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User:Gary An
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== Current Research == | == Current Research == | ||
| − | + | My research focuses on the utilization of agent-based modeling for multi-scale modeling of acute inflammation. Agent levels include cells and molecules, with the goal of simulating organ- and organism-level behaviors from these generative mechanisms. While the focus of my models have primarily been on the pathophysiology of sepsis and multiple organ failure, in a more general sense I am interested in using agent-based modeling as a means of dynamic knowledge representation to augment the biomedical research process. With respect to acute inflammation, the ubiquitousness of the underlying cellular and molecular mechanisms suggest the application of this methodology to such area as oncogenesis, transplant immunology/rejection, autoimmune disease, wound healing/scarring, atherosclerosis and aging. I am currently using NetLogo as my primary agent-based modeling platform, but am involved with the development of SPARK (Simple Platform for Agent-based Representation of Knowledge) currently being done at the University of Pittsburgh. | |
| − | + | I am also interested in automated text analysis/information extraction from biomedical texts, formal knowledge representation in biomedicine and the development of methods for evolving biomedical ontologies. These goals form a "front-end" to high-level modeling tools (such as MetaABM) and are intended to facilitate the ability for biomedical knowledge to be represented, communicated and evaluated via executable models. | |
== Complexity/Agent Based Modeling Publications == | == Complexity/Agent Based Modeling Publications == | ||
Revision as of 11:05, 25 November 2008
Contents |
Current Position:
Assistant Professor of Surgery
Division of Trauma/Critical Care
Department of Surgery
Northwestern University Feinberg School of Medicine
Contact Information
676 N. Saint Clair, #650
Chicago, IL 60611
Phone: 312-695-4838
Fax: 312-695-3644
Email: docgca@aol.com or docgca@gmail.com
Current Research
My research focuses on the utilization of agent-based modeling for multi-scale modeling of acute inflammation. Agent levels include cells and molecules, with the goal of simulating organ- and organism-level behaviors from these generative mechanisms. While the focus of my models have primarily been on the pathophysiology of sepsis and multiple organ failure, in a more general sense I am interested in using agent-based modeling as a means of dynamic knowledge representation to augment the biomedical research process. With respect to acute inflammation, the ubiquitousness of the underlying cellular and molecular mechanisms suggest the application of this methodology to such area as oncogenesis, transplant immunology/rejection, autoimmune disease, wound healing/scarring, atherosclerosis and aging. I am currently using NetLogo as my primary agent-based modeling platform, but am involved with the development of SPARK (Simple Platform for Agent-based Representation of Knowledge) currently being done at the University of Pittsburgh. I am also interested in automated text analysis/information extraction from biomedical texts, formal knowledge representation in biomedicine and the development of methods for evolving biomedical ontologies. These goals form a "front-end" to high-level modeling tools (such as MetaABM) and are intended to facilitate the ability for biomedical knowledge to be represented, communicated and evaluated via executable models.
Complexity/Agent Based Modeling Publications
An G. A model of TLR4 signaling and tolerance using a qualitative, particle-event-based method: Introduction of Spatially Configured Stochastic Reaction Chambers (SCSRC). Mathematical Biosciences, in press.
An G. Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation. Theoretical Biology and Medical Modelling 2008; 5:11 (May 27, 2008).
Vodovotz Y, Csete M, Bartels J, Chang S and An G. Translational Systems Biology of Inflammation. PLoS Comput Biol 4(4): e1000014. doi:10.1371/journal.pcbi.1000014
An G, Faeder J and Vodovotz Y. A Review of Translational Systems Biology as applied to Inflammation: Introduction of an Engineering Approach to the Pathophysiology of the Burn Patient. J Burn Care Res 2008; 29(2):277-285.
Folcik VA, An G and Orosz CG. The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theoretical Biology and Medical Modelling 2007; 4:39, Publish ahead of print September 27, 2007.
An, G: Agent Based Modeling and Endothelial Biomedicine. In Aird, W. (ed): Endothelial Biomedicine: A Comprehensive Treatise. Cambridge University Press, 2007. Pages 1754-1759.
An G, Hunt CA, Clermont G, Neugebauer EA and Vodovotz Y. Challenges and Rewards on the Road to Translational Systems Biology in Acute Illness: Four Case Reports from Interdisciplinary Teams. Journal of Critical Care 2007; 22(2):169-175.
Vodovotz Y, Clermont G, Hunt CA, Lefering R, Bartels J, Seydel R, Hotchkiss J, Ta’asan S, Neugebauer EA and An G. Evidence-based Modeling of Critical Illness: An Initial Consensus from the Society of Complexity in Acute Illness. Journal of Critical Care 2007; 22(1):77-84.
Wakeland, W., Macovsky, L. and An, G.. A Hybrid Simulation for Studying Acute Inflammatory Response. Proceedings of the 2007 Spring Simulation Multiconference (Agent-directed Simulation Symposium). 1:39-46.
An G. Concepts for developing a collaborative in-silico model of the acute inflammatory response using agent based modeling. Journal of Critical Care 2006; 21(1): 105-110.
An G. Phenomenological issues related to measurement, mechanisms and manipulation of complex biological systems. Critical Care Medicine 2006; 34(1): 245-246. (Editorial)
An G. Introduction of an in-sIlico syntactical grammar for translating basic science research into agent based models of the acute inflammatory response. Proceedings from the 11th Congress European Shock Society 2005, H Redl editor. 161-165.
An G. Mathematical modeling in medicine: A means not an end. Critical Care Medicine 2005; 33(1): 253-254. (Editorial)
Vodovotz Y, Clermont G, Chow C, An G. Mathematical models of the acute inflammatory response. Current Opinions in Critical Care 2004; 10:383-390.
An G. In-silico experiments of existing and hypothetical cytokine-directed clinical trials using agent based modeling. Critical Care Medicine 2004; 32(10): 2050-2060..
An G. Complexity theory and surgery: Introducing and integrating a new analytical paradigm. New Surgery 2001; 1(3): 175-179.
An G. Agent-based computer simulation and SIRS: Building a bridge between basic science and clinical trials. Shock 2001; 16(4): 266-273.
An G, Lee I. Agent-Based Computer simulation (ABCS) and the inflammatory response: Building a tool to study Systemic Inflammatory Response Syndrome (SIRS). Simulation and Gaming 2001; 32(3): 344-361.
An G, Lee I. Complexity, Emergence and Pathophysiology: Using Agent Based Computer Simulation to characterize the Non-Adaptive Inflammatory Response. InterJournal Complex Systems: http://www.interjournal.org. Manuscript # [344]. May, 2000.
Links
Link to Society of Complexity in Acute Illness (SCAI). This is an organization of physicians and biomedical researchers committed to promoting the use of mathematical modeling and computational methods to analyze the pathophysiology of acute illnesses with a focus on inflammation. http://www.scai-med.org
Link to the annual meeting of SCAI, called the International Conference on Complexity in Acute Illness (ICCAI). http://www.iccia.org
Link to Modeling Glossary developed and maintained by the Biosystems Research Group at the University of California, San Francisco under the leadership of C. Anthony Hunt. This Glossary can be used as a reference point by those interested in biomedical modeling as a means of fostering communication between modelers and domain specialists. http://biosystems.ucsf.edu/Researc/dictionary.html