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For: Walker DC, Southgate J. The virtual cell--a candidate co-ordinator for 'middle-out' modelling of biological systems. Brief Bioinform 2009;10:450-61. [PMID: 19293250 DOI: 10.1093/bib/bbp010] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
Number Cited by Other Article(s)
1
Krix S, Wilczynski E, Falgàs N, Sánchez-Valle R, Yoles E, Nevo U, Baruch K, Fröhlich H. Towards early diagnosis of Alzheimer's disease: advances in immune-related blood biomarkers and computational approaches. Front Immunol 2024;15:1343900. [PMID: 38720902 PMCID: PMC11078023 DOI: 10.3389/fimmu.2024.1343900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024]  Open
2
Riggi M, Torrez RM, Iwasa JH. 3D animation as a tool for integrative modeling of dynamic molecular mechanisms. Structure 2024;32:122-130. [PMID: 38183978 PMCID: PMC10872329 DOI: 10.1016/j.str.2023.12.007] [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: 09/22/2023] [Revised: 11/01/2023] [Accepted: 12/12/2023] [Indexed: 01/08/2024]
3
Nanda P, Budak M, Michael CT, Krupinsky K, Kirschner DE. Development and Analysis of Multiscale Models for Tuberculosis: From Molecules to Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566861. [PMID: 38014103 PMCID: PMC10680629 DOI: 10.1101/2023.11.13.566861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
4
Reyes-Aldasoro CC. Modelling the Tumour Microenvironment, but What Exactly Do We Mean by "Model"? Cancers (Basel) 2023;15:3796. [PMID: 37568612 PMCID: PMC10416922 DOI: 10.3390/cancers15153796] [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: 06/28/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]  Open
5
Griesemer M, Sindi SS. Rules of Engagement: A Guide to Developing Agent-Based Models. Methods Mol Biol 2022;2349:367-380. [PMID: 34719003 DOI: 10.1007/978-1-0716-1585-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
6
Derbal Y. Modeling Cancer Dynamics. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020;2020:2455-2458. [PMID: 33018503 DOI: 10.1109/embc44109.2020.9175155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
7
Liberman A, Mussel M, Kario D, Sprinzak D, Nevo U. Modelling cell surface dynamics and cell-cell interactions using Cell Studio: a three-dimensional visualization tool based on gaming technology. J R Soc Interface 2019;16:20190264. [PMID: 31771451 DOI: 10.1098/rsif.2019.0264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
8
Reynolds ER, Himmelwright R, Sanginiti C, Pfaffmann JO. An agent-based model of the Notch signaling pathway elucidates three levels of complexity in the determination of developmental patterning. BMC SYSTEMS BIOLOGY 2019;13:7. [PMID: 30642357 PMCID: PMC6332573 DOI: 10.1186/s12918-018-0672-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 12/17/2018] [Indexed: 01/15/2023]
9
Systems biology primer: the basic methods and approaches. Essays Biochem 2018;62:487-500. [PMID: 30287586 DOI: 10.1042/ebc20180003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
10
Liberman A, Kario D, Mussel M, Brill J, Buetow K, Efroni S, Nevo U. Cell studio: A platform for interactive, 3D graphical simulation of immunological processes. APL Bioeng 2018;2:026107. [PMID: 31069304 PMCID: PMC6481718 DOI: 10.1063/1.5039473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 05/04/2018] [Indexed: 12/27/2022]  Open
11
Melnikova NB, Svitenkov AI, Hose DR, Hoekstra AG. A cell-based mechanical model of coronary artery tunica media. J R Soc Interface 2018;14:rsif.2017.0028. [PMID: 28679664 DOI: 10.1098/rsif.2017.0028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/05/2017] [Indexed: 12/23/2022]  Open
12
Ingham-Dempster T, Walker DC, Corfe BM. An agent-based model of anoikis in the colon crypt displays novel emergent behaviour consistent with biological observations. ROYAL SOCIETY OPEN SCIENCE 2017;4:160858. [PMID: 28484606 PMCID: PMC5414243 DOI: 10.1098/rsos.160858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/14/2017] [Indexed: 05/07/2023]
13
Osborne JM, Fletcher AG, Pitt-Francis JM, Maini PK, Gavaghan DJ. Comparing individual-based approaches to modelling the self-organization of multicellular tissues. PLoS Comput Biol 2017;13:e1005387. [PMID: 28192427 PMCID: PMC5330541 DOI: 10.1371/journal.pcbi.1005387] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 02/28/2017] [Accepted: 01/28/2017] [Indexed: 12/28/2022]  Open
14
Hoekstra AG, Alowayyed S, Lorenz E, Melnikova N, Mountrakis L, van Rooij B, Svitenkov A, Závodszky G, Zun P. Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016;374:rsta.2016.0146. [PMID: 27698036 PMCID: PMC5052730 DOI: 10.1098/rsta.2016.0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/14/2016] [Indexed: 05/27/2023]
15
A hybrid agent-based model of the developing mammary terminal end bud. J Theor Biol 2016;407:259-270. [PMID: 27475843 DOI: 10.1016/j.jtbi.2016.07.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/15/2016] [Accepted: 07/25/2016] [Indexed: 12/13/2022]
16
Multi-scale Modeling of the Cardiovascular System: Disease Development, Progression, and Clinical Intervention. Ann Biomed Eng 2016;44:2642-60. [PMID: 27138523 DOI: 10.1007/s10439-016-1628-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
17
Appleby PA, Shabir S, Southgate J, Walker D. Sources of variability in cytosolic calcium transients triggered by stimulation of homogeneous uro-epithelial cell monolayers. J R Soc Interface 2015;12:rsif.2014.1403. [PMID: 25694543 PMCID: PMC4387530 DOI: 10.1098/rsif.2014.1403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]  Open
18
An G. Introduction of a Framework for Dynamic Knowledge Representation of the Control Structure of Transplant Immunology: Employing the Power of Abstraction with a Solid Organ Transplant Agent-Based Model. Front Immunol 2015;6:561. [PMID: 26594211 PMCID: PMC4635853 DOI: 10.3389/fimmu.2015.00561] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 10/19/2015] [Indexed: 12/22/2022]  Open
19
Cilfone NA, Kirschner DE, Linderman JJ. Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems. Cell Mol Bioeng 2015;8:119-136. [PMID: 26366228 PMCID: PMC4564133 DOI: 10.1007/s12195-014-0363-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
20
Wang Z, Butner JD, Cristini V, Deisboeck TS. Integrated PK-PD and agent-based modeling in oncology. J Pharmacokinet Pharmacodyn 2015;42:179-89. [PMID: 25588379 DOI: 10.1007/s10928-015-9403-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/08/2015] [Indexed: 01/11/2023]
21
Molecular Modeling. SYSTEMS AND SYNTHETIC BIOLOGY 2015. [DOI: 10.1007/978-94-017-9514-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
22
Johnson D, Connor AJ, McKeever S, Wang Z, Deisboeck TS, Quaiser T, Shochat E. Semantically linking in silico cancer models. Cancer Inform 2014;13:133-43. [PMID: 25520553 PMCID: PMC4260769 DOI: 10.4137/cin.s13895] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 01/23/2023]  Open
23
Fisher CP, Kierzek AM, Plant NJ, Moore JB. Systems biology approaches for studying the pathogenesis of non-alcoholic fatty liver disease. World J Gastroenterol 2014;20:15070-15078. [PMID: 25386055 PMCID: PMC4223240 DOI: 10.3748/wjg.v20.i41.15070] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/13/2014] [Indexed: 02/06/2023]  Open
24
Peer X, An G. Agent-based model of fecal microbial transplant effect on bile acid metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection. J Pharmacokinet Pharmacodyn 2014;41:493-507. [PMID: 25168489 DOI: 10.1007/s10928-014-9381-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 08/19/2014] [Indexed: 01/05/2023]
25
Wang Z, Butner JD, Kerketta R, Cristini V, Deisboeck TS. Simulating cancer growth with multiscale agent-based modeling. Semin Cancer Biol 2014;30:70-8. [PMID: 24793698 DOI: 10.1016/j.semcancer.2014.04.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/18/2014] [Accepted: 04/04/2014] [Indexed: 01/01/2023]
26
Najafi A, Bidkhori G, Bozorgmehr JH, Koch I, Masoudi-Nejad A. Genome scale modeling in systems biology: algorithms and resources. Curr Genomics 2014;15:130-59. [PMID: 24822031 PMCID: PMC4009841 DOI: 10.2174/1389202915666140319002221] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 02/16/2014] [Accepted: 03/17/2014] [Indexed: 12/18/2022]  Open
27
Treloar KK, Simpson MJ, Haridas P, Manton KJ, Leavesley DI, McElwain DLS, Baker RE. Multiple types of data are required to identify the mechanisms influencing the spatial expansion of melanoma cell colonies. BMC SYSTEMS BIOLOGY 2013;7:137. [PMID: 24330479 PMCID: PMC3878834 DOI: 10.1186/1752-0509-7-137] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/05/2013] [Indexed: 12/25/2022]
28
Autism and EMF? Plausibility of a pathophysiological link part II. ACTA ACUST UNITED AC 2013;20:211-34. [PMID: 24113318 DOI: 10.1016/j.pathophys.2013.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
29
Keurentjes JJB, Molenaar J, Zwaan BJ. Predictive modelling of complex agronomic and biological systems. PLANT, CELL & ENVIRONMENT 2013;36:1700-10. [PMID: 23777295 DOI: 10.1111/pce.12156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 06/02/2013] [Accepted: 06/11/2013] [Indexed: 05/24/2023]
30
Sarpe V, Jacob C. Simulating the decentralized processes of the human immune system in a virtual anatomy model. BMC Bioinformatics 2013;14 Suppl 6:S2. [PMID: 23734994 PMCID: PMC3633010 DOI: 10.1186/1471-2105-14-s6-s2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
31
Yang A. On the Common Conceptual and Computational Frameworks for Multiscale Modeling. Ind Eng Chem Res 2013. [DOI: 10.1021/ie303123s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
32
Skibinski G, Finkbeiner S. Longitudinal measures of proteostasis in live neurons: features that determine fate in models of neurodegenerative disease. FEBS Lett 2013;587:1139-46. [PMID: 23458259 DOI: 10.1016/j.febslet.2013.02.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 02/21/2013] [Indexed: 12/20/2022]
33
Cannata N, Corradini F, Merelli E, Tesei L. Agent-based models of cellular systems. Methods Mol Biol 2013;930:399-426. [PMID: 23086852 DOI: 10.1007/978-1-62703-059-5_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
34
Walker DC, Southgate J. The modulatory effect of cell–cell contact on the tumourigenic potential of pre-malignant epithelial cells: a computational exploration. J R Soc Interface 2012;10:20120703. [PMID: 23097504 DOI: 10.1098/rsif.2012.0703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]  Open
35
Cheng TMK, Goehring L, Jeffery L, Lu YE, Hayles J, Novák B, Bates PA. A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins. PLoS Comput Biol 2012;8:e1002738. [PMID: 23093928 PMCID: PMC3475653 DOI: 10.1371/journal.pcbi.1002738] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 08/23/2012] [Indexed: 12/27/2022]  Open
36
Computer simulations of in vitro morphogenesis. Biosystems 2012;109:430-43. [DOI: 10.1016/j.biosystems.2012.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/15/2012] [Accepted: 06/15/2012] [Indexed: 01/08/2023]
37
In silico modelling of tumour margin diffusion and infiltration: review of current status. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2012;2012:672895. [PMID: 22919432 PMCID: PMC3418724 DOI: 10.1155/2012/672895] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/11/2012] [Indexed: 11/17/2022]
38
Klann M, Koeppl H. Spatial simulations in systems biology: from molecules to cells. Int J Mol Sci 2012;13:7798-7827. [PMID: 22837728 PMCID: PMC3397560 DOI: 10.3390/ijms13067798] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/08/2012] [Accepted: 06/12/2012] [Indexed: 12/23/2022]  Open
39
Burkitt M, Walker D, Romano DM, Fazeli A. Computational modelling of maternal interactions with spermatozoa: potentials and prospects. Reprod Fertil Dev 2012;23:976-89. [PMID: 22127003 DOI: 10.1071/rd11032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 07/12/2011] [Indexed: 12/20/2022]  Open
40
Horn F, Heinekamp T, Kniemeyer O, Pollmächer J, Valiante V, Brakhage AA. Systems biology of fungal infection. Front Microbiol 2012;3:108. [PMID: 22485108 PMCID: PMC3317178 DOI: 10.3389/fmicb.2012.00108] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/05/2012] [Indexed: 12/26/2022]  Open
41
Deisboeck TS, Wang Z, Macklin P, Cristini V. Multiscale cancer modeling. Annu Rev Biomed Eng 2012;13:127-55. [PMID: 21529163 DOI: 10.1146/annurev-bioeng-071910-124729] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
42
Swarm-Based Computational Development. MORPHOGENETIC ENGINEERING 2012. [DOI: 10.1007/978-3-642-33902-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
43
Jacob C, von Mammen S, Davison T, Sarraf-Shirazi A, Sarpe V, Esmaeili A, Phillips D, Yazdanbod I, Novakowski S, Steil S, Gingras C, Jamniczky H, Hallgrimsson B, Wright B. LINDSAY Virtual Human: Multi-scale, Agent-based, and Interactive. ADVANCES IN INTELLIGENT MODELLING AND SIMULATION 2012. [DOI: 10.1007/978-3-642-30154-4_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
44
Machado D, Costa RS, Rocha M, Ferreira EC, Tidor B, Rocha I. Modeling formalisms in Systems Biology. AMB Express 2011;1:45. [PMID: 22141422 PMCID: PMC3285092 DOI: 10.1186/2191-0855-1-45] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/05/2011] [Indexed: 12/18/2022]  Open
45
Antony PMA, Balling R, Vlassis N. From systems biology to systems biomedicine. Curr Opin Biotechnol 2011;23:604-8. [PMID: 22119097 DOI: 10.1016/j.copbio.2011.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 11/06/2011] [Indexed: 12/22/2022]
46
Systems biology of kidney diseases. Kidney Int 2011;81:22-39. [PMID: 21881558 DOI: 10.1038/ki.2011.314] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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An G, Christley S. Agent‐based modeling and biomedical ontologies: a roadmap. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/wics.167] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Lucas M, Laplaze L, Bennett MJ. Plant systems biology: network matters. PLANT, CELL & ENVIRONMENT 2011;34:535-53. [PMID: 21309807 DOI: 10.1111/j.1365-3040.2010.02273.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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Dada JO, Mendes P. Multi-scale modelling and simulation in systems biology. Integr Biol (Camb) 2011;3:86-96. [DOI: 10.1039/c0ib00075b] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wang Z, Bordas V, Deisboeck TS. Discovering Molecular Targets in Cancer with Multiscale Modeling. Drug Dev Res 2010;72:45-52. [PMID: 21572568 DOI: 10.1002/ddr.20401] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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