405. [PMID: 28154501 PMCID: PMC5283826 DOI: 10.3934/dcdsb.2016103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
5
Liu ZP. Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data. Curr Genomics 2015;16:3-22. [PMID: 25937810 PMCID: PMC4412962 DOI: 10.2174/1389202915666141110210634] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 09/05/2014] [Accepted: 09/05/2014] [Indexed: 12/17/2022]  Open
6
Emmrich PMF, Roberts HE, Pancaldi V. A Boolean gene regulatory model of heterosis and speciation. BMC Evol Biol 2015;15:24. [PMID: 25888139 PMCID: PMC4349475 DOI: 10.1186/s12862-015-0298-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 01/27/2015] [Indexed: 11/11/2022]  Open
7
Austin D, Dinwoodie IH. MONOMIALS AND BASIN CYLINDERS FOR NETWORK DYNAMICS. SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS 2015;14:25-42. [PMID: 25620893 PMCID: PMC4299671 DOI: 10.1137/140975929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
8
Andrieux G, Le Borgne M, Théret N. An integrative modeling framework reveals plasticity of TGF-β signaling. BMC SYSTEMS BIOLOGY 2014;8:30. [PMID: 24618419 PMCID: PMC4007780 DOI: 10.1186/1752-0509-8-30] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/03/2014] [Indexed: 11/10/2022]
9
Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D. Integrative modelling of the influence of MAPK network on cancer cell fate decision. PLoS Comput Biol 2013;9:e1003286. [PMID: 24250280 PMCID: PMC3821540 DOI: 10.1371/journal.pcbi.1003286] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 09/02/2013] [Indexed: 02/04/2023]  Open
10
Somvanshi PR, Venkatesh KV. A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics. SYSTEMS AND SYNTHETIC BIOLOGY 2013;8:99-116. [PMID: 24592295 DOI: 10.1007/s11693-013-9125-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 09/10/2013] [Indexed: 12/28/2022]
11
Flöttmann M, Krause F, Klipp E, Krantz M. Reaction-contingency based bipartite Boolean modelling. BMC SYSTEMS BIOLOGY 2013;7:58. [PMID: 23835289 PMCID: PMC3710479 DOI: 10.1186/1752-0509-7-58] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 06/14/2013] [Indexed: 11/26/2022]
12
Rother M, Münzner U, Thieme S, Krantz M. Information content and scalability in signal transduction network reconstruction formats. MOLECULAR BIOSYSTEMS 2013;9:1993-2004. [PMID: 23636168 DOI: 10.1039/c3mb00005b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
13
Kazemzadeh L, Cvijovic M, Petranovic D. Boolean model of yeast apoptosis as a tool to study yeast and human apoptotic regulations. Front Physiol 2012;3:446. [PMID: 23233838 PMCID: PMC3518040 DOI: 10.3389/fphys.2012.00446] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 11/07/2012] [Indexed: 01/14/2023]  Open
14
Fearnley LG, Nielsen LK. PATHLOGIC-S: a scalable Boolean framework for modelling cellular signalling. PLoS One 2012;7:e41977. [PMID: 22879903 PMCID: PMC3413702 DOI: 10.1371/journal.pone.0041977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/27/2012] [Indexed: 11/18/2022]  Open
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