-
2
-
-
0141561891
-
Integrating 'omic' information: A bridge between genomics and systems biology
-
Ge H, Walhout AJM, Vidal M. Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet. 2003;19(10):551.
-
(2003)
Trends Genet.
, vol.19
, Issue.10
, pp. 551
-
-
Ge, H.1
Walhout, A.J.M.2
Vidal, M.3
-
3
-
-
33644527950
-
The model organism as a system: Integrating 'omics' data sets
-
doi:10.1038/nrm1857
-
Joyce AR, Palsson B. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol. 2006;7(3),198. doi:10.1038/nrm1857.
-
(2006)
Nat Rev Mol Cell Biol.
, vol.7
, Issue.3
, pp. 198
-
-
Joyce, A.R.1
Palsson, B.2
-
4
-
-
10044298236
-
Reductionism and complexity in molecular biology
-
doi:10.1038/sj. embor.7400284
-
Regenmortel MHVV. Reductionism and complexity in molecular biology. EMBO Rep. 2004;5(11):1016. doi:10.1038/sj. embor.7400284.
-
(2004)
EMBO Rep.
, vol.5
, Issue.11
, pp. 1016
-
-
Regenmortel, M.H.V.V.1
-
5
-
-
33847626655
-
Multiscale modeling in biology
-
doi:10.1511/2007.64.1018
-
Schnell S, Grima R, Maini PK. Multiscale modeling in biology. Am Sci. 2007;95(2):134. doi:10.1511/2007.64.1018.
-
(2007)
Am Sci.
, vol.95
, Issue.2
, pp. 134
-
-
Schnell, S.1
Grima, R.2
Maini, P.K.3
-
6
-
-
45449110225
-
Systems biology of persistent infection: Tuberculosis as a case study
-
doi:10.1038/nrmicro1919
-
Young D, Stark J, Kirschner D. Systems biology of persistent infection: tuberculosis as a case study. Nat Rev Microbiol. 2008; 6(7):520. doi:10.1038/nrmicro1919.
-
(2008)
Nat Rev Microbiol.
, vol.6
, Issue.7
, pp. 520
-
-
Young, D.1
Stark, J.2
Kirschner, D.3
-
7
-
-
33645276014
-
A plaidoyer for systems immunology
-
doi:10.1111/j.0105- 2896. 2006.00374.x. URL
-
Benoist C, Germain RN, Mathis D. A plaidoyer for systems immunology. Immunol Rev. 2006;210(1):229. doi:10.1111/j.0105- 2896.2006.00374.x. URL http://www.ingentaconnect.com/content/ mksg/imr/2006/00000210/00000001/art00015.
-
(2006)
Immunol Rev.
, vol.210
, Issue.1
, pp. 229
-
-
Benoist, C.1
Germain, R.N.2
Mathis, D.3
-
8
-
-
0036500993
-
Systems biology: A brief overview
-
doi:10.1126/science.1069492
-
Kitano H. Systems biology: a brief overview. Science. 2002;295(5560):1662. doi:10.1126/science.1069492.
-
(2002)
Science.
, vol.295
, Issue.5560
, pp. 1662
-
-
Kitano, H.1
-
9
-
-
79953242705
-
How scientific models can explain
-
eprint 1. doi:10.1007/s11229-009-9565-1
-
Bokulich A. How scientific models can explain. Synthese. 2009; eprint 1. doi:10.1007/s11229-009-9565-1.
-
(2009)
Synthese.
-
-
Bokulich, A.1
-
10
-
-
33751524084
-
When mechanistic models explain
-
doi:10.1007/s11229-006-9097-x
-
Craver C. When mechanistic models explain. Synthese. 2006; 153(3):355. doi:10.1007/s11229-006-9097-x.
-
(2006)
Synthese.
, vol.153
, Issue.3
, pp. 355
-
-
Craver, C.1
-
11
-
-
33947181077
-
Deciphering the complexity of acute inflammation using mathematical models
-
doi:10.1385/IR:36:1:237
-
Vodovotz Y. Deciphering the complexity of acute inflammation using mathematical models. Immunol Res. 2006;36(1-3):237. doi:10.1385/IR:36:1:237.
-
(2006)
Immunol Res.
, vol.36
, Issue.1-3
, pp. 237
-
-
Vodovotz, Y.1
-
12
-
-
77952791119
-
Computational systems biology in cancer: Modeling methods and applications
-
Materi W, Wishart DS. Computational systems biology in cancer: modeling methods and applications. Gene Regul Syst Bio. 2007;1:91.
-
(2007)
Gene Regul Syst Bio.
, vol.1
, pp. 91
-
-
Materi, W.1
Wishart, D.S.2
-
13
-
-
54249142981
-
A hybrid agent-based approach for modeling microbiological systems
-
doi:10.1016/j.jtbi.2008.08.008
-
Guo Z, Sloot PMA, Tay JC. A hybrid agent-based approach for modeling microbiological systems. J Theor Biol. 2008;255(2): 163. doi:10.1016/j.jtbi. 2008.08.008.
-
(2008)
J Theor Biol.
, vol.255
, Issue.2
, pp. 163
-
-
Guo, Z.1
Sloot, P.M.A.2
Tay, J.C.3
-
14
-
-
36148952900
-
Multiscale models for vertebrate limb development
-
doi:10.1016/S0070-2153(07)81011-8
-
Newman SA, Christley S, Glimm T, Hentschel HGE, Kazmierczak B, Zhang YT, Zhu J, Alber M. Multiscale models for vertebrate limb development. Curr Top Dev Biol. 2008;81:311. doi:10.1016/S0070-2153(07)81011-8.
-
(2008)
Curr Top Dev Biol.
, vol.81
, pp. 311
-
-
Newman, S.A.1
Christley, S.2
Glimm, T.3
Hentschel, H.G.E.4
Kazmierczak, B.5
Zhang, Y.T.6
Zhu, J.7
Alber, M.8
-
15
-
-
36049044199
-
Executable cell biology
-
doi:10.1038/nbt1356
-
Fisher J, Henzinger TA. Executable cell biology. Nat Biotechnol. 2007;25(11):1239. doi:10.1038/nbt1356.
-
(2007)
Nat Biotechnol.
, vol.25
, Issue.11
, pp. 1239
-
-
Fisher, J.1
Henzinger, T.A.2
-
16
-
-
0345863935
-
The kegg resource for deciphering the genome
-
doi:10.1093/nar/gkh063
-
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The kegg resource for deciphering the genome. Nucleic Acids Res. 2004;32(Database issue):D277. doi:10.1093/nar/gkh063.
-
(2004)
Nucleic Acids Res.
, vol.32
, Issue.DATABASE ISSUE
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
17
-
-
18244391495
-
A versatile petri net based architecture for modeling and simulation of complex biological processes
-
Nagasaki M, Doi A, Matsuno H, Miyano S. A versatile petri net based architecture for modeling and simulation of complex biological processes. Genome Inform. 2004;15(1):180.
-
(2004)
Genome Inform.
, vol.15
, Issue.1
, pp. 180
-
-
Nagasaki, M.1
Doi, A.2
Matsuno, H.3
Miyano, S.4
-
18
-
-
34548458823
-
Computational systems biology
-
(Elsevier, Amsterdam [u.a.]), chap
-
Eils J, Lawerenz C, Astrahantseff K, Ginkel M, Eils R. Computational systems biology (Elsevier, Amsterdam [u.a.]), chap. Databases for systems biology; 2005. p. 15-38.
-
(2005)
Databases for Systems Biology
, pp. 15-38
-
-
Eils, J.1
Lawerenz, C.2
Astrahantseff, K.3
Ginkel, M.4
Eils, R.5
-
19
-
-
33845451529
-
Resources for integrative systems biology: From data through databases to networks and dynamic system models
-
doi:10.1093/bib/bbl036
-
Ng A, Bursteinas B, Gao Q, Mollison E, Zvelebil M. Resources for integrative systems biology: from data through databases to networks and dynamic system models. Brief Bioinform. 2006;7(4):318. doi:10.1093/bib/bbl036.
-
(2006)
Brief Bioinform.
, vol.7
, Issue.4
, pp. 318
-
-
Ng, A.1
Bursteinas, B.2
Gao, Q.3
Mollison, E.4
Zvelebil, M.5
-
20
-
-
58149229704
-
Systems biology model databases and resources
-
doi:10.1042/BSE0450223
-
van Gend C, Snoep JL. Systems biology model databases and resources. Essays Biochem. 2008;45:223. doi:10.1042/BSE0450223.
-
(2008)
Essays Biochem.
, vol.45
, pp. 223
-
-
Van Gend, C.1
Snoep, J.L.2
-
21
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
doi:10.1146/annurev.physchem. 58.032806.104637
-
Gillespie DT. Stochastic simulation of chemical kinetics. Annu Rev Phys Chem. 2007;58:35. doi:10.1146/annurev.physchem. 58.032806.104637.
-
(2007)
Annu Rev Phys Chem.
, vol.58
, pp. 35
-
-
Gillespie, D.T.1
-
22
-
-
0035465048
-
An approach to modelling in immunology
-
Yates A, Chan CC, Callard RE, George AJ, Stark J. An approach to modelling in immunology. Brief Bioinform. 2001;2(3):245.
-
(2001)
Brief Bioinform.
, vol.2
, Issue.3
, pp. 245
-
-
Yates, A.1
Chan, C.C.2
Callard, R.E.3
George, A.J.4
Stark, J.5
-
23
-
-
34248209065
-
Rival approaches to mathematical modelling in immunology
-
Andrew SM, Baker CT, Bocharov GA. Rival approaches to mathematical modelling in immunology. J Comput Appl Math. 2007;205(2):669. URL http://www.sciencedirect.com/science/ article/B6TYH-4KGPND0-7/2/ 879347b51f188098ab9e03e0fb0 612a8.
-
(2007)
J Comput Appl Math.
, vol.205
, Issue.2
, pp. 669
-
-
Andrew, S.M.1
Baker, C.T.2
Bocharov, G.A.3
-
24
-
-
71549163142
-
Modeling and simulation of the immune system as a self-regulating network
-
doi:10.1016/S0076-6879(09)67004-X
-
Kim PS, Levy D, Lee PP. Modeling and simulation of the immune system as a self-regulating network. Methods Enzymol. 2009;467:79. doi:10.1016/S0076- 6879(09)67004-X.
-
(2009)
Methods Enzymol.
, vol.467
, Issue.79
-
-
Kim, P.S.1
Levy, D.2
Lee, P.P.3
-
25
-
-
79551568071
-
A helminth immunomodulator exploits host signaling events to regulate cytokine production in macrophages
-
Klotz C, Ziegler T, Figueiredo A, Rausch S, Hepworth M, Obsivac N, Sers C, Lang R, Hammerstein P, Lucius R, et al. A helminth immunomodulator exploits host signaling events to regulate cytokine production in macrophages. PLoS Pathogens. 2011;7(1):e1001248.
-
(2011)
PLoS Pathogens.
, vol.7
, Issue.1
-
-
Klotz, C.1
Ziegler, T.2
Figueiredo, A.3
Rausch, S.4
Hepworth, M.5
Obsivac, N.6
Sers, C.7
Lang, R.8
Hammerstein, P.9
Lucius, R.10
-
26
-
-
53749087283
-
Model-based analysis of interferon-b induced signaling pathway
-
Smieja J, Jamaluddin M, Brasier A, Kimmel M. Model-based analysis of interferon-b induced signaling pathway. Bioinformatics. 2008;24(20):2363.
-
(2008)
Bioinformatics.
, vol.24
, Issue.20
, pp. 2363
-
-
Smieja, J.1
Jamaluddin, M.2
Brasier, A.3
Kimmel, M.4
-
27
-
-
0037044575
-
The ikappab- nf-kappab signaling module: Temporal control and selective gene activation
-
doi:10.1126/ science.1071914
-
Hoffmann A, Levchenko A, Scott ML, Baltimore D. The ikappab- nf-kappab signaling module: temporal control and selective gene activation. Science. 2002;298(5596):1241. doi:10.1126/ science.1071914.
-
(2002)
Science.
, vol.298
, Issue.5596
, pp. 1241
-
-
Hoffmann, A.1
Levchenko, A.2
Scott, M.L.3
Baltimore, D.4
-
28
-
-
1942421298
-
Mathematical model of nf-kappab regulatory module
-
doi:10.1016/j.jtbi.2004.01.001
-
Lipniacki T, Paszek P, Brasier ARAR, Luxon B, Kimmel M. Mathematical model of nf-kappab regulatory module. J Theor Biol. 2004;228(2):195. doi:10.1016/j.jtbi.2004.01.001.
-
(2004)
J Theor Biol.
, vol.228
, Issue.2
, pp. 195
-
-
Lipniacki, T.1
Paszek, P.2
Brasier, A.R.A.R.3
Luxon, B.4
Kimmel, M.5
-
29
-
-
24744472075
-
A validated mathematical model of cellmediated immune response to tumor growth
-
de Pillis L, Radunskaya A, Wiseman C. A validated mathematical model of cellmediated immune response to tumor growth. Cancer Research. 2005;65(17):7950.
-
(2005)
Cancer Research.
, vol.65
, Issue.17
, pp. 7950
-
-
De Pillis, L.1
Radunskaya, A.2
Wiseman, C.3
-
32
-
-
0019797316
-
A model of the role of natural killer cells in immune surveillance
-
Merill SJ. A model of the role of natural killer cells in immune surveillance. J Math Biol. 1981;12:363.
-
(1981)
J Math Biol.
, vol.12
, pp. 363
-
-
Merill, S.J.1
-
33
-
-
0025296465
-
Dynamics of a class of immune networks i. global stability of idiotype interactions
-
Varela F, Stewart J. Dynamics of a class of immune networks i. global stability of idiotype interactions. J Theor Biol. 1990; 144(1):93.
-
(1990)
J Theor Biol.
, vol.144
, Issue.1
, pp. 93
-
-
Varela, F.1
Stewart, J.2
-
34
-
-
0025849021
-
Size and connectivity as emergent properties of a developing immune network
-
De Boer R, Perelson A. Size and connectivity as emergent properties of a developing immune network. J Theor Biol. 1991;149(3):381.
-
(1991)
J Theor Biol.
, vol.149
, Issue.3
, pp. 381
-
-
De Boer, R.1
Perelson, A.2
-
35
-
-
77955171002
-
An ode model of early stages of atherosclerosis: Mechanisms of the inflammatory response
-
Ougrinovskaia A, Thompson RS, Myerscough MR. An ode model of early stages of atherosclerosis: mechanisms of the inflammatory response. Bull Math Biol 2010;72(6):1534. URL http://www.ncbi.nlm.nih.gov/pubmed/20440571.
-
(2010)
Bull Math Biol
, vol.72
, Issue.6
, pp. 1534
-
-
Ougrinovskaia, A.1
Thompson, R.S.2
Myerscough, M.R.3
-
36
-
-
0028116794
-
Modeling hiv infection of cd4? t-cell subpopulations
-
Essunger P, Perelson AS. Modeling hiv infection of cd4? t-cell subpopulations. J Theor Biol. 1994;170(4):367.
-
(1994)
J Theor Biol.
, vol.170
, Issue.4
, pp. 367
-
-
Essunger, P.1
Perelson, A.S.2
-
37
-
-
0032494689
-
Mathematical model of a virusneutralizing immunglobulin response
-
Funk G, Barbour A, Hengartner H, Kalinke U. Mathematical model of a virusneutralizing immunglobulin response. J Theor Biol. 1998;195(1):41.
-
(1998)
J Theor Biol.
, vol.195
, Issue.1
, pp. 41
-
-
Funk, G.1
Barbour, A.2
Hengartner, H.3
Kalinke, U.4
-
38
-
-
24144457002
-
Effect of the ctl proliferation program on virus dynamics
-
Wodarz D, Thomsen A. Effect of the ctl proliferation program on virus dynamics. Int Immunol. 2005;17(9):1269.
-
(2005)
Int Immunol.
, vol.17
, Issue.9
, pp. 1269
-
-
Wodarz, D.1
Thomsen, A.2
-
39
-
-
81855176270
-
A model of cytotoxic t antitumor activation stimulated by pulsed dendritic cells
-
Simos TE, Psihoyios G, Tsitouras C, Anastassi Z, editors. American Institute of Physics Conference Series
-
Pennisi M, Pappalardo F, Chiacchio F, Motta S. A model of cytotoxic t antitumor activation stimulated by pulsed dendritic cells. In: Simos TE, Psihoyios G, Tsitouras C, Anastassi Z, editors. American Institute of Physics Conference Series, American Institute of Physics Conference Series, vol. 1389, American Institute of Physics Conference Series. 2011. p. 1236-1239.
-
(2011)
American Institute of Physics Conference Series, American Institute of Physics Conference Series
, vol.1389
, pp. 1236-1239
-
-
Pennisi, M.1
Pappalardo, F.2
Chiacchio, F.3
Motta, S.4
-
40
-
-
48749085156
-
Encoding nf-jb temporal control in response to tnf: Distinct roles for the negative regulators ijba and a20
-
Werner S, Kearns J, Zadorozhnaya V, Lynch C, ODea E, Boldin M, Ma A, Baltimore D, Hoffmann A. Encoding nf-jb temporal control in response to tnf: distinct roles for the negative regulators ijba and a20. Genes Dev. 2008;22(15):2093.
-
(2008)
Genes Dev.
, vol.22
, Issue.15
, pp. 2093
-
-
Werner, S.1
Kearns, J.2
Zadorozhnaya, V.3
Lynch, C.4
Odea, E.5
Boldin, M.6
Ma, A.7
Baltimore, D.8
Hoffmann, A.9
-
41
-
-
66449092314
-
Kinetic control of negative feedback regulators of NFkappaB/ RelA determines their pathogen- and cytokine-receptor signaling specificity
-
doi:10.1073/pnas.0812367106
-
Shih VF, Kearns JD, Basak S, Savinova OV, Ghosh G, Hoffmann A. Kinetic control of negative feedback regulators of NFkappaB/ RelA determines their pathogen- and cytokine-receptor signaling specificity. Proc Nat Acad Sci. 2009;106(24):9619. doi:10.1073/pnas.0812367106.
-
(2009)
Proc Nat Acad Sci.
, vol.106
, Issue.24
, pp. 9619
-
-
Shih, V.F.1
Kearns, J.D.2
Basak, S.3
Savinova, O.V.4
Ghosh, G.5
Hoffmann, A.6
-
42
-
-
0035193294
-
Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations
-
doi:10.1016/S0006-3495(01)75949-8
-
Kepler TB, Elston TC. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys J. 2001;81(6):3116. doi:10.1016/S0006-3495(01)75949-8.
-
(2001)
Biophys J.
, vol.81
, Issue.6
, pp. 3116
-
-
Kepler, T.B.1
Elston, T.C.2
-
43
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected escherichia coli cells
-
Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected escherichia coli cells. Genetics 1998;149(4):1633.
-
(1998)
Genetics
, vol.149
, Issue.4
, pp. 1633
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
44
-
-
77950525353
-
Stochastic modeling of b lymphocyte terminal differentiation and its suppression by dioxin
-
doi:10.1186/1752-0509-4-40
-
Zhang Q, Bhattacharya S, Kline DE, Crawford RB, Conolly RB, Thomas RS, Kaminski NE, Andersen ME. Stochastic modeling of b lymphocyte terminal differentiation and its suppression by dioxin. BMC Syst Biol.2010;4:40. doi:10.1186/1752-0509-4-40.
-
(2010)
BMC Syst Biol.
, vol.4
, pp. 40
-
-
Zhang, Q.1
Bhattacharya, S.2
Kline, D.E.3
Crawford, R.B.4
Conolly, R.B.5
Thomas, R.S.6
Kaminski, N.E.7
Andersen, M.E.8
-
45
-
-
29244462834
-
Transcriptional stochasticity in gene expression
-
doi:10.1016/j.jtbi.2005.05.032
-
Lipniacki T, Paszek P, Marciniak-Czochra A, Brasier AR, Kimmel M. Transcriptional stochasticity in gene expression. J Theor Biol. 2006;238(2):348. doi:10.1016/j.jtbi.2005.05.032.
-
(2006)
J Theor Biol.
, vol.238
, Issue.2
, pp. 348
-
-
Lipniacki, T.1
Paszek, P.2
Marciniak-Czochra, A.3
Brasier, A.R.4
Kimmel, M.5
-
46
-
-
66549109067
-
Optimization of immunoglobulin substitution therapy by a stochastic immune response model
-
Figge M. Optimization of immunoglobulin substitution therapy by a stochastic immune response model. PloS one. 2009;4(5): e5685.
-
(2009)
PloS One.
, vol.4
, Issue.5
-
-
Figge, M.1
-
47
-
-
0036400749
-
Stochastic vs. deterministic modeling of intracellular viral kinetics
-
Srivastava R, You L, Summers J, Yin J. Stochastic vs. deterministic modeling of intracellular viral kinetics. J Theor Biol. 2002;218(3):309.
-
(2002)
J Theor Biol.
, vol.218
, Issue.3
, pp. 309
-
-
Srivastava, R.1
You, L.2
Summers, J.3
Yin, J.4
-
48
-
-
0037342537
-
The systems biology markup language (sbml): A medium for representation and exchange of biochemical network models
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Novre NL, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J, Forum SBML. The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19(4):524.
-
(2003)
Bioinformatics.
, vol.19
, Issue.4
, pp. 524
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, M.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.H.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Novre, N.L.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Nakayama, Y.31
Nelson, M.R.32
Nielsen, P.F.33
Sakurada, T.34
Schaff, J.C.35
Shapiro, B.E.36
Shimizu, T.S.37
Spence, H.D.38
Stelling, J.39
Takahashi, K.40
Tomita, M.41
Wagner, J.42
Wang, J.43
Forum, S.B.M.L.44
more..
-
49
-
-
2442595958
-
Cellml: Its future, present and past
-
doi:10.1016/j.pbiomolbio.2004.01.004
-
Lloyd CM, Halstead MDB, Nielsen PF. Cellml: its future, present and past. Prog Biophys Mol Biol. (2004);85(2-3):433. doi:10.1016/j.pbiomolbio.2004.01. 004.
-
(2004)
Prog Biophys Mol Biol.
, vol.85
, Issue.2-3
, pp. 433
-
-
Lloyd, C.M.1
Halstead, M.D.B.2
Nielsen, P.F.3
-
51
-
-
0021755192
-
Cellular automata as models of complexity
-
Wolfram S. Cellular automata as models of complexity. Nature. 1984;311(5985):419.
-
(1984)
Nature.
, vol.311
, Issue.5985
, pp. 419
-
-
Wolfram, S.1
-
52
-
-
0030026711
-
Affinity maturation and hypermutation in a simulation of the humoral immune response
-
Celada F, Seiden P. Affinity maturation and hypermutation in a simulation of the humoral immune response. Eu J Immunol. 1996;26(6):1350.
-
(1996)
Eu J Immunol.
, vol.26
, Issue.6
, pp. 1350
-
-
Celada, F.1
Seiden, P.2
-
53
-
-
0031571212
-
A solution to the rheumatoid factor paradox: Pathologic rheumatoid factors can be tolerized by competition with natural rheumatoid factors
-
Stewart J, Agosto H, Litwin S, Welsh J, Shlomchik M, Weigert M, Seiden P. A solution to the rheumatoid factor paradox: pathologic rheumatoid factors can be tolerized by competition with natural rheumatoid factors. J Immunol. 1997;159(4):1728.
-
(1997)
J Immunol.
, vol.159
, Issue.4
, pp. 1728
-
-
Stewart, J.1
Agosto, H.2
Litwin, S.3
Welsh, J.4
Shlomchik, M.5
Weigert, M.6
Seiden, P.7
-
54
-
-
0035824717
-
A cellular automaton model of early tumor growth and invasion
-
doi:10.1006/jtbi.2001.2385
-
Patel AA, Gawlinski ET, Lemieux SK, Gatenby RA. A cellular automaton model of early tumor growth and invasion. J Theor Biol. 2001;213(3):315. doi:10.1006/jtbi.2001.2385.
-
(2001)
J Theor Biol.
, vol.213
, Issue.3
, pp. 315
-
-
Patel, A.A.1
Gawlinski, E.T.2
Lemieux, S.K.3
Gatenby, R.A.4
-
55
-
-
1542344734
-
Modeling of self-organized avascular tumor growth with a hybrid cellular automaton
-
Dormann S, Deutsch A. Modeling of self-organized avascular tumor growth with a hybrid cellular automaton. In Silico Biol. 2002;2(3):393.
-
(2002)
In Silico Biol.
, vol.2
, Issue.3
, pp. 393
-
-
Dormann, S.1
Deutsch, A.2
-
56
-
-
33750715064
-
Modeling the effects of vasculature evolution on early brain tumor growth
-
doi:10.1016/j.jtbi.2006.07.002
-
Gevertz JL, Torquato S. Modeling the effects of vasculature evolution on early brain tumor growth. J Theor Biol. 2006;243(4): 517. doi:10.1016/j.jtbi. 2006.07.002.
-
(2006)
J Theor Biol.
, vol.243
, Issue.4
, pp. 517
-
-
Gevertz, J.L.1
Torquato, S.2
-
57
-
-
33644890522
-
A cellular automata model of tumorimmune system interactions
-
doi:10.1016/j.jtbi.2005.08.002
-
Mallet DG, Pillis LGD. A cellular automata model of tumorimmune system interactions. J Theor Biol. 2006;239(3):334. doi:10.1016/j.jtbi.2005.08.002.
-
(2006)
J Theor Biol.
, vol.239
, Issue.3
, pp. 334
-
-
Mallet, D.G.1
Pillis, L.G.D.2
-
58
-
-
34247619795
-
Cellular automaton simulation examining progenitor hierarchy structure effects on mammary ductal carcinoma in situ
-
doi:10.1016/j.jtbi.2007.01.011
-
Bankhead A, Magnuson NS, Heckendorn RB. Cellular automaton simulation examining progenitor hierarchy structure effects on mammary ductal carcinoma in situ. J Theor Biol. 2007; 246(3):491. doi:10.1016/j.jtbi.2007.01.011.
-
(2007)
J Theor Biol.
, vol.246
, Issue.3
, pp. 491
-
-
Bankhead, A.1
Magnuson, N.S.2
Heckendorn, R.B.3
-
59
-
-
34248216634
-
An evolutionary hybrid cellular automaton model of solid tumour growth
-
doi:10.1016/j.jtbi.2007.01.027
-
Gerlee P, Anderson ARA. An evolutionary hybrid cellular automaton model of solid tumour growth. J Theor Biol. 2007;246(4):583. doi:10.1016/j.jtbi.2007. 01.027.
-
(2007)
J Theor Biol.
, vol.246
, Issue.4
, pp. 583
-
-
Gerlee, P.1
Anderson, A.R.A.2
-
60
-
-
38649099056
-
A hybrid cellular automaton model of clonal evolution in cancer: The emergence of the glycolytic phenotype
-
doi:10.1016/j.jtbi. 2007.10.038
-
Gerlee P, Anderson ARA. A hybrid cellular automaton model of clonal evolution in cancer: the emergence of the glycolytic phenotype. J Theor Biol. 2008;250(4):705. doi:10.1016/j.jtbi. 2007.10.038.
-
(2008)
J Theor Biol.
, vol.250
, Issue.4
, pp. 705
-
-
Gerlee, P.1
Anderson, A.R.A.2
-
61
-
-
70149105936
-
The role of transforming growth factor-beta-mediated tumor-stroma interactions in prostate cancer progression: An integrative approach
-
doi:10.1158/0008-5472.CAN-08-3957
-
Basanta D, Strand DW, Lukner RB, Franco OE, Cliffel DE, Ayala GE, Hayward SW, Anderson ARA. The role of transforming growth factor-beta-mediated tumor-stroma interactions in prostate cancer progression: an integrative approach. Cancer Res. 2009;69(17):7111. doi:10.1158/0008-5472.CAN-08-3957.
-
(2009)
Cancer Res.
, vol.69
, Issue.17
, pp. 7111
-
-
Basanta, D.1
Strand, D.W.2
Lukner, R.B.3
Franco, O.E.4
Cliffel, D.E.5
Ayala, G.E.6
Hayward, S.W.7
Anderson, A.R.A.8
-
62
-
-
70349655451
-
Chlamydial infection and spatial ascension of the female genital tract: A novel hybrid cellular automata and continuum mathematical model
-
doi:10.1111/j.1574-695X.2009.00596.x
-
Mallet DG, Heymer KJ, Rank RG, Wilson DP. Chlamydial infection and spatial ascension of the female genital tract: a novel hybrid cellular automata and continuum mathematical model. FEMS Immunol Med Microbiol. 2009;57(2):173. doi:10.1111/j.1574-695X.2009.00596.x.
-
(2009)
FEMS Immunol Med Microbiol.
, vol.57
, Issue.2
, pp. 173
-
-
Mallet, D.G.1
Heymer, K.J.2
Rank, R.G.3
Wilson, D.P.4
-
63
-
-
77954627336
-
Diffusion-limited tumour growth: Simulations and analysis
-
Gerlee P, Anderson ARA. Diffusion-limited tumour growth: simulations and analysis. Math Biosci Eng. 2010;7(2):385.
-
(2010)
Math Biosci Eng.
, vol.7
, Issue.2
, pp. 385
-
-
Gerlee, P.1
Anderson, A.R.A.2
-
64
-
-
77950934594
-
Episodic, transient systemic acidosis delays evolution of the malignant phenotype: Possible mechanism for cancer prevention by increased physical activity
-
doi:10.1186/1745-6150-5-22
-
Smallbone K, Maini PK, Gatenby RA. Episodic, transient systemic acidosis delays evolution of the malignant phenotype: Possible mechanism for cancer prevention by increased physical activity. Biol Direct. 2010;5:22. doi:10.1186/1745-6150-5-22.
-
(2010)
Biol Direct.
, vol.5
, pp. 22
-
-
Smallbone, K.1
Maini, P.K.2
Gatenby, R.A.3
-
65
-
-
42749102416
-
Dynamics of hiv infection: A cellular automata approach
-
Zorzenon dos Santos R, Coutinho S. Dynamics of hiv infection: a cellular automata approach. Phys Rev Lett. 2001;87(16): 168102.
-
(2001)
Phys Rev Lett.
, vol.87
, Issue.16
, pp. 168102
-
-
Zorzenon Dos Santos, R.1
Coutinho, S.2
-
66
-
-
0036403760
-
Spatiotemporal dynamics of hiv propagation
-
Strain M, Richman D, Wong J, Levine H. Spatiotemporal dynamics of hiv propagation. J Theor Biol. 2002;218(1):85.
-
(2002)
J Theor Biol.
, vol.218
, Issue.1
, pp. 85
-
-
Strain, M.1
Richman, D.2
Wong, J.3
Levine, H.4
-
67
-
-
34447298881
-
Simulating epstein-barr virus infection with c-immsim
-
Castiglione F, Duca K, Jarrah A, Laubenbacher R, Hochberg D, Thorley-Lawson D. Simulating epstein-barr virus infection with c-immsim. Bioinformatics. 2007;23(11):1371.
-
(2007)
Bioinformatics.
, vol.23
, Issue.11
, pp. 1371
-
-
Castiglione, F.1
Duca, K.2
Jarrah, A.3
Laubenbacher, R.4
Hochberg, D.5
Thorley-Lawson, D.6
-
68
-
-
33750735048
-
Modeling intercellular interactions in early mycobacterium infection
-
Warrender C, Forrest S, Koster F. Modeling intercellular interactions in early mycobacterium infection. Bull Math Biol. 2006;68(8):2233.
-
(2006)
Bull Math Biol.
, vol.68
, Issue.8
, pp. 2233
-
-
Warrender, C.1
Forrest, S.2
Koster, F.3
-
70
-
-
0035790856
-
The immune system as a reactive system: Modeling t cell activation with statecharts
-
ed. by Cohen IR, Harel D., doi: 10.1109/HCC.2001.995228
-
Kam N. The immune system as a reactive system: Modeling t cell activation with statecharts. In: Human-centric computing languages and environments, IEEE CS International Symposium on, vol. 0, ed. by Cohen IR, Harel D. 2001;vol. 0, p. 15-15. doi: 10.1109/HCC.2001.995228.
-
(2001)
Human-centric Computing Languages and Environments IEEE CS International Symposium on
, pp. 15-15
-
-
Kam, N.1
-
71
-
-
0242574975
-
Toward rigorous comprehension of biological complexity: Modeling, execution, and visualization of thymic t-cell maturation
-
doi: 10.1101/gr.1215303
-
Efroni S, Harel D, Cohen IR. Toward rigorous comprehension of biological complexity: modeling, execution, and visualization of thymic t-cell maturation. Genome Res. 2003;13(11), 2485. doi: 10.1101/gr.1215303.
-
(2003)
Genome Res.
, vol.13
, Issue.11
, pp. 2485
-
-
Efroni, S.1
Harel, D.2
Cohen, I.R.3
-
72
-
-
33846542982
-
Emergent dynamics of thymocyte development and lineage determination
-
doi:10.1371/journal.pcbi.0030013
-
Efroni S, Harel D, Cohen IR. Emergent dynamics of thymocyte development and lineage determination. PLoS Comput Biol. 2007;3(1):e13. doi:10.1371/journal. pcbi.0030013.
-
(2007)
PLoS Comput Biol.
, vol.3
, Issue.1
-
-
Efroni, S.1
Harel, D.2
Cohen, I.R.3
-
73
-
-
47949098283
-
The lymph node b cell immune response: Dynamic analysis in-silico
-
Naamah S, David CIRH. The lymph node b cell immune response: dynamic analysis in-silico. Proc IEEE. 2008;96(8): 1421.
-
(2008)
Proc IEEE
, vol.96
, Issue.8
, pp. 1421
-
-
Naamah, S.1
David, C.I.R.H.2
-
74
-
-
0026556477
-
A computer model of cellular interactions in the immune system
-
Celada F, Seiden P. A computer model of cellular interactions in the immune system. Immunol Today. 1992;13(2):56.
-
(1992)
Immunol Today.
, vol.13
, Issue.2
, pp. 56
-
-
Celada, F.1
Seiden, P.2
-
75
-
-
0036640183
-
Immsim, a flexible model for in machina experiments on immune system responses
-
Puzone R, Kohler B, Seiden P, Celada F. Immsim, a flexible model for in machina experiments on immune system responses. Fut Gen Comput Syst. 2002;18(7):961.
-
(2002)
Fut Gen Comput Syst.
, vol.18
, Issue.7
, pp. 961
-
-
Puzone, R.1
Kohler, B.2
Seiden, P.3
Celada, F.4
-
77
-
-
80054829961
-
Biocharts: A visual formalism for complex biological systems
-
Kugler H, Larjo A, Harel D. Biocharts: a visual formalism for complex biological systems. J R Soc Interface. 2009. URL http://www.biomedsearch.com/ nih/Biocharts-visual-formalismcomplex- biological/20022895.html.
-
(2009)
J R Soc Interface.
-
-
Kugler, H.1
Larjo, A.2
Harel, D.3
-
78
-
-
0035491584
-
Agent-based computer simulation and sirs: Building a bridge between basic science and clinical trials
-
An G. Agent-based computer simulation and sirs: building a bridge between basic science and clinical trials. Shock. 2001; 16(4):266.
-
(2001)
Shock.
, vol.16
, Issue.4
, pp. 266
-
-
An, G.1
-
79
-
-
33645957683
-
Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling
-
doi:10.1016/j.jcrc.2005.11.012
-
An G. Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling. J Crit Care. 2006;21(1):105. doi:10.1016/j.jcrc.2005.11.012.
-
(2006)
J Crit Care.
, vol.21
, Issue.1
, pp. 105
-
-
An, G.1
-
80
-
-
34249826054
-
Challenges and rewards on the road to translational systems biology in acute illness: Four case reports from interdisciplinary teams
-
doi:10.1016/j.jcrc.2006.12.011
-
An G, Hunt CA, Clermont G, Neugebauer E, Vodovotz Y. Challenges and rewards on the road to translational systems biology in acute illness: four case reports from interdisciplinary teams. J Crit Care. 2007;22(2):169. doi:10.1016/j.jcrc.2006.12.011.
-
(2007)
J Crit Care.
, vol.22
, Issue.2
, pp. 169
-
-
An, G.1
Hunt, C.A.2
Clermont, G.3
Neugebauer, E.4
Vodovotz, Y.5
-
81
-
-
73949109493
-
Nitrite protects against morbidity and mortality associated with tnf- or lps-induced shock in a soluble guanylate cyclase-dependent manner
-
doi:10.1084/jem.20091236
-
Cauwels A, Buys ES, Thoonen R, Geary L, Delanghe J, Shiva S, Brouckaert P. Nitrite protects against morbidity and mortality associated with tnf- or lps-induced shock in a soluble guanylate cyclase-dependent manner. J Exp Med. 2009;206(13):2915. doi:10.1084/jem.20091236.
-
(2009)
J Exp Med.
, vol.206
, Issue.13
, pp. 2915
-
-
Cauwels, A.1
Buys, E.S.2
Thoonen, R.3
Geary, L.4
Delanghe, J.5
Shiva, S.6
Brouckaert, P.7
-
82
-
-
34249663748
-
Multi-cell agent-based simulation of the microvasculature to study the dynamics of circulating inflammatory cell trafficking
-
doi:10.1007/s10439-007-9266-1
-
Bailey AM, Thorne BC, Peirce SM. Multi-cell agent-based simulation of the microvasculature to study the dynamics of circulating inflammatory cell trafficking. Ann Biomed Eng. 2007;35(6):916. doi:10.1007/s10439-007-9266-1.
-
(2007)
Ann Biomed Eng.
, vol.35
, Issue.6
, pp. 916
-
-
Bailey, A.M.1
Thorne, B.C.2
Peirce, S.M.3
-
83
-
-
34848830242
-
Agentbased model of inflammation and wound healing: Insights into diabetic foot ulcer pathology and the role of transforming growth factor-beta1
-
doi:10.1111/j.1524-475X.2007.00271.x
-
Mi Q, Rivire B, Clermont G, Steed DL, Vodovotz Y. Agentbased model of inflammation and wound healing: insights into diabetic foot ulcer pathology and the role of transforming growth factor-beta1. Wound Repair Regen. 2007;15(5):671. doi:10.1111/j.1524-475X.2007.00271.x.
-
(2007)
Wound Repair Regen.
, vol.15
, Issue.5
, pp. 671
-
-
Mi, Q.1
Rivire, B.2
Clermont, G.3
Steed, D.L.4
Vodovotz, Y.5
-
84
-
-
46449119246
-
Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation
-
doi:10.1186/ 1742-4682-5-11
-
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. doi:10.1186/ 1742-4682-5-11.
-
(2008)
Theor Biol Med Model.
, vol.5
, Issue.11
-
-
An, G.1
-
85
-
-
77949496645
-
Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes
-
doi:10.1371/journal.pone.0009249
-
Dong X, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes. PLoS One. 2010;5(2): e9249. doi:10.1371/journal.pone.0009249.
-
(2010)
PLoS One.
, vol.5
, Issue.2
-
-
Dong, X.1
Foteinou, P.T.2
Calvano, S.E.3
Lowry, S.F.4
Androulakis, I.P.5
-
86
-
-
51749108892
-
Development of a twodimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation
-
doi:10.1093/bioinformatics/btn362
-
Galvo V, Miranda JGV, dos Santos RR. Development of a twodimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation. Bioinformatics. 2008;24(18):2051. doi:10.1093/bioinformatics/ btn362.
-
(2008)
Bioinformatics.
, vol.24
, Issue.18
, pp. 2051
-
-
Galvo, V.1
Miranda, J.G.V.2
Dos Santos, R.R.3
-
87
-
-
77952545257
-
A three-dimensional multi-agent-based model for the evolution of chagas' disease
-
doi:10.1016/j.biosystems.2010.03.007
-
Galvo V, Miranda JGV. A three-dimensional multi-agent-based model for the evolution of chagas' disease. Biosystems. 2010; 100(3):225. doi:10.1016/j.biosystems.2010.03.007.
-
(2010)
Biosystems.
, vol.100
, Issue.3
, pp. 225
-
-
Galvo, V.1
Miranda, J.G.V.2
-
88
-
-
50949091234
-
A patient-specific in silico model of inflammation and healing tested in acute vocal fold injury
-
doi:10.1371/journal.pone.0002789
-
Li NYK, Verdolini K, Clermont G, Mi Q, Rubinstein EN, Hebda PA, Vodovotz Y. A patient-specific in silico model of inflammation and healing tested in acute vocal fold injury. PLoS One. 2008;3(7):e2789. doi:10.1371/journal.pone. 0002789.
-
(2008)
PLoS One.
, vol.3
, Issue.7
-
-
Li, N.Y.K.1
Verdolini, K.2
Clermont, G.3
Mi, Q.4
Rubinstein, E.N.5
Hebda, P.A.6
Vodovotz, Y.7
-
89
-
-
61449164943
-
Agent-based model of therapeutic adipose-derived stromal cell trafficking during ischemia predicts ability to roll on p-selectin
-
doi:10.1371/journal. pcbi.1000294
-
Bailey AM, Lawrence MB, Shang H, Katz AJ, Peirce SM. Agent-based model of therapeutic adipose-derived stromal cell trafficking during ischemia predicts ability to roll on p-selectin. PLoS Comput Biol. 2009;5(2):e1000294. doi:10.1371/journal. pcbi.1000294.
-
(2009)
PLoS Comput Biol.
, vol.5
, Issue.2
-
-
Bailey, A.M.1
Lawrence, M.B.2
Shang, H.3
Katz, A.J.4
Peirce, S.M.5
-
90
-
-
77649207414
-
Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion
-
doi:10.1371/journal.pcbi.1000681
-
Tang J, Hunt CA. Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion. PLoS Comput Biol. 2010;6(2):e1000681. doi:10.1371/journal.pcbi.1000681.
-
(2010)
PLoS Comput Biol.
, vol.6
, Issue.2
-
-
Tang, J.1
Hunt, C.A.2
-
91
-
-
77952477710
-
Development of a three dimensional multiscale computational model of the human epidermis
-
doi:10.1371/journal.pone.0008511
-
Adra S, Sun T, MacNeil S, Holcombe M, Smallwood R. Development of a three dimensional multiscale computational model of the human epidermis. PLoS One. 2010;5(1):e8511. doi:10.1371/journal.pone.0008511.
-
(2010)
PLoS One.
, vol.5
, Issue.1
-
-
Adra, S.1
Sun, T.2
MacNeil, S.3
Holcombe, M.4
Smallwood, R.5
-
92
-
-
6344281115
-
Identifying control mechanisms of granuloma formation during m. tuberculosis infection using an agent-based model
-
doi:10.1016/j.jtbi.2004.06.031
-
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(3):357. doi:10.1016/j.jtbi.2004.06.031.
-
(2004)
J Theor Biol.
, vol.231
, Issue.3
, pp. 357
-
-
Segovia-Juarez, J.L.1
Ganguli, S.2
Kirschner, D.3
-
93
-
-
48249141403
-
Modeling immune system control of atherogenesis
-
doi: 10.1093/bioinformatics/btn306
-
Pappalardo F, Musumeci S, Motta S. Modeling immune system control of atherogenesis. Bioinformatics. 2008;24(15):1715. doi: 10.1093/bioinformatics/ btn306.
-
(2008)
Bioinformatics.
, vol.24
, Issue.15
, pp. 1715
-
-
Pappalardo, F.1
Musumeci, S.2
Motta, S.3
-
94
-
-
36048953983
-
A virtual look at epstein-barr virus infection: Biological interpretations
-
doi: 10.1371/journal.ppat.0030137
-
Duca KA, Shapiro M, Delgado-Eckert E, Hadinoto V, Jarrah AS, Laubenbacher R, Lee K, Luzuriaga K, Polys NF, Thorley- Lawson DA. A virtual look at epstein-barr virus infection: biological interpretations. PLoS Pathog. 2007;3(10):1388. doi: 10.1371/journal.ppat.0030137.
-
(2007)
PLoS Pathog.
, vol.3
, Issue.10
, pp. 1388
-
-
Duca, K.A.1
Shapiro, M.2
Delgado-Eckert, E.3
Hadinoto, V.4
Jarrah, A.S.5
Laubenbacher, R.6
Lee, K.7
Luzuriaga, K.8
Polys, N.F.9
Thorley- Lawson, D.A.10
-
95
-
-
23744434889
-
Agent-based modeling of the context dependency in t cell recognition
-
doi:10.1016/j.jtbi.2005.03.019
-
Casal A, Sumen C, Reddy TE, Alber MS, Lee PP. Agent-based modeling of the context dependency in t cell recognition. J Theor Biol. 2005;236(4):376. doi:10.1016/j.jtbi.2005.03.019.
-
(2005)
J Theor Biol.
, vol.236
, Issue.4
, pp. 376
-
-
Casal, A.1
Sumen, C.2
Reddy, T.E.3
Alber, M.S.4
Lee, P.P.5
-
96
-
-
68749120548
-
In-silico cell surface modeling reveals mechanism for initial steps of b-cell receptor signal transduction
-
doi: 10.1016/j.molimm.2009.03.027
-
Nudelman G, Weigert M, Louzoun Y. In-silico cell surface modeling reveals mechanism for initial steps of b-cell receptor signal transduction. Mol Immunol. 2009;46(15):3141. doi: 10.1016/j.molimm.2009.03.027.
-
(2009)
Mol Immunol.
, vol.46
, Issue.15
, pp. 3141
-
-
Nudelman, G.1
Weigert, M.2
Louzoun, Y.3
-
97
-
-
77149134316
-
Agent-based simulation of t-cell activation and proliferation within a lymph node
-
doi:10.1038/icb.2009.78
-
Bogle G, Dunbar PR. Agent-based simulation of t-cell activation and proliferation within a lymph node. Immunol Cell Biol. 2010;88(2):172. doi:10.1038/icb.2009.78.
-
(2010)
Immunol Cell Biol.
, vol.88
, Issue.2
, pp. 172
-
-
Bogle, G.1
Dunbar, P.R.2
-
98
-
-
33750108678
-
An analysis of b cell selection mechanisms in germinal centers
-
doi:10.1093/imammb/dql012
-
Meyer-Hermann ME, Maini PK, Iber D. An analysis of b cell selection mechanisms in germinal centers. Math Med Biol. 2006;23(3):255. doi:10.1093/imammb/dql012.
-
(2006)
Math Med Biol.
, vol.23
, Issue.3
, pp. 255
-
-
Meyer-Hermann, M.E.1
Maini, P.K.2
Iber, D.3
-
99
-
-
44349185622
-
Implementation of a regulatory gene network to simulate the th1/2 differentiation in an agent-based model of hypersensitivity reactions
-
doi:10.1093/bioinformatics/btn135
-
Santoni D, Pedicini M, Castiglione F. Implementation of a regulatory gene network to simulate the th1/2 differentiation in an agent-based model of hypersensitivity reactions. Bioinformatics. 2008;24(11):1374. doi:10.1093/bioinformatics/btn135.
-
(2008)
Bioinformatics.
, vol.24
, Issue.11
, pp. 1374
-
-
Santoni, D.1
Pedicini, M.2
Castiglione, F.3
-
100
-
-
58249107138
-
A discrete computer model of the immune system reveals competitive interactions between the humoral and cellular branch and between cross-reacting memory and nave responses
-
doi:10.1016/j.vaccine.2008.11.109
-
Cheng Y, Ghersi D, Calcagno C, Selin LK, Puzone R, Celada F. A discrete computer model of the immune system reveals competitive interactions between the humoral and cellular branch and between cross-reacting memory and nave responses. Vaccine. 2009;27(6):833. doi:10.1016/j.vaccine.2008.11.109.
-
(2009)
Vaccine.
, vol.27
, Issue.6
, pp. 833
-
-
Cheng, Y.1
Ghersi, D.2
Calcagno, C.3
Selin, L.K.4
Puzone, R.5
Celada, F.6
-
101
-
-
34248390839
-
An enhanced agent based model of the immune system response
-
doi:10.1016/j.cellimm.2006.12.006
-
Baldazzi V, Castiglione F, Bernaschi M. An enhanced agent based model of the immune system response. Cell Immunol. 2006;244(2):77. doi:10.1016/j.cellimm. 2006.12.006.
-
(2006)
Cell Immunol.
, vol.244
, Issue.2
, pp. 77
-
-
Baldazzi, V.1
Castiglione, F.2
Bernaschi, M.3
-
102
-
-
38049136890
-
The basic immune simulator: An agent-based model to study the interactions between innate and adaptive immunity
-
doi: 10.1186/1742-4682-4-39
-
Folcik VA, An GC, Orosz CG. The basic immune simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theor Biol Med Model. 2007;4:39. doi: 10.1186/1742-4682-4-39.
-
(2007)
Theor Biol Med Model.
, vol.4
, pp. 39
-
-
Folcik, V.A.1
An, G.C.2
Orosz, C.G.3
-
103
-
-
45549108791
-
The multiscale systems immunology project: Software for cell-based immunological simulation
-
doi: 10.1186/1751-0473-3-6
-
Mitha F, Lucas TA, Feng F, Kepler TB, Chan C. The multiscale systems immunology project: software for cell-based immunological simulation. Source Code Biol Med. 2008;3:6. doi: 10.1186/1751-0473-3-6.
-
(2008)
Source Code Biol Med.
, vol.3
, pp. 6
-
-
Mitha, F.1
Lucas, T.A.2
Feng, F.3
Kepler, T.B.4
Chan, C.5
-
104
-
-
77953494820
-
Immunogrid: Towards agent-based simulations of the human immune system at a natural scale
-
doi:10.1098/rsta.2010.0067
-
Halling-Brown M, Pappalardo F, Rapin N, Zhang P, Alemani D, Emerson A, Castiglione F, Duroux P, Pennisi M, Miotto O, Churchill D, Rossi E, Moss DS, Sansom CE, Bernaschi M, Lefranc MP, Brunak S, Lund O, Motta S, Lollini PL, Murgo A, Palladini A, Basford KE, Brusic V, Shepherd AJ. Immunogrid: towards agent-based simulations of the human immune system at a natural scale. Philos Transact A Math Phys Eng Sci. 2010;368(1920):2799. doi:10.1098/rsta.2010.0067.
-
(2010)
Philos Transact A Math Phys Eng Sci.
, vol.368
, Issue.1920
, pp. 2799
-
-
Halling-Brown, M.1
Pappalardo, F.2
Rapin, N.3
Zhang, P.4
Alemani, D.5
Emerson, A.6
Castiglione, F.7
Duroux, P.8
Pennisi, M.9
Miotto, O.10
Churchill, D.11
Rossi, E.12
Moss, D.S.13
Sansom, C.E.14
Bernaschi, M.15
Lefranc, M.P.16
Brunak, S.17
Lund, O.18
Motta, S.19
Lollini, P.L.20
Murgo, A.21
Palladini, A.22
Basford, K.E.23
Brusic, V.24
Shepherd, A.J.25
more..
-
105
-
-
77956357957
-
Computational immunology meets bioinformatics: The use of prediction tools for molecular binding in the simulation of the immune system
-
doi:10.1371/journal.pone.0009862
-
Rapin N, Lund O, Bernaschi M, Castiglione F. Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS One. 2010;5(4):e9862. doi:10.1371/journal. pone.0009862.
-
(2010)
PLoS One.
, vol.5
, Issue.4
-
-
Rapin, N.1
Lund, O.2
Bernaschi, M.3
Castiglione, F.4
-
106
-
-
84858613793
-
-
Wikipedia, http://en.wikipedia.org/wiki/comparison-of-agentbased- modeling-software.
-
Wikipedia
-
-
-
107
-
-
84872215252
-
-
Swarm, http://www.swarm.org/index.php/tools-for-agent-based- modelling.
-
Swarm
-
-
-
108
-
-
0141877349
-
-
Wilensky U. Netlogo. http://ccl.northwestern.edu/netlogo/. (1999).
-
(1999)
Netlogo
-
-
Wilensky, U.1
-
109
-
-
84866733126
-
-
(Springer, London), chap. From artificial life to in silico medicine: Net- Logo as a means of translational knowledge representation in biomedical research;
-
An G, Wilensky U. Artificial life models in software. (Springer, London), chap. From artificial life to in silico medicine: Net- Logo as a means of translational knowledge representation in biomedical research; 2009. p. 183-214.
-
(2009)
Artificial Life Models in Software
, pp. 183-214
-
-
An, G.1
Wilensky, U.2
-
110
-
-
38549114452
-
From logical regulatory graphs to standard petri nets: Dynamical roles and functionality of feedback circuits
-
Priami C, Ingolfsdottir A, Mishra B, Riis Nielson H, editors. Springer, Berlin/Heidelberg;
-
Remy E, Ruet P, Mendoza L, Thieffry D, Chaouiya C. From logical regulatory graphs to standard petri nets: Dynamical roles and functionality of feedback circuits. In: Priami C, Ingolfsdottir A, Mishra B, Riis Nielson H, editors. Transactions on Computational Systems Biology VII, Lecture Notes in Computer Science, vol. 4230. Springer, Berlin/Heidelberg; 2006. p. 56-72.
-
(2006)
Transactions on Computational Systems Biology VII, Lecture Notes in Computer Science
, vol.4230
, pp. 56-72
-
-
Remy, E.1
Ruet, P.2
Mendoza, L.3
Thieffry, D.4
Chaouiya, C.5
-
111
-
-
33646345600
-
A network model for the control of the differentiation process in th cells
-
doi:10.1016/j.biosystems.2005.10.004
-
Mendoza L. A network model for the control of the differentiation process in th cells. Biosystems. 2006;84(2):101. doi:10.1016/j.biosystems.2005.10.004.
-
(2006)
Biosystems.
, vol.84
, Issue.2
, pp. 101
-
-
Mendoza, L.1
-
112
-
-
34548431024
-
A logical model provides insights into t cell receptor signaling
-
doi: 10.1371/journal.pcbi.0030163
-
Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus UU, Weismantel R, Gilles ED, Klamt S, Schraven B. A logical model provides insights into t cell receptor signaling. PLoS Comput Biol. 2007;3(8):e163. doi: 10.1371/journal.pcbi.0030163.
-
(2007)
PLoS Comput Biol.
, vol.3
, Issue.8
-
-
Saez-Rodriguez, J.1
Simeoni, L.2
Lindquist, J.A.3
Hemenway, R.4
Bommhardt, U.5
Arndt, B.6
Haus, U.U.7
Weismantel, R.8
Gilles, E.D.9
Klamt, S.10
Schraven, B.11
-
113
-
-
71449120701
-
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
-
doi:10.1038/msb.2009.87
-
Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol. 2009;5:331. doi:10.1038/msb.2009.87.
-
(2009)
Mol Syst Biol.
, vol.5
, pp. 331
-
-
Saez-Rodriguez, J.1
Alexopoulos, L.G.2
Epperlein, J.3
Samaga, R.4
Lauffenburger, D.A.5
Klamt, S.6
Sorger, P.K.7
-
114
-
-
40149109180
-
Hostpathogen systems biology: Logical modelling of hepatocyte growth factor and helicobacter pylori induced c-met signal transduction
-
doi: 10.1186/1752-0509-2-4
-
Franke R, Mller M, Wundrack N, Gilles ED, Klamt S, Khne T, Naumann M. Hostpathogen systems biology: logical modelling of hepatocyte growth factor and helicobacter pylori induced c-met signal transduction. BMC Syst Biol. 2008;2:4. doi: 10.1186/1752-0509-2-4.
-
(2008)
BMC Syst Biol.
, vol.2
, pp. 4
-
-
Franke, R.1
Mller, M.2
Wundrack, N.3
Gilles, E.D.4
Klamt, S.5
Khne, T.6
Naumann, M.7
-
115
-
-
34548302044
-
Petri net modelling of biological networks
-
doi:10.1093/bib/bbm029
-
Chaouiya C. Petri net modelling of biological networks. Brief Bioinform. 2007;8(4):210. doi:10.1093/bib/bbm029.
-
(2007)
Brief Bioinform.
, vol.8
, Issue.4
, pp. 210
-
-
Chaouiya, C.1
-
116
-
-
0035235039
-
Representation and simulation of biochemical processes using the pi-calculus process algebra
-
Regev A, Silverman W, Shapiro E. Representation and simulation of biochemical processes using the pi-calculus process algebra. Pac Symp Biocomput; 2001:459-470.
-
(2001)
Pac Symp Biocomput;
, pp. 459-470
-
-
Regev, A.1
Silverman, W.2
Shapiro, E.3
-
118
-
-
26944469780
-
Integration of immune models using petri nets
-
Nicosia Giuseppe, Cutello Vincenzo, Bentley Peter J, et al, editors., ICARIS 2004, Catania, Sicily, Italy, September 13-16, 2004- Vol 3239 of Lecture Notes in Computer Science. Berlin: Springer
-
Na D, Park I, Lee KH, Lee D. Integration of immune models using petri nets. In: Nicosia Giuseppe, Cutello Vincenzo, Bentley Peter J, et al, editors. Proceedings of Artificial Immune Systems: Third International Conference, ICARIS 2004, Catania, Sicily, Italy, September 13-16, 2004-Vol 3239 of Lecture Notes in Computer Science. Berlin: Springer; 2004. p. 205-216.
-
(2004)
Proceedings of Artificial Immune Systems: Third International Conference
, pp. 205-216
-
-
Na, D.1
Park, I.2
Lee, K.H.3
Lee, D.4
-
120
-
-
84866734307
-
-
CoSBi (Center for Computational and Systems Biology), University of Trento;
-
Guerriero ML, Prandi D, Priami C, Quaglia P. Process calculi abstractions for biology. Tech. Rep. Technical Report TR-13-2006, CoSBi (Center for Computational and Systems Biology), University of Trento; 2006.
-
(2006)
Process Calculi Abstractions for Biology. Tech. Rep. Technical Report TR-13-2006
-
-
Guerriero, M.L.1
Prandi, D.2
Priami, C.3
Quaglia, P.4
-
121
-
-
38949179852
-
Stochastic p systems and the simulation of biochemical processes with dynamic compartments
-
doi: 10.1016/j.biosystems.2006.12.009
-
Spicher A, Michel O, Cieslak M, Giavitto JL, Prusinkiewicz P. Stochastic p systems and the simulation of biochemical processes with dynamic compartments. Biosystems. 2008;91(3):458. doi: 10.1016/j.biosystems.2006.12.009.
-
(2008)
Biosystems.
, vol.91
, Issue.3
, pp. 458
-
-
Spicher, A.1
Michel, O.2
Cieslak, M.3
Giavitto, J.L.4
Prusinkiewicz, P.5
-
122
-
-
38949165633
-
Dynamics of hiv infection studied with cellular automata and conformon-p systems
-
doi:10.1016/j.biosystems.2007.01.007
-
Corne DW, Frisco P. Dynamics of hiv infection studied with cellular automata and conformon-p systems. Biosystems. 2008; 91(3):531. doi:10.1016/j.biosystems.2007.01.007.
-
(2008)
Biosystems.
, vol.91
, Issue.3
, pp. 531
-
-
Corne, D.W.1
Frisco, P.2
-
124
-
-
80054718671
-
Acomputational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology disease biology and molecular reaction networks
-
Eissing T, Kuepfer L, Becker C, Block M, Coboeken K, Gaub T, Goerlitz L, Jaeger J, Loosen R, Ludewig B, et al.Acomputational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks. Front Physiol. 2011;2.
-
(2011)
Front Physiol.
, pp. 2
-
-
Eissing, T.1
Kuepfer, L.2
Becker, C.3
Block, M.4
Coboeken, K.5
Gaub, T.6
Goerlitz, L.7
Jaeger, J.8
Loosen, R.9
Ludewig, B.10
-
125
-
-
63949087100
-
Adaptation of hiv-1 to human leukocyte antigen class i
-
Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, Gatanaga H, Fujiwara M, Hachiya A., Koizumi H., et al. Adaptation of hiv-1 to human leukocyte antigen class i. Nature. 2009;458(7238):641.
-
(2009)
Nature.
, vol.458
, Issue.7238
, pp. 641
-
-
Kawashima, Y.1
Pfafferott, K.2
Frater, J.3
Matthews, P.4
Payne, R.5
Addo, M.6
Gatanaga, H.7
Fujiwara, M.8
Hachiya, A.9
Koizumi, H.10
-
126
-
-
73449137909
-
Quantifying adaptive evolution in the drosophila immune system
-
Obbard D, Welch J, Kim K, Jiggins F. Quantifying adaptive evolution in the drosophila immune system. PLoS Genet. 2009;5(10):e1000698.
-
(2009)
PLoS Genet.
, vol.5
, Issue.10
-
-
Obbard, D.1
Welch, J.2
Kim, K.3
Jiggins, F.4
-
127
-
-
46149127936
-
The immune system, adaptation, and machine learning
-
Farmer J, Packard N, Perelson A. The immune system, adaptation, and machine learning. Phys D: Nonlinear Phenomena. 1986;22(1-3):187.
-
(1986)
Phys D: Nonlinear Phenomena.
, vol.22
, Issue.1-3
, pp. 187
-
-
Farmer, J.1
Packard, N.2
Perelson, A.3
-
128
-
-
0023063205
-
Adaptive dynamic networks as models for the immune system and autocatalytic sets
-
Farmer J, Kauffman S, Packard N, Perelson A. Adaptive dynamic networks as models for the immune system and autocatalytic sets. Ann N Y Acad Sci. 1987;504(1):118.
-
(1987)
Ann N y Acad Sci.
, vol.504
, Issue.1
, pp. 118
-
-
Farmer, J.1
Kauffman, S.2
Packard, N.3
Perelson, A.4
-
130
-
-
0032313108
-
Simulated evolution of antibody gene libraries under pathogen selection
-
Oprea M, Forrest S. Simulated evolution of antibody gene libraries under pathogen selection. In: Systems, Man, and Cybernetics, 1998. 1998 IEEE International Conference on, vol 4. 1998;4:3793-3798.
-
(1998)
Systems, Man, and Cybernetics, 1998. 1998 IEEE International Conference On, Vol 4
, vol.4
, pp. 3793-3798
-
-
Oprea, M.1
Forrest, S.2
-
131
-
-
3543122436
-
Immune memory and gene library evolution in the dynamic clonal selection algorithm
-
Kim J, Bentley P. Immune memory and gene library evolution in the dynamic clonal selection algorithm. Genet Program Evolvable Mach. 2004;5(4):361.
-
(2004)
Genet Program Evolvable Mach.
, vol.5
, Issue.4
, pp. 361
-
-
Kim, J.1
Bentley, P.2
-
133
-
-
33947193447
-
Computer immunology
-
doi:10.1111/j.1600-065X.2007.00499.x
-
Forrest S, Beauchemin C. Computer immunology. Immunol Rev. 2007;216:176. doi:10.1111/j.1600-065X.2007.00499.x.
-
(2007)
Immunol Rev.
, vol.216
, pp. 176
-
-
Forrest, S.1
Beauchemin, C.2
-
134
-
-
34147122539
-
Self-organizing behavior in a lattice model for co-evolution of virus and immune systems
-
Izmailian N, Papoyan V, Priezzhev V, Hu C, et al. Self-organizing behavior in a lattice model for co-evolution of virus and immune systems. Phys Rev E, Stat Nonlinear Soft Matter Phys. 2007;75(4 Pt 1):041104.
-
(2007)
Phys Rev e Stat Nonlinear Soft Matter Phys.
, vol.75
, Issue.4 PART 1
, pp. 041104
-
-
Izmailian, N.1
Papoyan, V.2
Priezzhev, V.3
Hu, C.4
-
135
-
-
84866733281
-
Short-time evolution in the adaptive immune system
-
Guttenberg N, Ali Tabei SM, Dinner AR. Short-time evolution in the adaptive immune system. Phys Rev E. 2011;84(3):031932.
-
(2011)
Phys Rev E.
, vol.84
, Issue.3
, pp. 031932
-
-
Guttenberg, N.1
Ali Tabei, S.M.2
Dinner, A.R.3
-
136
-
-
82255186689
-
Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes
-
Lieberman T, Michel J, Aingaran M, Potter-Bynoe G, Roux D, Davis M Jr, Skurnik D, Leiby N, LiPuma J, Goldberg J, et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat Genet; 2011.
-
(2011)
Nat Genet;
-
-
Lieberman, T.1
Michel, J.2
Aingaran, M.3
Potter-Bynoe, G.4
Roux, D.5
Davis Jr., M.6
Skurnik, D.7
Leiby, N.8
Lipuma, J.9
Goldberg, J.10
-
137
-
-
33750533388
-
Physicochemical modelling of cell signalling pathways
-
doi:10.1038/ncb1497
-
Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK. Physicochemical modelling of cell signalling pathways. Nat Cell Biol. 2006;8(11):1195. doi:10.1038/ncb1497.
-
(2006)
Nat Cell Biol.
, vol.8
, Issue.11
, pp. 1195
-
-
Aldridge, B.B.1
Burke, J.M.2
Lauffenburger, D.A.3
Sorger, P.K.4
-
138
-
-
33745075591
-
Tools for kinetic modeling of biochemical networks
-
doi:10.1038/nbt0606-667
-
Alves R, Antunes F, Salvador A. Tools for kinetic modeling of biochemical networks. Nat Biotechnol. 2006;24(6):667. doi:10.1038/nbt0606-667.
-
(2006)
Nat Biotechnol.
, vol.24
, Issue.6
, pp. 667
-
-
Alves, R.1
Antunes, F.2
Salvador, A.3
-
139
-
-
58549110252
-
Stochastic modelling for quantitative description of heterogeneous biological systems
-
doi:10.1038/nrg2509
-
Wilkinson DJ. Stochastic modelling for quantitative description of heterogeneous biological systems. Nat Rev Genet. 2009.10(2): 122. doi:10.1038/nrg2509.
-
(2009)
Nat Rev Genet.
, vol.10
, Issue.2
, pp. 122
-
-
Wilkinson, D.J.1
-
141
-
-
71549131604
-
Discrete dynamic modeling of cellular signaling networks
-
doi:10.1016/ S0076-6879(09)67011-7
-
Albert R, Wang RS. Discrete dynamic modeling of cellular signaling networks. Methods Enzymol. 2009;467:281. doi:10.1016/ S0076-6879(09)67011-7.
-
(2009)
Methods Enzymol.
, vol.467
, Issue.281
-
-
Albert, R.1
Wang, R.S.2
-
142
-
-
34047105227
-
Explaining a complex living system: Dynamics, multi-scaling and emergence
-
doi:10.1098/rsif.2006.0173
-
Cohen IR, Harel D. Explaining a complex living system: dynamics, multi-scaling and emergence. J R Soc Interface. 2007;4(13):175. doi:10.1098/rsif.2006.0173.
-
(2007)
J R Soc Interface.
, vol.4
, Issue.13
, pp. 175
-
-
Cohen, I.R.1
Harel, D.2
-
143
-
-
77950347868
-
The executable pathway to biological networks
-
doi:10.1093/bfgp/ elp054
-
Fisher J, Piterman N. The executable pathway to biological networks. Brief Funct Genomics. 2010;9(1):79. doi:10.1093/bfgp/ elp054.
-
(2010)
Brief Funct Genomics.
, vol.9
, Issue.1
, pp. 79
-
-
Fisher, J.1
Piterman, N.2
-
144
-
-
67650242026
-
Modular assembly of cell systems biology models using p systems
-
doi:10.1142/S0129054109006668
-
Romero-Campero FJ, Twycross J, Camara M, Bennett M, Gheorghe M, Krasnogor N. Modular assembly of cell systems biology models using p systems. Int J Found Comput Sci. 2009;3:427 doi:10.1142/S0129054109006668.
-
(2009)
Int J Found Comput Sci.
, vol.3
, pp. 427
-
-
Romero-Campero, F.J.1
Twycross, J.2
Camara, M.3
Bennett, M.4
Gheorghe, M.5
Krasnogor, N.6
-
145
-
-
84872214045
-
-
Swarm, http://www.swarm.org/wiki/agent-based-models-in- biology-and-medicine.
-
Swarm
-
-
-
146
-
-
33747366698
-
Rules for modeling signal-transduction systems
-
doi:10.1126/stke.3442006re6
-
Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W. Rules for modeling signal-transduction systems. Sci STKE. 2006;2006(344):re6. doi:10.1126/stke.3442006re6.
-
(2006)
Sci STKE
, vol.2006
, Issue.344
-
-
Hlavacek, W.S.1
Faeder, J.R.2
Blinov, M.L.3
Posner, R.G.4
Hucka, M.5
Fontana, W.6
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