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For: Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Quantitative information management for the biochemical computation of cellular networks. Sci Signal 2004;2004:pl11. [PMID: 15340175 DOI: 10.1126/stke.2482004pl11] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
1
Random parameter sampling of a generic three-tier MAPK cascade model reveals major factors affecting its versatile dynamics. PLoS One 2013;8:e54441. [PMID: 23365667 PMCID: PMC3554771 DOI: 10.1371/journal.pone.0054441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 12/13/2012] [Indexed: 01/04/2023]  Open
2
Costa R, Rocha I, Ferreira E, Machado D. Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling. IET Syst Biol 2011;5:157-63. [DOI: 10.1049/iet-syb.2009.0058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
3
Kohl M. Standards, databases, and modeling tools in systems biology. Methods Mol Biol 2011;696:413-27. [PMID: 21063963 DOI: 10.1007/978-1-60761-987-1_26] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
4
Zhang Z, Larner SF, Kobeissy F, Hayes RL, Wang KKW. Systems biology and theranostic approach to drug discovery and development to treat traumatic brain injury. Methods Mol Biol 2010;662:317-29. [PMID: 20824479 DOI: 10.1007/978-1-60761-800-3_16] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
5
Bebek G, Patel V, Chance MR. PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling. BMC Bioinformatics 2010;11:596. [PMID: 21144021 PMCID: PMC3016410 DOI: 10.1186/1471-2105-11-596] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 12/13/2010] [Indexed: 11/19/2022]  Open
6
Peng HH, Dong C. Systemic Analysis of Tumor Cell-Induced Endothelial Calcium Signaling and Junction Disassembly. Cell Mol Bioeng 2009;2:375-385. [PMID: 19915693 DOI: 10.1007/s12195-009-0067-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
7
Qutub AA, Mac Gabhann F, Karagiannis ED, Vempati P, Popel AS. Multiscale models of angiogenesis. IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE : THE QUARTERLY MAGAZINE OF THE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY 2009;28:14-31. [PMID: 19349248 PMCID: PMC3077679 DOI: 10.1109/memb.2009.931791] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
8
Ma'ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R. SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC SYSTEMS BIOLOGY 2009;3:10. [PMID: 19154595 PMCID: PMC2637233 DOI: 10.1186/1752-0509-3-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 01/20/2009] [Indexed: 01/06/2023]
9
Systems biology model databases and resources. Essays Biochem 2008;45:223-36. [PMID: 18793135 DOI: 10.1042/bse0450223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
10
Chang CW, Poteet E, Schetz JA, Gümüş ZH, Weinstein H. Towards a quantitative representation of the cell signaling mechanisms of hallucinogens: measurement and mathematical modeling of 5-HT1A and 5-HT2A receptor-mediated ERK1/2 activation. Neuropharmacology 2008;56 Suppl 1:213-25. [PMID: 18762202 PMCID: PMC2635340 DOI: 10.1016/j.neuropharm.2008.07.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 07/23/2008] [Accepted: 07/25/2008] [Indexed: 11/27/2022]
11
Cooley PC, Roberts D, Bakalov VD, Bikmal S, Cantor S, Costandine T, Ganapathi L, Golla BJ, Grubbs G, Hollingsworth C, Li S, Qin Y, Savage W, Simoni D, Solano E, Wagener D. The model repository of the models of infectious disease agent study. IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE : A PUBLICATION OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY 2008;12:513-22. [PMID: 18632331 PMCID: PMC2741407 DOI: 10.1109/titb.2007.910354] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 02/28/2007] [Indexed: 11/09/2022]
12
Bebek G, Yang J. PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics 2007;8:335. [PMID: 17854489 PMCID: PMC2100073 DOI: 10.1186/1471-2105-8-335] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 09/13/2007] [Indexed: 11/12/2022]  Open
13
Computational prediction of protein-protein interactions. Mol Biotechnol 2007;38:1-17. [PMID: 18095187 DOI: 10.1007/s12033-007-0069-2] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Accepted: 07/16/2007] [Indexed: 01/19/2023]
14
Kinzer-Ursem TL, Linderman JJ. Both ligand- and cell-specific parameters control ligand agonism in a kinetic model of g protein-coupled receptor signaling. PLoS Comput Biol 2007;3:e6. [PMID: 17222056 PMCID: PMC1769407 DOI: 10.1371/journal.pcbi.0030006] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 11/30/2006] [Indexed: 12/17/2022]  Open
15
Cerami EG, Bader GD, Gross BE, Sander C. cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 2006;7:497. [PMID: 17101041 PMCID: PMC1660554 DOI: 10.1186/1471-2105-7-497] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 11/13/2006] [Indexed: 11/10/2022]  Open
16
Le Novère N. Model storage, exchange and integration. BMC Neurosci 2006;7 Suppl 1:S11. [PMID: 17118155 PMCID: PMC1775041 DOI: 10.1186/1471-2202-7-s1-s11] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
17
Kholodenko BN. Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol 2006;7:165-76. [PMID: 16482094 PMCID: PMC1679905 DOI: 10.1038/nrm1838] [Citation(s) in RCA: 895] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
18
Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006;34:D689-91. [PMID: 16381960 PMCID: PMC1347454 DOI: 10.1093/nar/gkj092] [Citation(s) in RCA: 458] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
19
Weinstein H. Hallucinogen actions on 5-HT receptors reveal distinct mechanisms of activation and signaling by G protein-coupled receptors. AAPS JOURNAL 2006;7:E871-84. [PMID: 16594640 PMCID: PMC2750957 DOI: 10.1208/aapsj070485] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
20
Ma’ayan A, Blitzer RD, Iyengar R. Toward predictive models of mammalian cells. ACTA ACUST UNITED AC 2005;34:319-49. [PMID: 15869393 PMCID: PMC3035045 DOI: 10.1146/annurev.biophys.34.040204.144415] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
21
Hucka M, Finney A. Escalating model sizes and complexities call for standardized forms of representation. Mol Syst Biol 2005;1:2005.0011. [PMID: 16729046 PMCID: PMC1360139 DOI: 10.1038/msb4100015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
22
Searls DB. Data integration: challenges for drug discovery. Nat Rev Drug Discov 2005;4:45-58. [PMID: 15688072 DOI: 10.1038/nrd1608] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
23
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. BMC Bioinformatics 2005;6:5. [PMID: 15642112 PMCID: PMC545948 DOI: 10.1186/1471-2105-6-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Accepted: 01/10/2005] [Indexed: 11/10/2022]  Open
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