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For: Lemons NW, Hu B, Hlavacek WS. Hierarchical graphs for rule-based modeling of biochemical systems. BMC Bioinformatics 2011;12:45. [PMID: 21288338 PMCID: PMC3152790 DOI: 10.1186/1471-2105-12-45] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 02/02/2011] [Indexed: 11/23/2022]  Open
Number Cited by Other Article(s)
1
Saha TK, Katebi A, Dhifli W, Al Hasan M. Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins Using Frequent Subgraph Mining. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:1537-1549. [PMID: 28961123 DOI: 10.1109/tcbb.2017.2756879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
2
Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics. Interdiscip Sci 2019;11:21-32. [PMID: 30790228 DOI: 10.1007/s12539-019-00323-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/28/2019] [Accepted: 02/02/2019] [Indexed: 12/22/2022]
3
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]
4
Sekar JAP, Tapia JJ, Faeder JR. Automated visualization of rule-based models. PLoS Comput Biol 2017;13:e1005857. [PMID: 29131816 PMCID: PMC5703574 DOI: 10.1371/journal.pcbi.1005857] [Citation(s) in RCA: 11] [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: 09/05/2016] [Revised: 11/27/2017] [Accepted: 10/30/2017] [Indexed: 11/19/2022]  Open
5
Xie L, Ge X, Tan H, Xie L, Zhang Y, Hart T, Yang X, Bourne PE. Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput Biol 2014;10:e1003554. [PMID: 24830652 PMCID: PMC4022462 DOI: 10.1371/journal.pcbi.1003554] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
6
Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2014;6:13-36. [PMID: 24123887 PMCID: PMC3947470 DOI: 10.1002/wsbm.1245] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 01/04/2023]
7
Ibrahim B, Henze R, Gruenert G, Egbert M, Huwald J, Dittrich P. Spatial rule-based modeling: a method and its application to the human mitotic kinetochore. Cells 2013;2:506-44. [PMID: 24709796 PMCID: PMC3972674 DOI: 10.3390/cells2030506] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/05/2013] [Accepted: 06/25/2013] [Indexed: 12/23/2022]  Open
8
Bonnici V, Giugno R, Pulvirenti A, Shasha D, Ferro A. A subgraph isomorphism algorithm and its application to biochemical data. BMC Bioinformatics 2013;14 Suppl 7:S13. [PMID: 23815292 PMCID: PMC3633016 DOI: 10.1186/1471-2105-14-s7-s13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
9
Geyer T. Modeling metabolic processes between molecular and systems biology. Curr Opin Struct Biol 2013;23:218-23. [DOI: 10.1016/j.sbi.2012.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
10
Maus C, Rybacki S, Uhrmacher AM. Rule-based multi-level modeling of cell biological systems. BMC SYSTEMS BIOLOGY 2011;5:166. [PMID: 22005019 PMCID: PMC3306009 DOI: 10.1186/1752-0509-5-166] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 10/17/2011] [Indexed: 11/10/2022]
11
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. Guidelines for visualizing and annotating rule-based models. MOLECULAR BIOSYSTEMS 2011;7:2779-95. [PMID: 21647530 PMCID: PMC3168731 DOI: 10.1039/c1mb05077j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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