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For: Warrender C, Forrest S, Koster F. Modeling intercellular interactions in early Mycobacterium infection. Bull Math Biol 2006;68:2233-61. [PMID: 17086496 DOI: 10.1007/s11538-006-9103-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 02/15/2006] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Petrucciani A, Hoerter A, Kotze L, Du Plessis N, Pienaar E. In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models. PLoS One 2024;19:e0299107. [PMID: 38517920 PMCID: PMC10959380 DOI: 10.1371/journal.pone.0299107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/05/2024] [Indexed: 03/24/2024]  Open
2
Acharya V, Choi D, Yener B, Beamer G. Prediction of Tuberculosis From Lung Tissue Images of Diversity Outbred Mice Using Jump Knowledge Based Cell Graph Neural Network. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2024;12:17164-17194. [PMID: 38515959 PMCID: PMC10956573 DOI: 10.1109/access.2024.3359989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
3
Darquenne C, Borojeni AA, Colebank MJ, Forest MG, Madas BG, Tawhai M, Jiang Y. Aerosol Transport Modeling: The Key Link Between Lung Infections of Individuals and Populations. Front Physiol 2022;13:923945. [PMID: 35795643 PMCID: PMC9251577 DOI: 10.3389/fphys.2022.923945] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/24/2022] [Indexed: 12/18/2022]  Open
4
Chen A, Wessler T, Daftari K, Hinton K, Boucher RC, Pickles R, Freeman R, Lai SK, Forest MG. Modeling insights into SARS-CoV-2 respiratory tract infections prior to immune protection. Biophys J 2022;121:1619-1631. [PMID: 35378080 PMCID: PMC8975607 DOI: 10.1016/j.bpj.2022.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/27/2021] [Accepted: 03/31/2022] [Indexed: 11/19/2022]  Open
5
Moses ME, Hofmeyr S, Cannon JL, Andrews A, Gridley R, Hinga M, Leyba K, Pribisova A, Surjadidjaja V, Tasnim H, Forrest S. Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection. PLoS Comput Biol 2021;17:e1009735. [PMID: 34941862 PMCID: PMC8740970 DOI: 10.1371/journal.pcbi.1009735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 01/07/2022] [Accepted: 12/09/2021] [Indexed: 01/03/2023]  Open
6
Lafuente-Gracia L, Borgiani E, Nasello G, Geris L. Towards in silico Models of the Inflammatory Response in Bone Fracture Healing. Front Bioeng Biotechnol 2021;9:703725. [PMID: 34660547 PMCID: PMC8514728 DOI: 10.3389/fbioe.2021.703725] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/07/2021] [Indexed: 12/21/2022]  Open
7
An agent-based simulator for the gastrointestinal pathway of Listeria monocytogenes. Int J Food Microbiol 2020;333:108776. [PMID: 32693315 DOI: 10.1016/j.ijfoodmicro.2020.108776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 11/29/2019] [Accepted: 06/28/2020] [Indexed: 12/17/2022]
8
Bayani A, Dunster JL, Crofts JJ, Nelson MR. Spatial considerations in the resolution of inflammation: Elucidating leukocyte interactions via an experimentally-calibrated agent-based model. PLoS Comput Biol 2020;16:e1008413. [PMID: 33137107 PMCID: PMC7660912 DOI: 10.1371/journal.pcbi.1008413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 11/12/2020] [Accepted: 10/01/2020] [Indexed: 01/13/2023]  Open
9
Best A, Jubrail J, Boots M, Dockrell D, Marriott H. A mathematical model shows macrophages delay Staphylococcus aureus replication, but limitations in microbicidal capacity restrict bacterial clearance. J Theor Biol 2020;497:110256. [PMID: 32304686 PMCID: PMC7262596 DOI: 10.1016/j.jtbi.2020.110256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 11/29/2022]
10
Bayani A, Dunster JL, Crofts JJ, Nelson MR. Mechanisms and Points of Control in the Spread of Inflammation: A Mathematical Investigation. Bull Math Biol 2020;82:45. [PMID: 32222839 PMCID: PMC7103018 DOI: 10.1007/s11538-020-00709-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/14/2020] [Indexed: 02/07/2023]
11
Shinde SB, Kurhekar MP. Review of the systems biology of the immune system using agent-based models. IET Syst Biol 2019;12:83-92. [PMID: 29745901 DOI: 10.1049/iet-syb.2017.0073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
12
Norton KA, Gong C, Jamalian S, Popel AS. Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment. Processes (Basel) 2019;7:37. [PMID: 30701168 PMCID: PMC6349239 DOI: 10.3390/pr7010037] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
13
Read MN, Alden K, Timmis J, Andrews PS. Strategies for calibrating models of biology. Brief Bioinform 2018;21:24-35. [PMID: 30239570 DOI: 10.1093/bib/bby092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/10/2018] [Accepted: 08/27/2018] [Indexed: 11/14/2022]  Open
14
Bhavanam S, Rayat GR, Keelan M, Kunimoto D, Drews SJ. Understanding the pathophysiology of the human TB lung granuloma using in vitro granuloma models. Future Microbiol 2016;11:1073-89. [PMID: 27501829 DOI: 10.2217/fmb-2016-0005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
15
Levin D, Forrest S, Banerjee S, Clay C, Cannon J, Moses M, Koster F. A spatial model of the efficiency of T cell search in the influenza-infected lung. J Theor Biol 2016;398:52-63. [PMID: 26920246 DOI: 10.1016/j.jtbi.2016.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 02/08/2016] [Accepted: 02/12/2016] [Indexed: 11/16/2022]
16
Sershen CL, Plimpton SJ, May EE. Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach. Front Cell Infect Microbiol 2016;6:6. [PMID: 26913242 PMCID: PMC4753379 DOI: 10.3389/fcimb.2016.00006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 01/13/2016] [Indexed: 11/17/2022]  Open
17
Coupling of Petri Net Models of the Mycobacterial Infection Process and Innate Immune Response. COMPUTATION 2015. [DOI: 10.3390/computation3020150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
18
The importance of liver microcirculation in promoting autoimmune hepatitis via maintaining an inflammatory cytokine milieu--a mathematical model study. J Theor Biol 2014;348:33-46. [PMID: 24486232 DOI: 10.1016/j.jtbi.2014.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 11/22/2013] [Accepted: 01/15/2014] [Indexed: 01/22/2023]
19
An agent-based model of cellular dynamics and circadian variability in human endotoxemia. PLoS One 2013;8:e55550. [PMID: 23383223 PMCID: PMC3559552 DOI: 10.1371/journal.pone.0055550] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 12/30/2012] [Indexed: 01/01/2023]  Open
20
Narang V, Decraene J, Wong SY, Aiswarya BS, Wasem AR, Leong SR, Gouaillard A. Systems immunology: a survey of modeling formalisms, applications and simulation tools. Immunol Res 2012;53:251-65. [PMID: 22528121 DOI: 10.1007/s12026-012-8305-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
21
Seal JB, Alverdy JC, Zaborina O, An G. Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis. Theor Biol Med Model 2011;8:33. [PMID: 21929759 PMCID: PMC3184268 DOI: 10.1186/1742-4682-8-33] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/19/2011] [Indexed: 01/07/2023]  Open
22
Marino S, Linderman J, Kirschner DE. A multifaceted approach to modeling the immune response in tuberculosis. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2011;3:479-89. [PMID: 21197656 PMCID: PMC3110521 DOI: 10.1002/wsbm.131] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
23
Fallahi-Sichani M, El-Kebir M, Marino S, Kirschner DE, Linderman JJ. Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011;186:3472-83. [PMID: 21321109 PMCID: PMC3127549 DOI: 10.4049/jimmunol.1003299] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
24
Higher level of replication efficiency of 2009 (H1N1) pandemic influenza virus than those of seasonal and avian strains: kinetics from epithelial cell culture and computational modeling. J Virol 2010;85:1125-35. [PMID: 21068247 DOI: 10.1128/jvi.01722-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
25
Kirschner DE, Young D, Flynn JL. Tuberculosis: global approaches to a global disease. Curr Opin Biotechnol 2010;21:524-31. [PMID: 20637596 PMCID: PMC2943033 DOI: 10.1016/j.copbio.2010.06.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Revised: 06/16/2010] [Accepted: 06/16/2010] [Indexed: 10/19/2022]
26
Bauer AL, Beauchemin CAA, Perelson AS. Agent-based modeling of host-pathogen systems: The successes and challenges. Inf Sci (N Y) 2009;179:1379-1389. [PMID: 20161146 PMCID: PMC2731970 DOI: 10.1016/j.ins.2008.11.012] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 11/10/2008] [Indexed: 02/02/2023]
27
Ray JCJ, Flynn JL, Kirschner DE. Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2009;182:3706-17. [PMID: 19265149 PMCID: PMC3182770 DOI: 10.4049/jimmunol.0802297] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
28
Lello J, Hussell T. Functional group/guild modelling of inter-specific pathogen interactions: a potential tool for predicting the consequences of co-infection. Parasitology 2008;135:825-39. [PMID: 18477416 DOI: 10.1017/s0031182008000383] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
29
Forrest S, Beauchemin C. Computer immunology. Immunol Rev 2007;216:176-97. [PMID: 17367343 DOI: 10.1111/j.1600-065x.2007.00499.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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