Literature DB >> 20835989

Agent-based models in translational systems biology.

Gary An1,2, Qi Mi3,2, Joyeeta Dutta-Moscato4,2, Yoram Vodovotz4,2.   

Abstract

Effective translational methodologies for knowledge representation are needed in order to make strides against the constellation of diseases that affect the world today. These diseases are defined by their mechanistic complexity, redundancy, and nonlinearity. Translational systems biology aims to harness the power of computational simulation to streamline drug/device design, simulate clinical trials, and eventually to predict the effects of drugs on individuals. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggests that this modeling framework is well suited for translational systems biology. This review describes agent-based modeling and gives examples of its translational applications in the context of acute inflammation and wound healing.

Entities:  

Mesh：

Year:  2009        PMID： 20835989      PMCID： PMC3640333          DOI： 10.1002/wsbm.45

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev Syst Biol Med        ISSN： 1939-005X


  48 in total

1.  Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer.

Authors:  Le Zhang; Chaitanya A Athale; Thomas S Deisboeck
Journal:  J Theor Biol       Date:  2006-07-27       Impact factor: 2.691

2.  In silico experiments of existing and hypothetical cytokine-directed clinical trials using agent-based modeling.

Authors:  Gary An
Journal:  Crit Care Med       Date:  2004-10       Impact factor: 7.598

3.  A life-like virtual cell membrane using discrete automata.

Authors:  Gordon Broderick; Melania Ru'aini; Eugene Chan; Michael J Ellison
Journal:  In Silico Biol       Date:  2005

4.  An agent-based computational approach for representing aspects of in vitro multi-cellular tumor spheroid growth.

Authors:  Song Chen; Suman Ganguli; C Anthony Hunt
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2004

5.  Simulating in vitro epithelial morphogenesis in multiple environments.

Authors:  M R Grant; S H J Kim; C A Hunt
Journal:  Comput Syst Bioinformatics Conf       Date:  2006

6.  Dichotomies between computational and mathematical models.

Authors:  C Anthony Hunt; Glen E P Ropella; Sunwoo Park; Jesse Engelberg
Journal:  Nat Biotechnol       Date:  2008-07       Impact factor: 54.908

7.  Simulating the hallmarks of cancer.

Authors:  Robert G Abbott; Stephanie Forrest; Kenneth J Pienta
Journal:  Artif Life       Date:  2006       Impact factor: 0.667

Review 8.  Cancer as an evolutionary and ecological process.

Authors:  Lauren M F Merlo; John W Pepper; Brian J Reid; Carlo C Maley
Journal:  Nat Rev Cancer       Date:  2006-11-16       Impact factor: 60.716

Review 9.  Mechanistic simulations of inflammation: current state and future prospects.

Authors:  Yoram Vodovotz; Gregory Constantine; Jonathan Rubin; Marie Csete; Eberhard O Voit; Gary An
Journal:  Math Biosci       Date:  2008-08-26       Impact factor: 2.144

10.  Essential operating principles for tumor spheroid growth.

Authors:  Jesse A Engelberg; Glen E P Ropella; C Anthony Hunt
Journal:  BMC Syst Biol       Date:  2008-12-23
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  94 in total

1.  Biosimulation of inflammation and healing in surgically injured vocal folds.

Authors:  Nicole Y K Li; Yoram Vodovotz; Patricia A Hebda; Katherine Verdolini Abbott
Journal:  Ann Otol Rhinol Laryngol       Date:  2010-06       Impact factor: 1.547

Review 2.  Translational systems approaches to the biology of inflammation and healing.

Authors:  Yoram Vodovotz; Gregory Constantine; James Faeder; Qi Mi; Jonathan Rubin; John Bartels; Joydeep Sarkar; Robert H Squires; David O Okonkwo; Jörg Gerlach; Ruben Zamora; Shirley Luckhart; Bard Ermentrout; Gary An
Journal:  Immunopharmacol Immunotoxicol       Date:  2010-06       Impact factor: 2.730

Review 3.  The role of the microbiome in exacerbations of chronic lung diseases.

Authors:  Robert P Dickson; Fernando J Martinez; Gary B Huffnagle
Journal:  Lancet       Date:  2014-08-23       Impact factor: 79.321

Review 4.  Issues in Reproducible Simulation Research.

Authors:  B G Fitzpatrick
Journal:  Bull Math Biol       Date:  2018-09-06       Impact factor: 1.758

5.  Computational Modeling of Inflammation and Wound Healing.

Authors:  Cordelia Ziraldo; Qi Mi; Gary An; Yoram Vodovotz
Journal:  Adv Wound Care (New Rochelle)       Date:  2013-11       Impact factor: 4.730

6.  Using an Agent-Based Model to Examine the Role of Dynamic Bacterial Virulence Potential in the Pathogenesis of Surgical Site Infection.

Authors:  Vissagan Gopalakrishnan; Moses Kim; Gary An
Journal:  Adv Wound Care (New Rochelle)       Date:  2013-11       Impact factor: 4.730

7.  Immature oxidative stress management as a unifying principle in the pathogenesis of necrotizing enterocolitis: insights from an agent-based model.

Authors:  Moses Kim; Scott Christley; John C Alverdy; Donald Liu; Gary An
Journal:  Surg Infect (Larchmt)       Date:  2012-01-04       Impact factor: 2.150

8.  Linking changes in epithelial morphogenesis to cancer mutations using computational modeling.

Authors:  Katarzyna A Rejniak; Shizhen E Wang; Nicole S Bryce; Hang Chang; Bahram Parvin; Jerome Jourquin; Lourdes Estrada; Joe W Gray; Carlos L Arteaga; Alissa M Weaver; Vito Quaranta; Alexander R A Anderson
Journal:  PLoS Comput Biol       Date:  2010-08-26       Impact factor: 4.475

9.  Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions.

Authors:  Elsje Pienaar; William M Matern; Jennifer J Linderman; Joel S Bader; Denise E Kirschner
Journal:  Infect Immun       Date:  2016-04-22       Impact factor: 3.441

10.  Multi-scale Modeling of the Cardiovascular System: Disease Development, Progression, and Clinical Intervention.

Authors:  Yanhang Zhang; Victor H Barocas; Scott A Berceli; Colleen E Clancy; David M Eckmann; Marc Garbey; Ghassan S Kassab; Donna R Lochner; Andrew D McCulloch; Roger Tran-Son-Tay; Natalia A Trayanova
Journal:  Ann Biomed Eng       Date:  2016-05-02       Impact factor: 3.934
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