Time Lapse Simulations of Agent Based Models
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I Identifying control mechanism of granuloma formation during M. tuberculosis infection using an agent based model
Jose L. Segovia-Juarez, Suman Ganguli, and Denise Kirschner, Journal of Theoretical Biology. Vol. 231, Issue 3, pp.357-376, 2004.
Granuloma Time-Lapse Simulations

II A comparison of random vs. chemotaxis-driven contacts of T-cells with dendritic cells during repertoire scanning
Thomas Riggs, Adrienne Walts, Nicolas Perry, Laura Bickle, Jennifer N. Lynch, Amy Myers, Joanne Flynn, Jennifer J. Linderman, Mark J. Miller, and Denise E. Kirschner, Journal of Theoretical Biology., Vol. 250, Issue 4, pp.732-751, 2008., doi:10.1016/j.jtbi.2007.10.015, PMID: 18068193, PMCID: PMC2548315
T cell Chemotaxis Time Lapse Simulations

III Characterizing the dynamics of CD4+ T cell priming within a lymph node
Jennifer J. Linderman, Thomas Riggs, Manjusha Pande, Simeone Marino, and Denise E. Kirschner, Journal of Immunology, 2010, 184: pp 2873-85, doi:10.4049/jimmunol.0903117, PMID: 20154206, PMCID: 3153313
LN T-zone Time Lapse Simulations

IV A Synergy between Individual TNF-Dependent Functions Determines Granuloma Performance for Controlling Mycobacterium tuberculosis Infection
J. Christian Ray, Joanne L. Flynn, and Denise Kirschner, Journal of Immunology, 2009, 182: pp 3706-3717, PMID: 19265149, PMCID: 3182770
Granuloma Time-Lapse Simulations

V Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation
Fallahi-Sichani M, El-Kebir M, Marino S, Kirschner DE, Linderman JJ., J Immunol. 2011 Mar 15;186(6):3472-83, PMID: 21321109, PMCID: 3127549.
Multiscale Granuloma Simulations

VI Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability
Mohammad Fallahi-Sichani, JoAnne L. Flynn, Jennifer J. Linderman, Denise E. Kirschner, The Journal of Immunology, 188, no. 7 (2012): 3169-78., PMID: 22379032, PMCID: 3311778
Multiscale Anti-TNF Drug Simulations

VII Microenvironments in Tuberculous Granulomas Are Delineated by Distinct Populations of Macrophage Subsets and Expression of Nitric Oxide Synthase and Arginase Isoforms
Joshua T. Mattila, Olabisi O. Ojo, Diane Kepka-Lenhart, Simeone Marino, Denise E. Kirschner, Laura E. Via, Clifton E. Barry, III, Korean MD, Philana Ling Lin, Edwin Klein, Sidney M. Morris Jr., JoAnne L. Flynn, J Immunol, July 15th 2013, 191, pages 773-784, PMID: 23749634, PMCID: 3746594
Multiscale M1-M2 Granuloma Simulations

VIII Predicting lymph node output efficiency through systems biology
Chang Gong, Joshua T. Mattila, Mark Miller, JoAnne L. Flynn, Jennifer J. Linderman, D. Kirschner, Journal of Theoretical Biology, Volume 335, October 21 2013, Pages 169-184, ePUB: June 29, 2013, PMID: 23816876, PMCID: 3783027
3d LN Simulations

IX A computational tool integrating host immunity with antibiotic dynamics to study tuberculosis treatment
Elsje Pienaar, Nicholas A. Cilfone, Philana Ling Lin, Veronique Dartois, Joshua T. Mattila, J. Russell Butler, JoAnne L. Flynn, Denise E. Kirschner, Jennifer J. Linderman, Journal of Theoretical Biology (2015), pp. 166-179, published online: 24-DEC-2014, DOI: 10.1016/j.jtbi.2014.11.021, PMID: 25497475, PMCID: 4332617
Antibiotic Treatment Simulations

X A systems pharmacology approach towards the design of inhaled formulations of rifampicin and isoniazid for treatment of tuberculosis
Nicholas A. Cilfone, Denise E. Kirschner, and Jennifer J. Linderman, 2015, Pharmacometrics and Systems Pharmacology, DOI: 10.1002/psp4.22, PMID: 26225241, PMCID: 4394619
Inhaled Antibiotic Treatment Simulations



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