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For: Soyer OS, Pfeiffer T, Bonhoeffer S. Simulating the evolution of signal transduction pathways. J Theor Biol 2006;241:223-32. [PMID: 16403533 DOI: 10.1016/j.jtbi.2005.11.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 11/04/2005] [Accepted: 11/18/2005] [Indexed: 11/15/2022]
Number Cited by Other Article(s)
1
Martin RA, Tate AT. Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signalling networks. Proc Biol Sci 2024;291:20240446. [PMID: 38835275 DOI: 10.1098/rspb.2024.0446] [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: 02/22/2024] [Accepted: 05/03/2024] [Indexed: 06/06/2024]  Open
2
Martin R, Tate AT. Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signaling networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561276. [PMID: 37873469 PMCID: PMC10592669 DOI: 10.1101/2023.10.06.561276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
3
Martin RA, Tate AT. Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution. PLoS Comput Biol 2023;19:e1010445. [PMID: 37022993 PMCID: PMC10079112 DOI: 10.1371/journal.pcbi.1010445] [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: 07/29/2022] [Accepted: 02/23/2023] [Indexed: 04/07/2023]  Open
4
Hemery M, François P. In Silico Evolution of Biochemical Log-Response. J Phys Chem B 2019;123:2235-2243. [PMID: 30779571 DOI: 10.1021/acs.jpcb.8b10974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
5
Schrom EC, Prada JM, Graham AL. Immune Signaling Networks: Sources of Robustness and Constrained Evolvability during Coevolution. Mol Biol Evol 2017;35:676-687. [PMID: 29294066 DOI: 10.1093/molbev/msx321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
6
Nakauma A, van Doorn GS. Reconstructing the genotype-to-fitness map for the bacterial chemotaxis network and its emergent behavioural phenotypes. J Theor Biol 2017;420:200-212. [PMID: 28322874 DOI: 10.1016/j.jtbi.2017.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/10/2017] [Accepted: 03/16/2017] [Indexed: 11/26/2022]
7
Kamiya T, Oña L, Wertheim B, van Doorn GS. Coevolutionary feedback elevates constitutive immune defence: a protein network model. BMC Evol Biol 2016;16:92. [PMID: 27150135 PMCID: PMC4858902 DOI: 10.1186/s12862-016-0667-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/23/2016] [Indexed: 11/19/2022]  Open
8
Feng S, Ollivier JF, Swain PS, Soyer OS. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Res 2015;43:e123. [PMID: 26101250 PMCID: PMC4627059 DOI: 10.1093/nar/gkv595] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 05/26/2015] [Indexed: 11/13/2022]  Open
9
Friedlander T, Mayo AE, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Comput Biol 2015;11:e1004055. [PMID: 25798588 PMCID: PMC4370773 DOI: 10.1371/journal.pcbi.1004055] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/21/2014] [Indexed: 12/11/2022]  Open
10
Gottstein W, Müller S, Herzel H, Steuer R. Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution. Biosystems 2014;117:68-76. [PMID: 24440082 DOI: 10.1016/j.biosystems.2013.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 11/28/2013] [Accepted: 12/19/2013] [Indexed: 01/23/2023]
11
Mozhayskiy V, Tagkopoulos I. Microbial evolution in vivo and in silico: methods and applications. Integr Biol (Camb) 2013;5:262-77. [PMID: 23096365 DOI: 10.1039/c2ib20095c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
12
Roh K, Safaei FRP, Hespanha JP, Proulx SR. Evolution of transcription networks in response to temporal fluctuations. Evolution 2012;67:1091-104. [PMID: 23550758 DOI: 10.1111/evo.12012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
François P, Siggia ED. Phenotypic models of evolution and development: geometry as destiny. Curr Opin Genet Dev 2012;22:627-33. [PMID: 23026724 DOI: 10.1016/j.gde.2012.09.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 08/10/2012] [Accepted: 09/09/2012] [Indexed: 11/24/2022]
14
Warmflash A, Francois P, Siggia ED. Pareto evolution of gene networks: an algorithm to optimize multiple fitness objectives. Phys Biol 2012;9:056001. [PMID: 22874123 DOI: 10.1088/1478-3975/9/5/056001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
15
François P. Evolution In Silico: From Network Structure to Bifurcation Theory. EVOLUTIONARY SYSTEMS BIOLOGY 2012;751:157-82. [DOI: 10.1007/978-1-4614-3567-9_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
16
Tyson JJ, Novák B. Functional motifs in biochemical reaction networks. Annu Rev Phys Chem 2010;61:219-40. [PMID: 20055671 DOI: 10.1146/annurev.physchem.012809.103457] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
17
Luo J, Wang J, Ma TM, Sun Z. Reverse engineering of bacterial chemotaxis pathway via frequency domain analysis. PLoS One 2010;5:e9182. [PMID: 20231879 PMCID: PMC2834735 DOI: 10.1371/journal.pone.0009182] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 01/24/2010] [Indexed: 12/01/2022]  Open
18
Masel J, Siegal ML. Robustness: mechanisms and consequences. Trends Genet 2009;25:395-403. [PMID: 19717203 DOI: 10.1016/j.tig.2009.07.005] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/11/2009] [Accepted: 07/13/2009] [Indexed: 01/09/2023]
19
Wang Z, Chen Q, Liu L. Relationship between topology and functions in metabolic network evolution. Sci Bull (Beijing) 2009. [DOI: 10.1007/s11434-009-0072-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
20
Loewe L. A framework for evolutionary systems biology. BMC SYSTEMS BIOLOGY 2009;3:27. [PMID: 19239699 PMCID: PMC2663779 DOI: 10.1186/1752-0509-3-27] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 02/24/2009] [Indexed: 12/02/2022]
21
Salathé M, Soyer OS. Parasites lead to evolution of robustness against gene loss in host signaling networks. Mol Syst Biol 2008;4:202. [PMID: 18628743 PMCID: PMC2516366 DOI: 10.1038/msb.2008.44] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 06/06/2008] [Indexed: 12/02/2022]  Open
22
Crombach A, Hogeweg P. Evolution of evolvability in gene regulatory networks. PLoS Comput Biol 2008;4:e1000112. [PMID: 18617989 PMCID: PMC2432032 DOI: 10.1371/journal.pcbi.1000112] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 06/03/2008] [Indexed: 11/25/2022]  Open
23
François P, Siggia ED. A case study of evolutionary computation of biochemical adaptation. Phys Biol 2008;5:026009. [PMID: 18577806 DOI: 10.1088/1478-3975/5/2/026009] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
24
Goldstein RA, Soyer OS. Evolution of taxis responses in virtual bacteria: non-adaptive dynamics. PLoS Comput Biol 2008;4:e1000084. [PMID: 18483577 PMCID: PMC2386285 DOI: 10.1371/journal.pcbi.1000084] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 04/07/2008] [Indexed: 11/17/2022]  Open
25
Hintze A, Adami C. Evolution of complex modular biological networks. PLoS Comput Biol 2008;4:e23. [PMID: 18266463 PMCID: PMC2233666 DOI: 10.1371/journal.pcbi.0040023] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 12/20/2007] [Indexed: 12/14/2022]  Open
26
Tagkopoulos I, Liu YC, Tavazoie S. Predictive behavior within microbial genetic networks. Science 2008;320:1313-7. [PMID: 18467556 DOI: 10.1126/science.1154456] [Citation(s) in RCA: 374] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
27
Márton ML, Dresselhaus T. A comparison of early molecular fertilization mechanisms in animals and flowering plants. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s00497-007-0062-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
28
Soyer OS. Emergence and maintenance of functional modules in signaling pathways. BMC Evol Biol 2007;7:205. [PMID: 17974002 PMCID: PMC2228312 DOI: 10.1186/1471-2148-7-205] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 10/31/2007] [Indexed: 11/26/2022]  Open
29
Schwacke JH, Voit EO. The potential for signal integration and processing in interacting MAP kinase cascades. J Theor Biol 2007;246:604-20. [PMID: 17337011 PMCID: PMC2707083 DOI: 10.1016/j.jtbi.2006.12.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 12/26/2006] [Accepted: 12/27/2006] [Indexed: 11/29/2022]
30
Soyer OS, Bonhoeffer S. Evolution of complexity in signaling pathways. Proc Natl Acad Sci U S A 2006;103:16337-42. [PMID: 17060629 PMCID: PMC1621048 DOI: 10.1073/pnas.0604449103] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
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