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For: Krause F, Schulz M, Ripkens B, Flöttmann M, Krantz M, Klipp E, Handorf T. Biographer: web-based editing and rendering of SBGN compliant biochemical networks. Bioinformatics 2013;29:1467-8. [PMID: 23574737 PMCID: PMC3661053 DOI: 10.1093/bioinformatics/btt159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
Number Cited by Other Article(s)
1
Alfaro-García JP, Granados-Alzate MC, Vicente-Manzanares M, Gallego-Gómez JC. An Integrated View of Virus-Triggered Cellular Plasticity Using Boolean Networks. Cells 2021;10:cells10112863. [PMID: 34831086 PMCID: PMC8616224 DOI: 10.3390/cells10112863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]  Open
2
Touré V, Dräger A, Luna A, Dogrusoz U, Rougny A. The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11515-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
3
Sarmah DT, Bairagi N, Chatterjee S. Tracing the footsteps of autophagy in computational biology. Brief Bioinform 2020;22:5985288. [PMID: 33201177 PMCID: PMC8293817 DOI: 10.1093/bib/bbaa286] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022]  Open
4
Heberle H, Carazzolle MF, Telles GP, Meirelles GV, Minghim R. CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components. BMC Bioinformatics 2017;18:395. [PMID: 28929969 PMCID: PMC5606216 DOI: 10.1186/s12859-017-1787-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
5
Elmarakeby H, Arefiyan M, Myers E, Li S, Grene R, Heath LS. Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language. J Comput Biol 2017;24:1226-1229. [PMID: 28846457 DOI: 10.1089/cmb.2017.0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
6
King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol 2015;11:e1004321. [PMID: 26313928 PMCID: PMC4552468 DOI: 10.1371/journal.pcbi.1004321] [Citation(s) in RCA: 238] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/05/2015] [Indexed: 01/19/2023]  Open
7
SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps. PLoS One 2015;10:e0128985. [PMID: 26030594 PMCID: PMC4451519 DOI: 10.1371/journal.pone.0128985] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/04/2015] [Indexed: 01/08/2023]  Open
8
Dräger A, Palsson BØ. Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol 2014;2:61. [PMID: 25538939 PMCID: PMC4259112 DOI: 10.3389/fbioe.2014.00061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/14/2014] [Indexed: 11/17/2022]  Open
9
Ariño J, Aydar E, Drulhe S, Ganser D, Jorrín J, Kahm M, Krause F, Petrezsélyová S, Yenush L, Zimmermannová O, van Heusden GPH, Kschischo M, Ludwig J, Palmer C, Ramos J, Sychrová H. Systems biology of monovalent cation homeostasis in yeast: the translucent contribution. Adv Microb Physiol 2014;64:1-63. [PMID: 24797924 DOI: 10.1016/b978-0-12-800143-1.00001-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
10
Bock M, Scharp T, Talnikar C, Klipp E. BooleSim: an interactive Boolean network simulator. Bioinformatics 2013;30:131-2. [DOI: 10.1093/bioinformatics/btt568] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
11
Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G. An online model composition tool for system biology models. BMC SYSTEMS BIOLOGY 2013;7:88. [PMID: 24006914 PMCID: PMC3846440 DOI: 10.1186/1752-0509-7-88] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 08/21/2013] [Indexed: 11/21/2022]
12
Flöttmann M, Krause F, Klipp E, Krantz M. Reaction-contingency based bipartite Boolean modelling. BMC SYSTEMS BIOLOGY 2013;7:58. [PMID: 23835289 PMCID: PMC3710479 DOI: 10.1186/1752-0509-7-58] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 06/14/2013] [Indexed: 11/26/2022]
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