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Volumn 6, Issue 4, 2014, Pages 289-309

Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models

Author keywords

[No Author keywords available]

Indexed keywords

CYTOKINE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TUMOR NECROSIS FACTOR ALPHA; TUMOR NECROSIS FACTOR RECEPTOR;

EID: 84902658640     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.1270     Document Type: Review
Times cited : (52)

References (106)
  • 1
    • 79953242705 scopus 로고    scopus 로고
    • How scientific models can explain
    • Bokulich A. How scientific models can explain. Synthese 2011, 180:33-45.
    • (2011) Synthese , vol.180 , pp. 33-45
    • Bokulich, A.1
  • 2
    • 62749163145 scopus 로고    scopus 로고
    • Thinking again about biological mechanisms
    • Darden L. Thinking again about biological mechanisms. Philos Sci 2008, 75:958-969.
    • (2008) Philos Sci , vol.75 , pp. 958-969
    • Darden, L.1
  • 3
    • 80255123663 scopus 로고    scopus 로고
    • Models and mechanisms in psychological explanation
    • Weiskopf DA. Models and mechanisms in psychological explanation. Synthese 2011, 183:313-338.
    • (2011) Synthese , vol.183 , pp. 313-338
    • Weiskopf, D.A.1
  • 4
    • 33751524084 scopus 로고    scopus 로고
    • When mechanistic models explain
    • Craver CF. When mechanistic models explain. Synthese 2006, 153:355-376.
    • (2006) Synthese , vol.153 , pp. 355-376
    • Craver, C.F.1
  • 5
    • 84870250065 scopus 로고    scopus 로고
    • Interweaving categories: styles, paradigms, and models
    • Winther RG. Interweaving categories: styles, paradigms, and models. Stud Hist Philos Sci A 2012, 43:628-639.
    • (2012) Stud Hist Philos Sci A , vol.43 , pp. 628-639
    • Winther, R.G.1
  • 8
    • 79953890886 scopus 로고    scopus 로고
    • Moving beyond in silico tools to in silico science in support of drug development research
    • Hunt CA, Ropella GEP. Moving beyond in silico tools to in silico science in support of drug development research. Drug Dev Res 2011, 72:153-161.
    • (2011) Drug Dev Res , vol.72 , pp. 153-161
    • Hunt, C.A.1    Ropella, G.E.P.2
  • 9
    • 84879287149 scopus 로고    scopus 로고
    • Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity
    • doi: 10.1002/wsbm.1222.
    • Hunt CA, Kennedy RC, Kim SHJ, Ropella GEP. Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity. WIREs Syst Biol Med 2013, 5:461-480. doi: 10.1002/wsbm.1222.
    • (2013) WIREs Syst Biol Med , vol.5 , pp. 461-480
    • Hunt, C.A.1    Kennedy, R.C.2    Kim, S.H.J.3    Ropella, G.E.P.4
  • 10
    • 84937217390 scopus 로고    scopus 로고
    • AToM(3): a tool for multi-formalism and meta-modelling
    • de Lara J, Vangheluwe H. AToM(3): a tool for multi-formalism and meta-modelling. Lect Notes Comput Sci 2002, 2306:174-188.
    • (2002) Lect Notes Comput Sci , vol.2306 , pp. 174-188
    • de Lara, J.1    Vangheluwe, H.2
  • 11
    • 79953194081 scopus 로고    scopus 로고
    • 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. Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation. J Immunol 2011, 186:3472-3483.
    • (2011) J Immunol , vol.186 , pp. 3472-3483
    • Fallahi-Sichani, M.1    El-Kebir, M.2    Marino, S.3    Kirschner, D.E.4    Linderman, J.J.5
  • 12
    • 77649218593 scopus 로고    scopus 로고
    • Computational complementation: a modelling approach to study signalling mechanisms during legume autoregulation of nodulation
    • Han LQ, Hanan J, Gresshoff PM. Computational complementation: a modelling approach to study signalling mechanisms during legume autoregulation of nodulation. PLoS Comput Biol 2010, 6:e1000685.
    • (2010) PLoS Comput Biol , vol.6
    • Han, L.Q.1    Hanan, J.2    Gresshoff, P.M.3
  • 13
    • 0346497702 scopus 로고    scopus 로고
    • A physiologically based approach for the estimation of recirculatory parameters
    • Karalis V, Dokoumetzidis A, Macheras P. A physiologically based approach for the estimation of recirculatory parameters. J Pharmacol Exp Ther 2004, 308:198-205.
    • (2004) J Pharmacol Exp Ther , vol.308 , pp. 198-205
    • Karalis, V.1    Dokoumetzidis, A.2    Macheras, P.3
  • 14
    • 77649207414 scopus 로고    scopus 로고
    • Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion
    • Tang J, Hunt CA. Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion. PLoS Comput Biol 2010, 6:e1000681.
    • (2010) PLoS Comput Biol , vol.6
    • Tang, J.1    Hunt, C.A.2
  • 15
    • 59149096719 scopus 로고    scopus 로고
    • Computational strategies unravel and trace how liver disease changes hepatic drug disposition
    • Park S, Ropella GE, Kim SH, Roberts MS, Hunt CA. Computational strategies unravel and trace how liver disease changes hepatic drug disposition. J Pharmacol Exp Ther 2009, 328:294-305.
    • (2009) J Pharmacol Exp Ther , vol.328 , pp. 294-305
    • Park, S.1    Ropella, G.E.2    Kim, S.H.3    Roberts, M.S.4    Hunt, C.A.5
  • 16
    • 84902672728 scopus 로고    scopus 로고
    • A systems biology approach for understanding granuloma formation and function in tuberculosis
    • In: McFadden J, Beste DJV, Kierzek AM, eds. . New York, NY: Springer; .
    • Fallahi-Sichani M, Marino S, Flynn JL, Linderman JJ, Kirschner DE. A systems biology approach for understanding granuloma formation and function in tuberculosis. In: McFadden J, Beste DJV, Kierzek AM, eds. Systems Biology of Tuberculosis. New York, NY: Springer; 2012.
    • (2012) Systems Biology of Tuberculosis
    • Fallahi-Sichani, M.1    Marino, S.2    Flynn, J.L.3    Linderman, J.J.4    Kirschner, D.E.5
  • 19
    • 79960158150 scopus 로고    scopus 로고
    • The use of multiscale systems biology approaches to facilitate understanding of complex control systems for airway protection
    • Bolser DC, Pitts TE, Morris KF. The use of multiscale systems biology approaches to facilitate understanding of complex control systems for airway protection. Curr Opin Pharmacol 2011, 11:272-277.
    • (2011) Curr Opin Pharmacol , vol.11 , pp. 272-277
    • Bolser, D.C.1    Pitts, T.E.2    Morris, K.F.3
  • 20
    • 80054770583 scopus 로고    scopus 로고
    • Multi-scale computational models of familial hypertrophic cardiomyopathy: genotype to phenotype
    • Campbell SG, McCulloch AD. Multi-scale computational models of familial hypertrophic cardiomyopathy: genotype to phenotype. J R Soc Interface 2011, 8:1550-1561.
    • (2011) J R Soc Interface , vol.8 , pp. 1550-1561
    • Campbell, S.G.1    McCulloch, A.D.2
  • 21
    • 85047688868 scopus 로고    scopus 로고
    • Multiscale systems biology and physics of thrombosis under flow
    • Flamm MH, Diamond SL. Multiscale systems biology and physics of thrombosis under flow. Ann Biomed Eng 2012, 40:2355-2364.
    • (2012) Ann Biomed Eng , vol.40 , pp. 2355-2364
    • Flamm, M.H.1    Diamond, S.L.2
  • 25
    • 84880559564 scopus 로고    scopus 로고
    • Multiscale computational models of complex biological systems
    • Walpole J, Papin JA, Peirce SM. Multiscale computational models of complex biological systems. Annu Rev Biomed Eng 2013, 15:137-154.
    • (2013) Annu Rev Biomed Eng , vol.15 , pp. 137-154
    • Walpole, J.1    Papin, J.A.2    Peirce, S.M.3
  • 26
    • 84868351003 scopus 로고    scopus 로고
    • Multiscale modeling of platelet adhesion and thrombus growth
    • Wang W, King MR. Multiscale modeling of platelet adhesion and thrombus growth. Ann Biomed Eng 2012, 40:2345-2354.
    • (2012) Ann Biomed Eng , vol.40 , pp. 2345-2354
    • Wang, W.1    King, M.R.2
  • 27
    • 33044506498 scopus 로고    scopus 로고
    • Modelling biological complexity: a physical scientist's perspective
    • Coveney PV, Fowler PW. Modelling biological complexity: a physical scientist's perspective. J R Soc Interface 2005, 2:267-280.
    • (2005) J R Soc Interface , vol.2 , pp. 267-280
    • Coveney, P.V.1    Fowler, P.W.2
  • 28
    • 84902649698 scopus 로고    scopus 로고
    • The multi-scale immune response to pathogens: M. tuberculosis as an example
    • In: Flower D, Timmis J, eds. . New York: Springer;
    • Kirschner D. The multi-scale immune response to pathogens: M. tuberculosis as an example. In: Flower D, Timmis J, eds. In Silico Immunology. New York: Springer; 2007, 289-311.
    • (2007) In Silico Immunology , pp. 289-311
    • Kirschner, D.1
  • 29
    • 32644484370 scopus 로고    scopus 로고
    • A review of multiscale analysis: examples from systems biology, materials engineering, and other fluid-surface interacting systems
    • Vlachos DG. A review of multiscale analysis: examples from systems biology, materials engineering, and other fluid-surface interacting systems. Adv Chem Eng 2005, 30:1-61.
    • (2005) Adv Chem Eng , vol.30 , pp. 1-61
    • Vlachos, D.G.1
  • 31
    • 0033555859 scopus 로고    scopus 로고
    • Emergent properties of networks of biological signaling pathways
    • Bhalla US, Iyengar R. Emergent properties of networks of biological signaling pathways. Science 1999, 283:381-387.
    • (1999) Science , vol.283 , pp. 381-387
    • Bhalla, U.S.1    Iyengar, R.2
  • 32
    • 84890408904 scopus 로고    scopus 로고
    • Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems
    • doi: 10.1002/wsbm.1245.
    • Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. WIREs Syst Biol Med 2014, 6:13-36. doi: 10.1002/wsbm.1245.
    • (2014) WIREs Syst Biol Med , vol.6 , pp. 13-36
    • Chylek, L.A.1    Harris, L.A.2    Tung, C.S.3    Faeder, J.R.4    Lopez, C.F.5    Hlavacek, W.S.6
  • 35
    • 84859994220 scopus 로고    scopus 로고
    • Computational approaches for analyzing information flow in biological networks
    • Kholodenko B, Yaffe MB, Kolch W. Computational approaches for analyzing information flow in biological networks. Sci Signal 2012, 5:re1.
    • (2012) Sci Signal , vol.5
    • Kholodenko, B.1    Yaffe, M.B.2    Kolch, W.3
  • 36
    • 84878041846 scopus 로고    scopus 로고
    • Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits
    • Marchisio MA, Colaiacovo M, Whitehead E, Stelling J. Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. BMC Syst Biol 2013, 7:42.
    • (2013) BMC Syst Biol , vol.7 , pp. 42
    • Marchisio, M.A.1    Colaiacovo, M.2    Whitehead, E.3    Stelling, J.4
  • 37
    • 84886490024 scopus 로고    scopus 로고
    • Reliable prediction of complex phenotypes from a modular design in free energy space: an extensive exploration of the lac operon
    • Vilar JM, Saiz L. Reliable prediction of complex phenotypes from a modular design in free energy space: an extensive exploration of the lac operon. ACS Synth Biol 2013, 2:576-586.
    • (2013) ACS Synth Biol , vol.2 , pp. 576-586
    • Vilar, J.M.1    Saiz, L.2
  • 38
    • 76749131557 scopus 로고    scopus 로고
    • Mechanistic insight from in silico pharmacokinetic experiments: roles of P-glycoprotein, Cyp3A4 enzymes, and microenvironments
    • Lam TN, Hunt CA. Mechanistic insight from in silico pharmacokinetic experiments: roles of P-glycoprotein, Cyp3A4 enzymes, and microenvironments. J Pharmacol Exp Ther 2010, 332:398-412.
    • (2010) J Pharmacol Exp Ther , vol.332 , pp. 398-412
    • Lam, T.N.1    Hunt, C.A.2
  • 40
    • 84858853541 scopus 로고    scopus 로고
    • Integrating intracellular dynamics using CompuCell3D and Bionetsolver: applications to multiscale modelling of cancer cell growth and invasion
    • Andasari V, Roper RT, Swat MH, Chaplain MA. Integrating intracellular dynamics using CompuCell3D and Bionetsolver: applications to multiscale modelling of cancer cell growth and invasion. PLoS One 2012, 7:e33726.
    • (2012) PLoS One , vol.7
    • Andasari, V.1    Roper, R.T.2    Swat, M.H.3    Chaplain, M.A.4
  • 43
    • 34547546965 scopus 로고    scopus 로고
    • Reproducible computational experiments using SCons. In: International Conference on Acoustics, Speech, 1257-1260.
    • Fomel S, Hennenfent G. Reproducible computational experiments using SCons. In: International Conference on Acoustics, Speech, 2007, 1257-1260.
    • (2007)
    • Fomel, S.1    Hennenfent, G.2
  • 44
    • 75649122581 scopus 로고    scopus 로고
    • Accessible reproducible research
    • Mesirov JP. Accessible reproducible research. Science 2010, 327:415-416.
    • (2010) Science , vol.327 , pp. 415-416
    • Mesirov, J.P.1
  • 46
    • 70149102312 scopus 로고    scopus 로고
    • Reproducible research and biostatistics
    • Peng RD. Reproducible research and biostatistics. Biostatistics 2009, 10:405-408.
    • (2009) Biostatistics , vol.10 , pp. 405-408
    • Peng, R.D.1
  • 47
    • 84902672730 scopus 로고    scopus 로고
    • The scientific method in practice: reproducibility in the computational sciences. MIT Sloan Research Paper 4773;, 10
    • Stodden V. The scientific method in practice: reproducibility in the computational sciences. MIT Sloan Research Paper 4773; 2010, 10
    • (2010)
    • Stodden, V.1
  • 48
    • 45449094504 scopus 로고    scopus 로고
    • A methodology for performing global uncertainty and sensitivity analysis in systems biology
    • Marino S, Hogue IB, Ray CJ, Kirschner DE. A methodology for performing global uncertainty and sensitivity analysis in systems biology. J Theor Biol 2008, 254:178-196.
    • (2008) J Theor Biol , vol.254 , pp. 178-196
    • Marino, S.1    Hogue, I.B.2    Ray, C.J.3    Kirschner, D.E.4
  • 49
    • 84895558372 scopus 로고    scopus 로고
    • Harnessing the heterogeneity of T cell differentiation fate to fine-tune generation of effector and memory T cells
    • Gong C, Linderman JJ, Kirschner DE. Harnessing the heterogeneity of T cell differentiation fate to fine-tune generation of effector and memory T cells. Front Immunol 2013, 5:57.
    • (2013) Front Immunol , vol.5 , pp. 57
    • Gong, C.1    Linderman, J.J.2    Kirschner, D.E.3
  • 50
    • 0027812507 scopus 로고
    • Families of models that cross levels of resolution - issues for design, calibration and management. In: 1993 Winter Simulation Conference Proceedings, 1003-1012.
    • Davis PK, Hillestad R. Families of models that cross levels of resolution - issues for design, calibration and management. In: 1993 Winter Simulation Conference Proceedings, 1993, 1003-1012.
    • (1993)
    • Davis, P.K.1    Hillestad, R.2
  • 51
    • 0030652179 scopus 로고    scopus 로고
    • MRE: a flexible approach to multi-resolution modeling. In: 11th Workshop on Parallel and Distributed Simulation, Proceedings, 156-163.
    • Natrajan A, Reynolds PF, Srinivasan S. MRE: a flexible approach to multi-resolution modeling. In: 11th Workshop on Parallel and Distributed Simulation, Proceedings, 1997, 156-163.
    • (1997)
    • Natrajan, A.1    Reynolds, P.F.2    Srinivasan, S.3
  • 52
    • 0036031533 scopus 로고    scopus 로고
    • Developing improved metamodels by combining phenomenological reasoning with statistical methods
    • Bigelow JH, Davis PK. Developing improved metamodels by combining phenomenological reasoning with statistical methods. Proc Soc Photo Opt Ins 2002, 4716:167-180.
    • (2002) Proc Soc Photo Opt Ins , vol.4716 , pp. 167-180
    • Bigelow, J.H.1    Davis, P.K.2
  • 53
    • 0034429255 scopus 로고    scopus 로고
    • Exploratory analysis enabled by multiresolultion, multiperspective modeling. In: Proceedings of the 2000 Winter Simulation Conference, Vols. 1 and 2, 293-302.
    • Davis PK. Exploratory analysis enabled by multiresolultion, multiperspective modeling. In: Proceedings of the 2000 Winter Simulation Conference, Vols. 1 and 2, 2000, 293-302.
    • (2000)
    • Davis, P.K.1
  • 54
    • 0034430882 scopus 로고    scopus 로고
    • Composable simulations. In: Proceedings of the 2000 Winter Simulation Conference, Vols. 1 and 2, 1577-1584.
    • Kasputis S, Ng HC. Composable simulations. In: Proceedings of the 2000 Winter Simulation Conference, Vols. 1 and 2, 2000, 1577-1584.
    • (2000)
    • Kasputis, S.1    Ng, H.C.2
  • 55
    • 33847721852 scopus 로고    scopus 로고
    • A methodology for developing simulation models of complex systems
    • Aumann CA. A methodology for developing simulation models of complex systems. Ecol Model 2007, 202:385-396.
    • (2007) Ecol Model , vol.202 , pp. 385-396
    • Aumann, C.A.1
  • 57
    • 34247470744 scopus 로고    scopus 로고
    • Simulation modelling of ecological hierarchies in constructive dynamical systems
    • Ratze C, Gillet F, Muller JP, Stoffel K. Simulation modelling of ecological hierarchies in constructive dynamical systems. Ecol Complex 2007, 4:13-25.
    • (2007) Ecol Complex , vol.4 , pp. 13-25
    • Ratze, C.1    Gillet, F.2    Muller, J.P.3    Stoffel, K.4
  • 58
    • 0037099993 scopus 로고    scopus 로고
    • A spatially explicit hierarchical approach to modeling complex ecological systems: theory and applications
    • Wu JG, David JL. A spatially explicit hierarchical approach to modeling complex ecological systems: theory and applications. Ecol Model 2002, 153:7-26.
    • (2002) Ecol Model , vol.153 , pp. 7-26
    • Wu, J.G.1    David, J.L.2
  • 59
    • 33947369051 scopus 로고    scopus 로고
    • Strategies and tactics in multiscale modeling of cell-to-organ systems
    • Bassingthwaighte JB, Chizeck HJ, Atlas LE. Strategies and tactics in multiscale modeling of cell-to-organ systems. Proc IEEE 2006, 94:819-831.
    • (2006) Proc IEEE , vol.94 , pp. 819-831
    • Bassingthwaighte, J.B.1    Chizeck, H.J.2    Atlas, L.E.3
  • 60
    • 73349122901 scopus 로고    scopus 로고
    • A multiformalism and multiresolution modelling environment: application to the cardiovascular system and its regulation
    • Hernandez AI, Le Rolle V, Defontaine A, Carrault G. A multiformalism and multiresolution modelling environment: application to the cardiovascular system and its regulation. Philos Trans R Soc A 2009, 367:4923-4940.
    • (2009) Philos Trans R Soc A , vol.367 , pp. 4923-4940
    • Hernandez, A.I.1    Le Rolle, V.2    Defontaine, A.3    Carrault, G.4
  • 62
    • 84902661815 scopus 로고    scopus 로고
    • Explanatory models versus predictive models: reduced complexity modeling in geomorphology
    • In: Vassilios Karakostos DD, ed. . New York, NY: Springer International Publishing;
    • Bokulich A. Explanatory models versus predictive models: reduced complexity modeling in geomorphology. In: Vassilios Karakostos DD, ed. EPSA11 Perspectives and Foundational Problems in Philosophy of Science. New York, NY: Springer International Publishing; 2013, 115-128.
    • (2013) EPSA11 Perspectives and Foundational Problems in Philosophy of Science , pp. 115-128
    • Bokulich, A.1
  • 63
    • 80955148324 scopus 로고    scopus 로고
    • A tentative taxonomy for predictive models in relation to their falsifiability
    • Viceconti M. A tentative taxonomy for predictive models in relation to their falsifiability. Philos Trans A Math Phys Eng Sci 2011, 369:4149-4161.
    • (2011) Philos Trans A Math Phys Eng Sci , vol.369 , pp. 4149-4161
    • Viceconti, M.1
  • 64
    • 80053362261 scopus 로고    scopus 로고
    • Relational grounding facilitates development of scientifically useful multiscale models
    • Hunt CA, Ropella GE, Lam T, Gewitz AD. Relational grounding facilitates development of scientifically useful multiscale models. Theor Biol Med Model 2011, 8:35.
    • (2011) Theor Biol Med Model , vol.8 , pp. 35
    • Hunt, C.A.1    Ropella, G.E.2    Lam, T.3    Gewitz, A.D.4
  • 65
    • 84902672723 scopus 로고    scopus 로고
    • Analogy and analogical reasoning. In: Zalta EN, ed. The Stanford Encyclopedia of Philosophy. Fall ed. Standford: The Metaphysics Research Lab, Center for the Study of Language and Information; . Available at:
    • Bartha P. Analogy and analogical reasoning. In: Zalta EN, ed. The Stanford Encyclopedia of Philosophy. Fall ed. Standford: The Metaphysics Research Lab, Center for the Study of Language and Information; 2013. Available at: http://plato.stanford.edu/archives/fall2013/entries/reasoning-analogy/.
    • (2013)
    • Bartha, P.1
  • 66
    • 20444419234 scopus 로고    scopus 로고
    • Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling
    • Conzelmann H, Saez-Rodriguez J, Sauter T, Bullinger E, Allgower F, Gilles ED. Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling. Syst Biol (Stevenage) 2004, 1:159-169.
    • (2004) Syst Biol (Stevenage) , vol.1 , pp. 159-169
    • Conzelmann, H.1    Saez-Rodriguez, J.2    Sauter, T.3    Bullinger, E.4    Allgower, F.5    Gilles, E.D.6
  • 67
    • 31144447003 scopus 로고    scopus 로고
    • Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module
    • Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S. Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module. Syst Biol (Stevenage) 2005, 152:229-242.
    • (2005) Syst Biol (Stevenage) , vol.152 , pp. 229-242
    • Maurya, M.R.1    Bornheimer, S.J.2    Venkatasubramanian, V.3    Subramaniam, S.4
  • 68
    • 30344478862 scopus 로고    scopus 로고
    • A systematic framework for the design of reduced-order models for signal transduction pathways from a control theoretic perspective
    • Maurya MR, Katare S, Patkar PR, Rundell AE, Venkatasubramanian V. A systematic framework for the design of reduced-order models for signal transduction pathways from a control theoretic perspective. Comput Chem Eng 2006, 30:437-452.
    • (2006) Comput Chem Eng , vol.30 , pp. 437-452
    • Maurya, M.R.1    Katare, S.2    Patkar, P.R.3    Rundell, A.E.4    Venkatasubramanian, V.5
  • 69
    • 6344281115 scopus 로고    scopus 로고
    • Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model
    • Segovia-Juarez JL, Ganguli S, Kirschner D. Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model. J Theor Biol 2004, 231:357-376.
    • (2004) J Theor Biol , vol.231 , pp. 357-376
    • Segovia-Juarez, J.L.1    Ganguli, S.2    Kirschner, D.3
  • 70
    • 65449166781 scopus 로고    scopus 로고
    • Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection
    • Ray JC, Flynn JL, Kirschner DE. Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection. J Immunol 2009, 182:3706-3717.
    • (2009) J Immunol , vol.182 , pp. 3706-3717
    • Ray, J.C.1    Flynn, J.L.2    Kirschner, D.E.3
  • 72
    • 3543037051 scopus 로고    scopus 로고
    • T cell-derived tumour necrosis factor is essential, but not sufficient, for protection against Mycobacterium tuberculosis infection
    • Saunders BM, Briscoe H, Britton WJ. T cell-derived tumour necrosis factor is essential, but not sufficient, for protection against Mycobacterium tuberculosis infection. Clin Exp Immunol 2004, 137:279-287.
    • (2004) Clin Exp Immunol , vol.137 , pp. 279-287
    • Saunders, B.M.1    Briscoe, H.2    Britton, W.J.3
  • 73
    • 2442667753 scopus 로고    scopus 로고
    • TNF influences chemokine expression of macrophages in vitro and that of CD11b+cells in vivo during Mycobacterium tuberculosis infection
    • Algood HM, Lin PL, Yankura D, Jones A, Chan J, Flynn JL. TNF influences chemokine expression of macrophages in vitro and that of CD11b+cells in vivo during Mycobacterium tuberculosis infection.J Immunol 2004, 172:6846-6857.
    • (2004) J Immunol , vol.172 , pp. 6846-6857
    • Algood, H.M.1    Lin, P.L.2    Yankura, D.3    Jones, A.4    Chan, J.5    Flynn, J.L.6
  • 75
    • 56749153497 scopus 로고    scopus 로고
    • Tumor necrosis factor blockers influence macrophage responses to Mycobacterium tuberculosis
    • Harris J, Hope JC, Keane J. Tumor necrosis factor blockers influence macrophage responses to Mycobacterium tuberculosis. J Infect Dis 2008, 198:1842-1850.
    • (2008) J Infect Dis , vol.198 , pp. 1842-1850
    • Harris, J.1    Hope, J.C.2    Keane, J.3
  • 76
    • 75749099727 scopus 로고    scopus 로고
    • Tumor necrosis factor neutralization results in disseminated disease in acute and latent Mycobacterium tuberculosis infection with normal granuloma structure in a cynomolgus macaque model
    • Lin PL, Myers A, Smith L, Bigbee C, Bigbee M, Fuhrman C, Grieser H, Chiosea I, Voitenek NN, Capuano SV, et al. Tumor necrosis factor neutralization results in disseminated disease in acute and latent Mycobacterium tuberculosis infection with normal granuloma structure in a cynomolgus macaque model. Arthritis Rheum 2010, 62:340-350.
    • (2010) Arthritis Rheum , vol.62 , pp. 340-350
    • Lin, P.L.1    Myers, A.2    Smith, L.3    Bigbee, C.4    Bigbee, M.5    Fuhrman, C.6    Grieser, H.7    Chiosea, I.8    Voitenek, N.N.9    Capuano, S.V.10
  • 77
    • 67651125074 scopus 로고    scopus 로고
    • Infectious complications of tumor necrosis factor blockade
    • Wallis RS. Infectious complications of tumor necrosis factor blockade. Curr Opin Infect Dis 2009, 22:403-409.
    • (2009) Curr Opin Infect Dis , vol.22 , pp. 403-409
    • Wallis, R.S.1
  • 78
    • 2342468669 scopus 로고    scopus 로고
    • Granulomatous infectious diseases associated with tumor necrosis factor antagonists
    • Wallis RS, Broder MS, Wong JY, Hanson ME, Beenhouwer DO. Granulomatous infectious diseases associated with tumor necrosis factor antagonists. Clin Infect Dis 2004, 38:1261-1265.
    • (2004) Clin Infect Dis , vol.38 , pp. 1261-1265
    • Wallis, R.S.1    Broder, M.S.2    Wong, J.Y.3    Hanson, M.E.4    Beenhouwer, D.O.5
  • 79
    • 67650096563 scopus 로고    scopus 로고
    • Risk of tuberculosis is higher with anti-tumor necrosis factor monoclonal antibody therapy than with soluble tumor necrosis factor receptor therapy: the three-year prospective French research axed on tolerance of biotherapies registry
    • Tubach F, Salmon D, Ravaud P, Allanore Y, Goupille P, Breban M, Pallot-Prades B, Pouplin S, Sacchi A, Chichemanian RM, et al. Risk of tuberculosis is higher with anti-tumor necrosis factor monoclonal antibody therapy than with soluble tumor necrosis factor receptor therapy: the three-year prospective French research axed on tolerance of biotherapies registry. Arthritis Rheum 2009, 60:1884-1894.
    • (2009) Arthritis Rheum , vol.60 , pp. 1884-1894
    • Tubach, F.1    Salmon, D.2    Ravaud, P.3    Allanore, Y.4    Goupille, P.5    Breban, M.6    Pallot-Prades, B.7    Pouplin, S.8    Sacchi, A.9    Chichemanian, R.M.10
  • 82
    • 84859377308 scopus 로고    scopus 로고
    • Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability
    • Fallahi-Sichani M, Flynn JL, Linderman JJ, Kirschner DE. Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability. J Immunol 2012, 188:3169-3178.
    • (2012) J Immunol , vol.188 , pp. 3169-3178
    • Fallahi-Sichani, M.1    Flynn, J.L.2    Linderman, J.J.3    Kirschner, D.E.4
  • 83
    • 84880273351 scopus 로고    scopus 로고
    • Multi-scale modeling predicts a balance of tumor necrosis factor-α and interleukin-10 controls the granuloma environment during Mycobacterium tuberculosis infection
    • Cilfone NA, Perry CR, Kirschner DE, Linderman JJ. Multi-scale modeling predicts a balance of tumor necrosis factor-α and interleukin-10 controls the granuloma environment during Mycobacterium tuberculosis infection. PLoS One 2013, 8:e68680.
    • (2013) PLoS One , vol.8
    • Cilfone, N.A.1    Perry, C.R.2    Kirschner, D.E.3    Linderman, J.J.4
  • 84
    • 53149144336 scopus 로고    scopus 로고
    • NF-kappa B activation controls phagolysosome fusion-mediated killing of mycobacteria by macrophages
    • Gutierrez MG, Mishra BB, Jordao L, Elliott E, Anes E, Griffiths G. NF-kappa B activation controls phagolysosome fusion-mediated killing of mycobacteria by macrophages. J Immunol 2008, 181:2651-2663.
    • (2008) J Immunol , vol.181 , pp. 2651-2663
    • Gutierrez, M.G.1    Mishra, B.B.2    Jordao, L.3    Elliott, E.4    Anes, E.5    Griffiths, G.6
  • 85
    • 56749174940 scopus 로고    scopus 로고
    • Exploring the full spectrum of macrophage activation
    • Mosser DM, Edwards JP. Exploring the full spectrum of macrophage activation. Nat Rev Immunol 2008, 8:958-969.
    • (2008) Nat Rev Immunol , vol.8 , pp. 958-969
    • Mosser, D.M.1    Edwards, J.P.2
  • 86
    • 0029976817 scopus 로고    scopus 로고
    • An essential role for NF-kappaB in preventing TNF-α-induced cell death
    • Beg AA, Baltimore D. An essential role for NF-kappaB in preventing TNF-α-induced cell death. Science 1996, 274:782-784.
    • (1996) Science , vol.274 , pp. 782-784
    • Beg, A.A.1    Baltimore, D.2
  • 88
    • 77954541844 scopus 로고    scopus 로고
    • Single-cell NF-κB dynamics reveal digital activation and analogue information processing
    • Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Single-cell NF-κB dynamics reveal digital activation and analogue information processing. Nature 2010, 466:267-271.
    • (2010) Nature , vol.466 , pp. 267-271
    • Tay, S.1    Hughey, J.J.2    Lee, T.K.3    Lipniacki, T.4    Quake, S.R.5    Covert, M.W.6
  • 89
    • 0036009115 scopus 로고    scopus 로고
    • NF-kappaB at the crossroads of life and death
    • Karin M, Lin A. NF-kappaB at the crossroads of life and death. Nat Immunol 2002, 3:221-227.
    • (2002) Nat Immunol , vol.3 , pp. 221-227
    • Karin, M.1    Lin, A.2
  • 90
    • 0036078710 scopus 로고    scopus 로고
    • Dissemination of Mycobacterium tuberculosis is influenced by host factors and precedes the initiation of T-cell immunity
    • Chackerian AA, Alt JM, Perera TV, Dascher CC, Behar SM. Dissemination of Mycobacterium tuberculosis is influenced by host factors and precedes the initiation of T-cell immunity. Infect Immun 2002, 70:4501-4509.
    • (2002) Infect Immun , vol.70 , pp. 4501-4509
    • Chackerian, A.A.1    Alt, J.M.2    Perera, T.V.3    Dascher, C.C.4    Behar, S.M.5
  • 91
    • 15444378745 scopus 로고    scopus 로고
    • Multiple mechanisms allow Mycobacterium tuberculosis to continuously inhibit MHC class II-mediated antigen presentation by macrophages
    • Chang ST, Linderman JJ, Kirschner DE. Multiple mechanisms allow Mycobacterium tuberculosis to continuously inhibit MHC class II-mediated antigen presentation by macrophages. Proc Natl Acad Sci USA 2005, 102:4530-4535.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 4530-4535
    • Chang, S.T.1    Linderman, J.J.2    Kirschner, D.E.3
  • 92
    • 0035877017 scopus 로고    scopus 로고
    • Infection of human macrophages and dendritic cells with Mycobacterium tuberculosis induces a differential cytokine gene expression that modulates T cell response
    • Giacomini E, Iona E, Ferroni L, Miettinen M, Fattorini L, Orefici G, Julkunen I, Coccia EM. Infection of human macrophages and dendritic cells with Mycobacterium tuberculosis induces a differential cytokine gene expression that modulates T cell response. J Immunol 2001, 166:7033-7041.
    • (2001) J Immunol , vol.166 , pp. 7033-7041
    • Giacomini, E.1    Iona, E.2    Ferroni, L.3    Miettinen, M.4    Fattorini, L.5    Orefici, G.6    Julkunen, I.7    Coccia, E.M.8
  • 93
    • 0036569397 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis induces differential cytokine production from dendritic cells and macrophages with divergent effects on naive T cell polarization
    • Hickman SP, Chan J, Salgame P. Mycobacterium tuberculosis induces differential cytokine production from dendritic cells and macrophages with divergent effects on naive T cell polarization. J Immunol 2002, 168:4636-4642.
    • (2002) J Immunol , vol.168 , pp. 4636-4642
    • Hickman, S.P.1    Chan, J.2    Salgame, P.3
  • 94
    • 79954611569 scopus 로고    scopus 로고
    • A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis
    • Marino S, El-Kebir M, Kirschner D. A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis. J Theor Biol 2011, 280:50-62.
    • (2011) J Theor Biol , vol.280 , pp. 50-62
    • Marino, S.1    El-Kebir, M.2    Kirschner, D.3
  • 95
    • 77954465946 scopus 로고    scopus 로고
    • TNF and IL-10 are major factors in modulation of the phagocytic cell environment in lung and lymph node in tuberculosis: a next-generation two-compartmental model
    • Marino S, Myers A, Flynn JL, Kirschner DE. TNF and IL-10 are major factors in modulation of the phagocytic cell environment in lung and lymph node in tuberculosis: a next-generation two-compartmental model. J Theor Biol 2010, 265:586-598.
    • (2010) J Theor Biol , vol.265 , pp. 586-598
    • Marino, S.1    Myers, A.2    Flynn, J.L.3    Kirschner, D.E.4
  • 96
    • 0036884522 scopus 로고    scopus 로고
    • Resident cell chemokine expression serves as the major mechanism for leukocyte recruitment during local inflammation
    • Garcia-Ramallo E, Marques T, Prats N, Beleta J, Kunkel SL, Godessart N. Resident cell chemokine expression serves as the major mechanism for leukocyte recruitment during local inflammation. J Immunol 2002, 169:6467-6473.
    • (2002) J Immunol , vol.169 , pp. 6467-6473
    • Garcia-Ramallo, E.1    Marques, T.2    Prats, N.3    Beleta, J.4    Kunkel, S.L.5    Godessart, N.6
  • 100
    • 46449119246 scopus 로고    scopus 로고
    • Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation
    • An G. Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation. Theor Biol Med Model 2008, 5:11.
    • (2008) Theor Biol Med Model , vol.5 , pp. 11
    • An, G.1
  • 101
    • 84902672724 scopus 로고    scopus 로고
    • Composite cell agent model of epithelial culture in vitro. In: Proceedings of the 2011 Workshop on Agent-Directed Simulation. Society for Computer Simulation International, 45-51.
    • Kim SH, Hunt CA. Composite cell agent model of epithelial culture in vitro. In: Proceedings of the 2011 Workshop on Agent-Directed Simulation. Society for Computer Simulation International, 2011, 45-51.
    • (2011)
    • Kim, S.H.1    Hunt, C.A.2
  • 103
    • 35848950784 scopus 로고    scopus 로고
    • Dynamics of in silico leukocyte rolling, activation, and adhesion
    • Tang J, Ley KF, Hunt CA. Dynamics of in silico leukocyte rolling, activation, and adhesion. BMC Syst Biol 2007, 1:14.
    • (2007) BMC Syst Biol , vol.1 , pp. 14
    • Tang, J.1    Ley, K.F.2    Hunt, C.A.3
  • 106
    • 80755141377 scopus 로고    scopus 로고
    • Ensuring congruency in multiscale modeling: towards linking agent based and continuum biomechanical models of arterial adaptation
    • Hayenga H, Thorne B, Peirce S, Humphrey J. Ensuring congruency in multiscale modeling: towards linking agent based and continuum biomechanical models of arterial adaptation. Ann Biomed Eng 2011, 39:2669-2682.
    • (2011) Ann Biomed Eng , vol.39 , pp. 2669-2682
    • Hayenga, H.1    Thorne, B.2    Peirce, S.3    Humphrey, J.4


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