Moving beyond in silico tools to in silico science in support of drug development research

Drug Development Research

Volumn 72, Issue 2, 2011, Pages 153-161

  Hunt, C Anthony ^a,b,c   Ropella, Glen E P ^a,b  

^a San Francisco   (United States)

^b TEMPUS DICTUM INC   (United States)

^c NONE   (United States)

Author keywords

agent based; mechanistic; modeling; predict; simulation; translation

Indexed keywords

ARTICLE; COMPUTER MODEL; DRUG RESEARCH; PERSONALIZED MEDICINE; PHYSICAL CHEMISTRY; SIMULATION; TRANSLATIONAL RESEARCH;

EID: 79953890886     PISSN: 02724391     EISSN: 10982299     Source Type: Journal    
DOI: 10.1002/ddr.20412     Document Type: Article

References (23)

1. Engelberg JA, Ropella GE, Hunt CA,. 2008. Essential operating principles for tumor spheroid growth. BMC Syst Biol 2: 110.
2. Hung DY, Chang P, Cheung K, McWhinney B, Masci PP, Weiss M, Roberts MS,. 2002. Cationic drug pharmacokinetics in diseased livers determined by fibrosis index, hepatic protein content, microsomal activity, and nature of drug. J Pharmacol Exp Ther 301: 1079-1087. (Pubitemid 34595100)
3. Hunt CA, Ropella GE, Yan L, Hung DY, Roberts MS,. 2006. Physiologically based synthetic models of hepatic disposition. J Pharmacokinet Pharmacodyn 33: 737-772. (Pubitemid 44819260)
4. Hunt CA, Baranzini S, Matthay MA, Park S,. 2008. A framework and mechanistically focused, in silico method for enabling rational translational research. AMIA summit on translational bioinformatics, San Francisco, CA, March 10-12, 2008.
5. Hunt CA, Ropella GE, Lam TN, Tang J, Kim SH, Engelberg JA, Sheikh-Bahaei S,. 2009. At the biological modeling and simulation frontier. Pharm Res 26: 2369-2400.
6. Kim SH, Debnath J, Mostov K, Park S, Hunt CA,. 2009a. A computational approach to resolve cell level contributions to early glandular epithelial cancer progression. BMC Syst Biol 3: 122.
7. Kim SH, Park S, Mostov K, Debnath J, Hunt CA,. 2009b. Computational investigation of epithelial cell dynamic phenotype in vitro. Theor Biol Med Model 6: 8.
8. Kim SH, Yu W, Mostov K, Matthay MA, Hunt CA,. 2009c. A computational approach to understand in vitro alveolar morphogenesis. PLoS One 4: e4819.
9. Kim SH, Matthay MA, Mostov K, Hunt CA,. 2010. Simulation of lung alveolar epithelial wound healing in vitro. J R Soc Interface 7: 1157-1170.
10. Lam TN, Hunt CA,. 2010. Mechanistic insight from in silico pharmacokinetic experiments: roles of P-glycoprotein, Cyp3A4 enzymes, and microenvironments. J Pharmacol Exp Ther 332: 398-412.
11. Luke S, Cioffi-Revilla C, Panait L, Sullivan K, Balan G,. 2005. MASON: a multiagent simulation environment. Simulation 81: 517-527.accessed 28 June 2010. (Pubitemid 41448648)
12. Minar N, Burkhart R, Langton C, Askenazi M,. 1996. The Swarm simulation system: a toolkit for building multi-agent simulations. Working Paper 96-06-042, Santa Fe Institute, Santa Fe, NM.accessed 28 June.
13. North M, Collier NT, Vos JR,. 2006. Experiences creating three implementations of the Repast agent modeling toolkit. ACM TOMACS 16:1-25. accessed 28 June 2010.
14. Park S, Ropella GE, Kim SH, Roberts MS, Hunt CA,. 2009. Computational strategies unravel and trace how liver disease changes hepatic drug disposition. J Pharmacol Exp Ther 328: 294-305.
15. Park S, Kim SH, Ropella GE, Roberts MS, Hunt CA,. 2010. Tracing multiscale mechanisms of drug disposition in normal and diseased livers. J Pharmacol Exp Ther 334: 124-136.
16. Sheikh-Bahaei S, Hunt CA,. 2006. Prediction of in vitro hepatic biliary excretion using stochastic agent-based modeling and fuzzy clustering. In:, Perrone LF, Wieland FP, Liu J, Lawson BG, Nicol DM, Fujimoto RM, editors. Proceedings of the 37th conference on Winter Simulation, Monterey, CA, December 3-6. p 1617-1624.
17. Sheikh-Bahaei S, Hunt CA,. 2007. Parameter estimation via analysis of fuzzy clusters (PEAF): an algorithm to estimate parameters of agent-based models. In:, Hu G, editor. Proceedings of the ISCA 20th International Conference on Comp Appl Ind Engr, ISCA, San Francisco, CA, November 7-9. p 23-27.
18. Sheikh-Bahaei S, Ropella GE, Hunt CA,. 2006. In silico hepatocyte: agent-based modeling of the biliary excretion of drugs in vitro. In:, Yilmaz L, et al., editors. Proceedings of the 2006 Agent-Director Simulation Symposium, Huntsville, AL, April 3-9. San Diego, CA: SCS Press. p 157-163.
19. Sheikh-Bahaei S, Maher JJ, Hunt CA,. 2010a. Computational experiments reveal plausible mechanisms for changing patterns of hepatic zonation of xenobiotic clearance and hepatotoxicity. J Theor Biol 265: 718-733.
20. Sheikh-Bahaei S, Ali KA, Bera SR, Hunt CA,. 2010b. Predicting human hepatic clearance using hypernet neural networks. In: 19th International Conference on Software Engineering and Data Engineering (SEDE-2010), San Francisco, CA, June 16-18. p 355-359.
21. Tang J, Hunt CA,. 2010. Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion. PLoS Comput Biol 6: e1000681.
22. Yan L, Sheihk-Bahaei S, Park S, Ropella GE, Hunt CA,. 2008a. Predictions of hepatic disposition properties using a mechanistically realistic, physiologically based model. Drug Metab Dispos 36: 759-768. (Pubitemid 351468384)
23. Yan L, Ropella GE, Park S, Roberts MS, Hunt CA,. 2008b. Modeling and simulation of hepatic drug disposition using a physiologically based, multi-agent in silico liver. Pharm Res 25: 1023-1036.