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For: Borisov NM, Markevich NI, Hoek JB, Kholodenko BN. Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity. Biophys J 2005;89:951-66. [PMID: 15923229 PMCID: PMC1366644 DOI: 10.1529/biophysj.105.060533] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
Number Cited by Other Article(s)
1
Patel H, Solanki N, Solanki A, Patel M, Patel S, Shah U. Mathematical modelling of Alzheimer's disease biomarkers: Targeting Amyloid beta, Tau protein, Apolipoprotein E and Apoptotic pathways. Am J Transl Res 2024;16:2777-2792. [PMID: 39114703 PMCID: PMC11301479 DOI: 10.62347/ujqf5204] [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: 01/09/2024] [Accepted: 05/15/2024] [Indexed: 08/10/2024]
2
Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023;28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023]  Open
3
Ovchinnikov A, Pérez Verona I, Pogudin G, Tribastone M. CLUE: Exact maximal reduction of kinetic models by constrained lumping of differential equations. Bioinformatics 2021;37:1732-1738. [PMID: 33532849 DOI: 10.1093/bioinformatics/btab010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/13/2020] [Accepted: 01/30/2021] [Indexed: 11/14/2022]  Open
4
Frøysa HG, Fallahi S, Blaser N. Evaluating model reduction under parameter uncertainty. BMC SYSTEMS BIOLOGY 2018;12:79. [PMID: 30053887 PMCID: PMC6062951 DOI: 10.1186/s12918-018-0602-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 07/09/2018] [Indexed: 11/10/2022]
5
Stepanov A, Karelina T, Markevich N, Demin O, Nicholas T. A mathematical model of multisite phosphorylation of tau protein. PLoS One 2018;13:e0192519. [PMID: 29408874 PMCID: PMC5800643 DOI: 10.1371/journal.pone.0192519] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/24/2018] [Indexed: 11/18/2022]  Open
6
Straube R. Analysis of network motifs in cellular regulation: Structural similarities, input-output relations and signal integration. Biosystems 2017;162:215-232. [PMID: 29107640 DOI: 10.1016/j.biosystems.2017.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023]
7
Snowden TJ, van der Graaf PH, Tindall MJ. Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends. Bull Math Biol 2017;79:1449-1486. [PMID: 28656491 PMCID: PMC5498684 DOI: 10.1007/s11538-017-0277-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 03/30/2017] [Indexed: 01/31/2023]
8
Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS DISCOVERY 2017;22:213-237. [PMID: 28231035 DOI: 10.1177/2472555216682725] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
9
Aliper AM, Korzinkin MB, Kuzmina NB, Zenin AA, Venkova LS, Smirnov PY, Zhavoronkov AA, Buzdin AA, Borisov NM. Mathematical Justification of Expression-Based Pathway Activation Scoring (PAS). Methods Mol Biol 2017;1613:31-51. [PMID: 28849557 DOI: 10.1007/978-1-4939-7027-8_3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
10
Lavrik IN, Samsonova MG. The systems biology of signaling pathways. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916010127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
11
Fey D, Halasz M, Dreidax D, Kennedy SP, Hastings JF, Rauch N, Munoz AG, Pilkington R, Fischer M, Westermann F, Kolch W, Kholodenko BN, Croucher DR. Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients. Sci Signal 2015;8:ra130. [DOI: 10.1126/scisignal.aab0990] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
12
Birtwistle MR. Analytical reduction of combinatorial complexity arising from multiple protein modification sites. J R Soc Interface 2015;12:rsif.2014.1215. [PMID: 25519995 DOI: 10.1098/rsif.2014.1215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
13
Hogg JS, Harris LA, Stover LJ, Nair NS, Faeder JR. Exact hybrid particle/population simulation of rule-based models of biochemical systems. PLoS Comput Biol 2014;10:e1003544. [PMID: 24699269 PMCID: PMC3974646 DOI: 10.1371/journal.pcbi.1003544] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 02/03/2014] [Indexed: 11/19/2022]  Open
14
Santra T, Kolch W, Kholodenko BN. Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PLoS Comput Biol 2014;10:e1003385. [PMID: 24550716 PMCID: PMC3923657 DOI: 10.1371/journal.pcbi.1003385] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
15
Duan G, Walther D, Schulze WX. Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2013;4:540. [PMID: 24400017 PMCID: PMC3872036 DOI: 10.3389/fpls.2013.00540] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/12/2013] [Indexed: 05/23/2023]
16
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: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
17
Moenke G, Falcke M, Thurley K. Hierarchic stochastic modelling applied to intracellular Ca(2+) signals. PLoS One 2012;7:e51178. [PMID: 23300536 PMCID: PMC3531454 DOI: 10.1371/journal.pone.0051178] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022]  Open
18
Fey D, Croucher DR, Kolch W, Kholodenko BN. Crosstalk and signaling switches in mitogen-activated protein kinase cascades. Front Physiol 2012;3:355. [PMID: 23060802 PMCID: PMC3449335 DOI: 10.3389/fphys.2012.00355] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/19/2012] [Indexed: 12/24/2022]  Open
19
Radulescu O, Gorban AN, Zinovyev A, Noel V. Reduction of dynamical biochemical reactions networks in computational biology. Front Genet 2012;3:131. [PMID: 22833754 PMCID: PMC3400272 DOI: 10.3389/fgene.2012.00131] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 06/26/2012] [Indexed: 12/23/2022]  Open
20
Heitzler D, Durand G, Gallay N, Rizk A, Ahn S, Kim J, Violin JD, Dupuy L, Gauthier C, Piketty V, Crépieux P, Poupon A, Clément F, Fages F, Lefkowitz RJ, Reiter E. Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling. Mol Syst Biol 2012;8:590. [PMID: 22735336 PMCID: PMC3397412 DOI: 10.1038/msb.2012.22] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 05/23/2012] [Indexed: 01/14/2023]  Open
21
Saiz L. The physics of protein-DNA interaction networks in the control of gene expression. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012;24:193102. [PMID: 22516977 DOI: 10.1088/0953-8984/24/19/193102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
22
Kholodenko B, Yaffe MB, Kolch W. Computational approaches for analyzing information flow in biological networks. Sci Signal 2012;5:re1. [PMID: 22510471 DOI: 10.1126/scisignal.2002961] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
23
Bigger, better, faster: principles and models of AKAP anchoring protein signaling. J Cardiovasc Pharmacol 2012;58:462-9. [PMID: 21562426 DOI: 10.1097/fjc.0b013e31822001e3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
24
Nguyen LK, Matallanas D, Croucher DR, von Kriegsheim A, Kholodenko BN. Signalling by protein phosphatases and drug development: a systems-centred view. FEBS J 2012;280:751-65. [PMID: 22340367 DOI: 10.1111/j.1742-4658.2012.08522.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
25
Modeling Signaling Networks Using High-throughput Phospho-proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012;736:19-57. [DOI: 10.1007/978-1-4419-7210-1_2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
26
Yang J, Meng X, Hlavacek WS. Rule-based modelling and simulation of biochemical systems with molecular finite automata. IET Syst Biol 2011;4:453-66. [PMID: 21073243 DOI: 10.1049/iet-syb.2010.0015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
27
Fragments-based Model Reduction: Some Case Studies. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.entcs.2010.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
28
Camporesi F, Feret J, Koeppl H, Petrov T. Combining Model Reductions. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.entcs.2010.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
29
Smith GR, Shanley DP. Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways. PLoS One 2010;5:e11092. [PMID: 20567500 PMCID: PMC2886341 DOI: 10.1371/journal.pone.0011092] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/01/2010] [Indexed: 01/10/2023]  Open
30
Ghaffari N, Ivanov I, Qian X, Dougherty ER. A CoD-based reduction algorithm for designing stationary control policies on Boolean networks. ACTA ACUST UNITED AC 2010;26:1556-63. [PMID: 20421196 DOI: 10.1093/bioinformatics/btq225] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
31
Sunnåker M, Schmidt H, Jirstrand M, Cedersund G. Zooming of states and parameters using a lumping approach including back-translation. BMC SYSTEMS BIOLOGY 2010;4:28. [PMID: 20298607 PMCID: PMC2853501 DOI: 10.1186/1752-0509-4-28] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 03/18/2010] [Indexed: 12/17/2022]
32
Costa MN, Radhakrishnan K, Wilson BS, Vlachos DG, Edwards JS. Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction. PLoS One 2009;4:e6316. [PMID: 19626123 PMCID: PMC2710010 DOI: 10.1371/journal.pone.0006316] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 06/17/2009] [Indexed: 01/24/2023]  Open
33
Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Mol Syst Biol 2009;5:256. [PMID: 19357636 PMCID: PMC2683723 DOI: 10.1038/msb.2009.19] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 02/23/2009] [Indexed: 01/01/2023]  Open
34
Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG. Simulation of large-scale rule-based models. Bioinformatics 2009;25:910-7. [PMID: 19213740 PMCID: PMC2660871 DOI: 10.1093/bioinformatics/btp066] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 01/13/2009] [Accepted: 01/27/2009] [Indexed: 01/26/2023]  Open
35
Bruggeman FJ, Snoep JL, Westerhoff HV. Control, responses and modularity of cellular regulatory networks: a control analysis perspective. IET Syst Biol 2009;2:397-410. [PMID: 19045835 DOI: 10.1049/iet-syb:20070065] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
36
Collins SD, Chatterjee A, Vlachos DG. Coarse-grained kinetic Monte Carlo models: Complex lattices, multicomponent systems, and homogenization at the stochastic level. J Chem Phys 2009;129:184101. [PMID: 19045380 DOI: 10.1063/1.3005225] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
37
Saiz L, Vilar JMG. Protein-protein/DNA interaction networks: versatile macromolecular structures for the control of gene expression. IET Syst Biol 2009;2:247-55. [PMID: 19045820 DOI: 10.1049/iet-syb:20080091] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
38
Borisov NM, Chistopolsky AS, Faeder JR, Kholodenko BN. Domain-oriented reduction of rule-based network models. IET Syst Biol 2009;2:342-51. [PMID: 19045829 DOI: 10.1049/iet-syb:20070081] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
39
Faeder JR, Blinov ML, Hlavacek WS. Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol 2009;500:113-67. [PMID: 19399430 DOI: 10.1007/978-1-59745-525-1_5] [Citation(s) in RCA: 232] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
40
Koschorreck M, Gilles ED. ALC: automated reduction of rule-based models. BMC SYSTEMS BIOLOGY 2008;2:91. [PMID: 18973705 PMCID: PMC2636783 DOI: 10.1186/1752-0509-2-91] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 10/31/2008] [Indexed: 01/01/2023]
41
Robust simplifications of multiscale biochemical networks. BMC SYSTEMS BIOLOGY 2008;2:86. [PMID: 18854041 PMCID: PMC2654786 DOI: 10.1186/1752-0509-2-86] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2008] [Accepted: 10/14/2008] [Indexed: 12/21/2022]
42
Gaffney EA, Heath JK, Kwiatkowska MZ. A mass action model of a Fibroblast Growth Factor signaling pathway and its simplification. Bull Math Biol 2008;70:2229-63. [PMID: 18841420 DOI: 10.1007/s11538-008-9342-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 05/23/2008] [Indexed: 10/21/2022]
43
Yang J, Monine MI, Faeder JR, Hlavacek WS. Kinetic Monte Carlo method for rule-based modeling of biochemical networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008;78:031910. [PMID: 18851068 PMCID: PMC2652652 DOI: 10.1103/physreve.78.031910] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 06/29/2008] [Indexed: 05/09/2023]
44
Conzelmann H, Fey D, Gilles ED. Exact model reduction of combinatorial reaction networks. BMC SYSTEMS BIOLOGY 2008;2:78. [PMID: 18755034 PMCID: PMC2570670 DOI: 10.1186/1752-0509-2-78] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 08/28/2008] [Indexed: 11/10/2022]
45
Saez-Rodriguez J, Hammerle-Fickinger A, Dalal O, Klamt S, Gilles ED, Conradi C. Multistability of signal transduction motifs. IET Syst Biol 2008;2:80-93. [PMID: 18397119 DOI: 10.1049/iet-syb:20070012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
46
Gomez-Uribe C, Verghese GC, Mirny LA. Operating regimes of signaling cycles: statics, dynamics, and noise filtering. PLoS Comput Biol 2008;3:e246. [PMID: 18159939 PMCID: PMC2230677 DOI: 10.1371/journal.pcbi.0030246] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 10/24/2007] [Indexed: 01/11/2023]  Open
47
Conzelmann H, Gilles ED. Dynamic pathway modeling of signal transduction networks: a domain-oriented approach. Methods Mol Biol 2008;484:559-78. [PMID: 18592201 DOI: 10.1007/978-1-59745-398-1_33] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
48
Saiz L, Vilar JMG. Ab initio thermodynamic modeling of distal multisite transcription regulation. Nucleic Acids Res 2007;36:726-31. [PMID: 18056082 PMCID: PMC2241893 DOI: 10.1093/nar/gkm1034] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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Koschorreck M, Conzelmann H, Ebert S, Ederer M, Gilles ED. Reduced modeling of signal transduction - a modular approach. BMC Bioinformatics 2007;8:336. [PMID: 17854494 PMCID: PMC2216040 DOI: 10.1186/1471-2105-8-336] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 09/13/2007] [Indexed: 12/18/2022]  Open
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Bruggeman FJ, Hornberg JJ, Boogerd FC, Westerhoff HV. Introduction to systems biology. EXS 2007;97:1-19. [PMID: 17432261 DOI: 10.1007/978-3-7643-7439-6_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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