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For: Suderman R, Mitra ED, Lin YT, Erickson KE, Feng S, Hlavacek WS. Generalizing Gillespie's Direct Method to Enable Network-Free Simulations. Bull Math Biol 2019;81:2822-48. [PMID: 29594824 DOI: 10.1007/s11538-018-0418-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/19/2018] [Indexed: 12/22/2022]
Number Cited by Other Article(s)
1
Mitra ED, Hlavacek WS. Parameter Estimation and Uncertainty Quantification for Systems Biology Models. CURRENT OPINION IN SYSTEMS BIOLOGY 2019;18:9-18. [PMID: 32719822 PMCID: PMC7384601 DOI: 10.1016/j.coisb.2019.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
2
Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM, Posner RG, Hlavacek WS. PyBioNetFit and the Biological Property Specification Language. iScience 2019;19:1012-1036. [PMID: 31522114 PMCID: PMC6744527 DOI: 10.1016/j.isci.2019.08.045] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/21/2019] [Accepted: 08/22/2019] [Indexed: 02/07/2023]  Open
3
Cao Y, Linda P, Seitaridou E. Stochastic Simulation of Biochemical Systems: In Memory of Dan T. Gillespie's contributions. Bull Math Biol 2019;81:2819-2821. [PMID: 31264134 DOI: 10.1007/s11538-019-00633-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
4
Lin YT, Feng S, Hlavacek WS. Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks. J Chem Phys 2019;150:244101. [PMID: 31255063 DOI: 10.1063/1.5096774] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
5
Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules. Methods Mol Biol 2019. [PMID: 30945241 DOI: 10.1007/978-1-4939-9102-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
6
Thomas MJ, Klein U, Lygeros J, Rodríguez Martínez M. A Probabilistic Model of the Germinal Center Reaction. Front Immunol 2019;10:689. [PMID: 31001283 PMCID: PMC6456718 DOI: 10.3389/fimmu.2019.00689] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/13/2019] [Indexed: 12/18/2022]  Open
7
Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS. Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. PLoS Comput Biol 2019;15:e1006706. [PMID: 30653502 PMCID: PMC6353226 DOI: 10.1371/journal.pcbi.1006706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 01/30/2019] [Accepted: 12/09/2018] [Indexed: 12/27/2022]  Open
8
Hlavacek WS, Csicsery-Ronay JA, Baker LR, Ramos Álamo MDC, Ionkov A, Mitra ED, Suderman R, Erickson KE, Dias R, Colvin J, Thomas BR, Posner RG. A Step-by-Step Guide to Using BioNetFit. Methods Mol Biol 2019;1945:391-419. [PMID: 30945257 DOI: 10.1007/978-1-4939-9102-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
9
Tapia JJ, Saglam AS, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Faeder JR. MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework. Methods Mol Biol 2019;1945:203-229. [PMID: 30945248 PMCID: PMC6580425 DOI: 10.1007/978-1-4939-9102-0_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
10
Suderman R, Deeds EJ. Intrinsic limits of information transmission in biochemical signalling motifs. Interface Focus 2018;8:20180039. [PMID: 30443336 DOI: 10.1098/rsfs.2018.0039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2018] [Indexed: 12/22/2022]  Open
11
Lin YT, Chylek LA, Lemons NW, Hlavacek WS. Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics. J Phys Chem B 2018;122:6351-6356. [PMID: 29851484 DOI: 10.1021/acs.jpcb.8b02960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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