Recent Publications

Articles in Peer Reviewed Journals

  1. In Silico Methods for Unraveling the Mechanistic Complexities of Intestinal Absorption: Metabolism–Efflux Transport Interactions.  Lana X. Garmire and C.A. Hunt.  Drug Metab Dispos e-pub: 24 April, 2008 (DOI: 10.1124/dmd.107.020164).
  2. New Simulation Methods to Facilitate Achieving a Mechanistic Understanding of Basic Pharmacology Principles in the Classroom.  A. Grover, T.N. Lam, and C.A. Hunt.  J Scie Ed Technol e-pub: 3 April, 2008 (DOI: 10.1007/s10956-008-9106-6).  <CLICK HERE FOR TUTORIAL>
  3. Predictions of Hepatic Disposition Properties Using a Mechanistically Realistic, Physiologically Based Model.  L. Yan, S. Sheihk-Bahaei, S. Park, G.E.P. Ropella, and C.A. Hunt.  Drug Metab Dispos 36(4): 759-768. E-pub: 28 January, 2008 (Featured Article) (DOI: 10.1124/dmd.107.019067).
  4. Modeling and Simulation of Hepatic Drug Disposition Using a Physiologically Based, Multi-agent In Silico Liver.  L. Yan, G.E.P. Ropella, S. Park, M.S. Roberts, and C.A. Hunt.  Pharm Res e-pub: 28 November, 2007 (DOI: 10.1007/s11095-007-9494-y).
  5. Synthetic Nano-LDL with Paclitaxel Oleate as a Targeted Drug Delivery Vehicle for Glioblastoma Multiforme.  M. Nikanjam, A.R. Gibbs, C.A. Hunt, T.F. Budinger, and T.M. Forte.  J Cont Release 24: 163-71 (2007).
  6. An In Silico Transwell Device for the Study of Drug Transport and Drug-Drug Interactions.  L.X. Garmire, D.G. Garmire, and C.A. Hunt.  Pharm Res 24: 2171-86 (2007) (Featured Article).
  7. Challenges and rewards on the road to translational systems biology in acute illness: four case reports from interdisciplinary teams.  G. An, C.A. Hunt, G. Clermont, E. Neugebauer, and Y Vodovotz.  J Crit Care 22:169-75 (2007).
  8. Dynamics of in Silico Leukocyte Rolling, Activation, and Adhesion.  J. Tang, K.F. Ley, and C.A. Hunt.  BMC Systems Biology 1: 14 (2007).
  9. Formation of cysts by alveolar type II cells in three-dimensional culture reveals a novel mechanism for epithelial morphogenesis.  W. Yu, X. Fang, A. Ewald, K. Wong, C.A. Hunt, Z. Werb, M.A. Matthay, and K. Mostov.  Mol Biol Cell 18(5): 1693-700 (2007).
  10. Cost-Based Partitioning For Distributed and Parallel Simulation of Decomposable Multiscale Constructive Models.  S. Park, C.A. Hunt, and B.P. Zeigler.  Simulation 82(12): 809-26 (2006).
  11. Physiologically Based Synthetic Models of Hepatic Disposition.  C.A. Hunt, G.E.P. Ropella, L. Yan, D.Y. Hung, and M.S. Roberts.  J Pharmacokin Pharmacodyn 33(6): 737-72 (2006).   Hunt_JPKPD_v33p737_2006.pdf
  12. Simulating Properties of In Vitro Epithelial Cell Morphogenesis.  M.R. Grant, K.E. Mostov, T.D. Tlsty, and C.A. Hunt.  PLoS Computational Biology 2(10): e129, 1193-1209 (2006).
  13. An In Silico Analogue of In Vitro Systems Used to Study Epithelial Cell Morphogenesis.  M.R. Grant and C.A. Hunt.  In: C. Priami (Ed.): CMSB 2006, LNCS 4210: 285-97 (2006).
  14. Mechanistic study of the interplay of intestinal transport and metabolism using the synthetic modeling method.  Y. Liu and C. A. Hunt.  Pharm Res 23(3): 493-505 (2006).   Liu_PharmRes_v23p493_2006.pdf
  15. Studies of Intestinal Drug Transport Using an In Silico Epithelio-Mimetic Device.  Y. Liu and C.A. Hunt.  Biosystems 82(2): 154-167 (2005).   Liu_Biosystems_v82p154_2005.pdf
  16. Biomimetic in silico devices.  C.A. Hunt, G.E.P. Ropella, M.S. Roberts, L. Yan.  In: V. Danos and V. Schachter (Eds.): CMBS 2004, LNCS 3082: 35-43 (2005).
  17. Glucose transport to the brain: A systems model.  A.A. Qutub and C.A. Hunt.  Brain Research Rev 49(3): 595-617 (2005).
  18. Plasticity of gene expression in injured human dorsal root ganglia revealed by GeneChip oligonucleotide microarrays.  D. Rabert, Y. Xiao, Y. Yiangou, D. Kreder, L. Sangameswaran, M.R. Segal, C.A. Hunt, R. Birch, P. Anand.   J Clin Neurosci 11(3): 289-99 (2004).

Peer Reviewed Articles in Proceedings

  1. In Silico White Blood Cell: Mechanisms Underlying Leukocyte Rolling and Adhesion during Inflammation.  Jon Tang and C. Anthony Hunt.  Spring Simulation Multiconference 2008, Agent-Directed Simulation Symposium (ADS'08), The Society for Modeling and Simulation International, San Diago, CA., pp. 170-76 (ISBN: 1-56555-319-5).  Tang_ADS2008.pdf
  2. Predicting Hepatic Disposition Properties of Cationic Drugs Using a Physiologically Based, Agent-Oriented In Silico Liver.  Li Yan, Sunwoo Park, Shahab Sheikh-Bahaei, Glen E. P. Ropella, and C. Anthony Hunt.  Spring Simulation Multiconference 2008, Agent-Directed Simulation Symposium (ADS'08), The Society for Modeling and Simulation International, San Diago, CA., pp. 162-69 (ISBN: 1-56555-319-5).  Yan_ADS2008.pdf
  3. A Framework and Mechanistically Focused, In Silico Method for Enabling Rational Translational Research.  C. Anthony Hunt, Sergio Baranzini, Michael A. Matthay, and Sunwoo Park.  2008 AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 10-12, 2008. Hunt_AMIA2008.pdf
  4. The multiscale in silico liver.  C. Anthony Hunt, Li Yan, Glen E.P. Ropella, Sunwoo Park, Shahab Sheikh-Bahaei and Michael S. Roberts.  J Crit Care 22: 348-49, Abstracts for the 2007 International Conference on Complexity in Acute Illness (ICCAI), Long Beach, CA, October 5-7, 2007.  Hunt_JCC2007.pdf
  5. Parameter Estimation via Analysis of Fuzzy Clusters (PEAF): An Algorithm to Estimate Parameters of Agent-Based Models.  Shahab Sheikh-Bahaei and C. Anthony Hunt.  In G. Hu, ed., Proc ISCA 20th Intern Conf Comp Appl Ind Engr, ISCA, Cary, NC (ISBN: 978-1-880843-65-9), San Francisco, CA, Novebmer 7-9, 2007. Sheikh-Bahaei_CAINE2007.pdf
  6. Systems Modeling of Alveolar Morphogenesis In Vitro.  Sean H. J. Kim, Sunwoo Park, Wei Yu, Keith E. Mostov, Michael A. Matthay, and C. Anthony Hunt.  op.cit., 141-4.  Kim_CAINE2007.pdf
  7. Tracking Compounds and Their Interactions within In Silico Liver.  Sunwoo Park, Sean H.J. Kim, Glen E.P. Ropella, and C. Anthony Hunt.  op.cit., 257-62.  Park_CAINE2007_01.pdf
  8. Affects of surface detection on shape and growth of model tumor spheroids.  Jesse Engelberg, Glen E. P. Ropella, and C. Anthony Hunt.  op.cit., 53-7.  Engelberg_CAINE2007.pdf
  9. Simulation Processors and Their Collaboration for DEVS Models Integrated with Universal Coupling Specification.  Sunwoo Park, Sean H.J. Kim, and C. Anthony Hunt.  op.cit., 151-5.  Park_CAINE2007.pdf
  10. DEVS Peer-to-Peer Protocol for Distributed and Parallel Simulation of Hierarchical and Decomposable DEVS Models.  Sunwoo Park, Sean H.J. Kim, C. Anthony Hunt, and Dongsun Park.  In Press: Proceedings of the International Symposium on Information Technology Convergence (ISITC), Jeonju, Korea, November 23-24, 2007.  Park_ISITC2007.pdf
  11. Prediction of In Vitro Hepatic Biliary Excretion Using Stochastic Agent-Based Modeling and Fuzzy Clustering.  Shahab Sheikh-Bahaei and C. Anthony Hunt.  In: L. F. Perrone, et al., eds., Proceedings of the 37th conference on Winter Simulation, Monterey, CA, Dec 03 - 06, 1617-24, 2006.  Sheikh-Bahaei_WSC2006.pdf
  12. Understanding Emergent Biological Behaviors: Agent Based Simulations of In vitro Epithelial Morphogenesis in Multiple Environments.  Mark R. Grant, Sean H. J. Kim, and C. Anthony Hunt.  In: Proceedings of the Sixth International Conference on Complex Systems, June 25-30, Boston, MA, Ed: A. Minai, D. Braha, Y. Bar-Yam, #42 (2006).  Grant_ICCS2006.pdf
  13. Simulating In Vitro Epithelial Morphogenesis in Multiple Environments.  Mark R. Grant, Sean H. J. Kim, and C. Anthony Hunt.  In: Proc 5th Comp Syst Bioinform Conf (CSB 2006), IEEE Computer Society Press, 381-4 (2006).  Grant_CSB2006.pdf
  14. Coupling Permutation and Model Migration Based on Dynamic and Adaptive Coupling Mechanisms.  Sunwoo Park and C. Anthony Hunt.  In: Proc 2006 DEVS Symp, Sp Simul Conf, (Huntsville, AL, Apr 2-6), SCS Press, San Diego, CA, 9-15 (2006).  Park_SprSim2006.pdf
  15. In Silico Hepatocyte: Agent-based Modeling of the Biliary Excretion of Drugs In Vitro.  Shahab Sheikh-Bahaei, Glen E. P. Ropella, and C. Anthony Hunt.  In: L. Yilmaz, et al., eds., Proc 2006 Agent-Direc Simul Symp (Huntsville, AL, Apr 3-9), SCS Press, San Diego, CA (ADS'06), 157-163 (2006).  Sheikh-Bahaei_SprSim2006.pdf
  16. Agent-Based Simulations of In Vitro Multicellular Tumor Spheroid Growth.  Engelberg, Jesse A., Ganguli, Suman, and C. Anthony Hunt.  op.cit., 141-148.  Engelberg_SprSim2006.pdf
  17. Similarity measures and validation in automated modeling.  D. A. Nag, Glen E. P. Ropella, and C. A. Hunt.  Proceedings: Huntsville Simulation Conference, Huntsville, AL, October 25-27, 2005.  Nag_HSC2005.pdf
  18. Modeling and Simulation of Hepatic Drug Metabolism: In Silico Hepatic Intrinsic Clearance.  Shahab Sheikh-Bahaei, Glen E. P. Ropella, C. Anthony Hunt, in Systems Engineering and Autonomous Control: A Tribute to Professor Mo Jamshidi, ed. Aly El-Osery and Edward Tunstel, TSI, Inc. San Antonio (ISBN: 1-889335-28-2) pp. 137-146 (2006).  Sheikh-Bahaei_SEAC2006.pdf
  19. Methodological Considerations of Heuristic Modeling of Biological Systems.  Glen E. P. Ropella, C. Anthony Hunt, and Shahab Sheikh-Bahaei.  In: Proc 9th World Multi-Conf Systemics, Cybernetics and Informatics, Orlando, FL July 10-13, 2005.  Ropella_WMSCI2005.pdf
  20. Using Heuristic Models to Bridge the Gap Between Analytic and Experimental Models in Biology.  Glen E. Ropella, C. Anthony Hunt, Dev A. Nag.  In: L. Yilmaz, ed., Proc 2005 Agent-Direc Simul Symp (San Diego, CA, Apr 2-8), Simulation Series 37(2), SCS Press, San Diego, CA (ADS'05), 182-190.  Ropella_ADS2005.pdf
  21. In Silico Modeling of Blood-Brain Barrier: An Agent-Based Simulation of Cerebral Glucose Transport.  Sean H.J. Kim, Amina Qutub, C. Anthony Hunt.  ADS'05, op.cit. 177-81.  Kim_ADS2005.pdf
  22. Agent-Based Simulation of In Vitro Hepatic Drug Metabolism: In Silico Hepatic Intrinsic Clearance.  Shahab Sheikh-Bahaei, Glen E. P. Ropella, and C. Anthony Hunt.  ADS'05, op.cit. 157-163.  Sheikh-Bahaei_ADS2005.pdf
  23. Generic Model Partitioning with LookAhead k: A Multi-Scale Partitioning Algorithm for DEVS Biomimetic In Silico Devices.  Sunwoo Park, C. Anthony Hunt, and Bernard P. Zeigler.  ADS'05, op.cit.  Park_ADS2005_01.pdf
  24. PISL: A Large-Scale In Silico Experimental Framework for Agent-Directed Physiological Models.  Sunwoo Park, C. Anthony Hunt, and Glen E.P. Ropella.  ADS'05, op.cit. 205-210.  Park_ADS2005_02.pdf
 
 

The premise of the agent paradigm, its related theory and methodologies together with advances in multilevel modeling of complex systems of interactions opened new frontiers for advancing the physical, natural, social, military, and information sciences and engineering...