A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNADavid J D'Onofrio
College of Arts and Science, Math Department, University of Phoenix, 5480 Corporate Drive, Troy, MI 48098, USA
Theor Biol Med Model 7:3. 2010
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- Computational disease modeling - fact or fiction?
Jesper N Tegnér
Computational Medicine group, Department of Medicine, Center for Molecular Medicine, Karolinska University Hospital, Solna, Stockholm, Sweden
BMC Syst Biol 3:56. 2009
..On the other hand, the physics-inspired top-down modeling strategy identifies and selects features of (presumably) essential relevance to the phenomena of interest and combines available data in models of modest complexity...
- A case report of thoracic compartment syndrome in the setting of penetrating chest trauma and review of the literature
Michael W Wandling
Department of Surgery, Section of General Surgery, University of Chicago Pritzker School of Medicine, 5841 South Maryland, S 032 MC5031, Chicago, IL, 60637, USA
World J Emerg Surg 5:22. 2010
..TCS is exceedingly rare in the trauma population. We present a case of TCS following surgical repair of a stab wound injury that necessitated decompressive thoracotomy and peri-operative open-chest management...
- Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation
Gary An
Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
Theor Biol Med Model 5:11. 2008
..They are intended to translate the knowledge derived from in vitro models of acute inflammation to clinically relevant phenomenon such as multiple organ failure...
- Challenges and rewards on the road to translational systems biology in acute illness: four case reports from interdisciplinary teams
Gary An
Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
J Crit Care 22:169-75. 2007
..However, the development of these groups must overcome domain-specific barriers to communication and understanding...
- Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling
Gary An
Department of Trauma, Cook County Hospital, Chicago, IL 60612, USA
J Crit Care 21:105-10; discussion 110-1. 2006
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- In silico and in vivo approach to elucidate the inflammatory complexity of CD14-deficient mice
Jose M Prince
Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
Mol Med 12:88-96. 2006
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- The role of initial trauma in the host's response to injury and hemorrhage: insights from a correlation of mathematical simulations and hepatic transcriptomic analysis
Claudio E Lagoa
Department of Surgery, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15213, USA
Shock 26:592-600. 2006
..Mathematical simulations and DNA microarrays, both systems biology tools, may provide valuable insight into the complex global physiological interactions that occur in response to trauma and hemorrhagic shock...
- In silico experiments of existing and hypothetical cytokine-directed clinical trials using agent-based modeling
Gary An
Department of Trauma, Cook County Hospital, Chicago, IL, USA
Crit Care Med 32:2050-60. 2004
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- Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patient
Gary An
Department of Surgery, Northwestern University, Chicago, IL 60611, USA
J Burn Care Res 29:277-85. 2008
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- Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning
Gary C An
Department of Surgery, Northwestern University, Chicago, IL 60611, USA
Math Biosci 217:53-63. 2009
..This approach is termed 'dynamic knowledge representation,' and is intended to be an integrated component of the iterative cycle of scientific discovery...
- Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research
Gary C An
Department of Surgery, Division of Trauma Critical Care, Northwestern University, Chicago, Illinois 60622, USA
Wound Repair Regen 18:8-12. 2010
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- In silico models of acute inflammation in animals
Yoram Vodovotz
Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
Shock 26:235-44. 2006
..Mathematical modeling may provide insights into the complex dynamics of acute inflammation in a manner that can be tested in vivo using many fewer animals than has been possible previously...
- Translational systems approaches to the biology of inflammation and healing
Yoram Vodovotz
Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
Immunopharmacol Immunotoxicol 32:181-95. 2010
..This plethora of computational and intertwined experimental/engineering approaches is the cornerstone of Translational Systems Biology approaches for inflammatory diseases...
- Mechanistic simulations of inflammation: current state and future prospects
Yoram Vodovotz
Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
Math Biosci 217:1-10. 2009
..Here we discuss the state of this emerging field. We note several common features of inflammation models, as well as challenges and prospects for future studies...
- An adequately robust early TNF-alpha response is a hallmark of survival following trauma/hemorrhage
Rajaie Namas
Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
PLoS ONE 4:e8406. 2009
..Trauma/hemorrhagic shock (T/HS) results in cytokine-mediated acute inflammation that is generally considered detrimental...
- Mathematical models of the acute inflammatory response
Yoram Vodovotz
Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
Curr Opin Crit Care 10:383-90. 2004
..There is a growing recognition that the complexity of the acute inflammatory response precludes the efficient development of therapies for sepsis and multiple organ failure until systems approaches are brought to bear on this problem...
- Dynamic knowledge representation using agent-based modeling: ontology instantiation and verification of conceptual models
Gary An
Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
Methods Mol Biol 500:445-68. 2009
..Thus, utilized in this fashion, ABM can provide a powerful adjunct to other computational methods within the research process, as well as providing a metamodeling framework to enhance the evolution of biomedical ontologies...
- Evidence-based modeling of critical illness: an initial consensus from the Society for Complexity in Acute Illness
Yoram Vodovotz
Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
J Crit Care 22:77-84. 2007
..Accordingly, SCAI identified a need for and carried out a critical appraisal of DMM as currently used in the setting of acute illness...
- Closing the scientific loop: bridging correlation and causality in the petaflop age
Gary An
Section of General Surgery, Department of Surgery, University of Chicago, Chicago, IL 60637, USA
Sci Transl Med 2:41ps34. 2010
..This combination provides a roadmap for closing the scientific loop between correlation and causality, a necessary step if translational endeavors are to succeed...
- A model of TLR4 signaling and tolerance using a qualitative, particle-event-based method: introduction of spatially configured stochastic reaction chambers (SCSRC)
Gary An
Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
Math Biosci 217:43-52. 2009
..Presented herein is an example of the SCSRC as applied to Toll-like receptor (TLR) 4 signaling and the inflammatory response...
- Translational systems biology of inflammation
Yoram Vodovotz
Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
PLoS Comput Biol 4:e1000014. 2008
..Future advances in understanding complex medical problems are highly dependent on methodological advances and integration of the computational systems biology community with biologists and clinicians...
- Mathematical modeling in medicine: a means, not an end
Gary An
Crit Care Med 33:253-4. 2005
