-
1
-
-
33845368513
-
COPASI--a COmplex PAthway SImulator
-
Hoops S, et al: COPASI--a COmplex PAthway SImulator. Bioinformatics. 2006, 22 (24): 3067-74. 10.1093/bioinformatics/btl485.
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
-
2
-
-
0035478586
-
The Virtual Cell: a software environment for computational cell biology
-
Loew LM, Schaff JC: The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol. 2001, 19 (10): 401-6. 10.1016/S0167-7799(01)01740-1.
-
(2001)
Trends Biotechnol
, vol.19
, Issue.10
, pp. 401-406
-
-
Loew, L.M.1
Schaff, J.C.2
-
4
-
-
38049136890
-
The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity
-
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: 39-10.1186/1742-4682-4-39.
-
(2007)
Theor Biol Med Model
, vol.4
, pp. 39
-
-
Folcik, V.A.1
An, G.C.2
Orosz, C.G.3
-
5
-
-
34250756654
-
NetLogo, a multi-agent simulation environment
-
Sklar E: NetLogo, a multi-agent simulation environment. Artif Life. 2007, 13 (3): 303-11. 10.1162/artl.2007.13.3.303.
-
(2007)
Artif Life
, vol.13
, Issue.3
, pp. 303-311
-
-
Sklar, E.1
-
8
-
-
84866510577
-
ENteric Immunity SImulator: A tool for in silico study of gastroenteric infections
-
Wendelsdorf K, et al: ENteric Immunity SImulator: A tool for in silico study of gastroenteric infections. IEEE Transactions on NanoBioScience. 2012, 11: 273-288.
-
(2012)
IEEE Transactions on NanoBioScience
, vol.11
, pp. 273-288
-
-
Wendelsdorf, K.1
-
11
-
-
0020972784
-
Mathematical modeling in immunology
-
DeLisi C: Mathematical modeling in immunology. Annu Rev Biophys Bioeng. 1983, 12: 117-38. 10.1146/annurev.bb.12.060183.001001.
-
(1983)
Annu Rev Biophys Bioeng
, vol.12
, pp. 117-138
-
-
DeLisi, C.1
-
12
-
-
0037079054
-
Computational systems biology
-
Kitano H: Computational systems biology. Nature. 2002, 420 (6912): 206-10. 10.1038/nature01254.
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 206-210
-
-
Kitano, H.1
-
13
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
Hucka M, et al: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 19 (4): 524-31. 10.1093/bioinformatics/btg015.
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
-
14
-
-
85012427182
-
Whither computational biology
-
Davison DB, et al: Whither computational biology. J Comput Biol. 1994, 1 (1): 1-2.
-
(1994)
J Comput Biol
, vol.1
, Issue.1
, pp. 1-2
-
-
Davison, D.B.1
-
15
-
-
0036607144
-
New computational approaches for analysis of cis-regulatory networks
-
Brown CT, et al: New computational approaches for analysis of cis-regulatory networks. Dev Biol. 2002, 246 (1): 86-102. 10.1006/dbio.2002.0619.
-
(2002)
Dev Biol
, vol.246
, Issue.1
, pp. 86-102
-
-
Brown, C.T.1
-
16
-
-
0032549745
-
Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene
-
Yuh CH, Bolouri H, Davidson EH: Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science. 1998, 279 (5358): 1896-902. 10.1126/science.279.5358.1896.
-
(1998)
Science
, vol.279
, Issue.5358
, pp. 1896-1902
-
-
Yuh, C.H.1
Bolouri, H.2
Davidson, E.H.3
-
17
-
-
84926059438
-
Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling
-
Ye H, et al: Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling. Proc Natl Acad Sci USA. 2015, 112 (13): E1569-76. 10.1073/pnas.1417063112.
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, Issue.13
, pp. E1569-E1576
-
-
Ye, H.1
-
18
-
-
0037203880
-
Inspired by immunity
-
Klarreich E: Inspired by immunity. Nature. 2002, 415 (6871): 468-70. 10.1038/415468a.
-
(2002)
Nature
, vol.415
, Issue.6871
, pp. 468-470
-
-
Klarreich, E.1
-
20
-
-
84876915404
-
Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity
-
Carbo A, et al: Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity. PLoS Comput Biol. 2013, 9 (4): e1003027-10.1371/journal.pcbi.1003027.
-
(2013)
PLoS Comput Biol
, vol.9
, Issue.4
, pp. e1003027
-
-
Carbo, A.1
-
21
-
-
84883495378
-
Predictive computational modeling of the mucosal immune responses during Helicobacter pylori infection
-
Carbo A, et al: Predictive computational modeling of the mucosal immune responses during Helicobacter pylori infection. PLoS One. 2013, 8 (9): e73365-10.1371/journal.pone.0073365.
-
(2013)
PLoS One
, vol.8
, Issue.9
, pp. e73365
-
-
Carbo, A.1
-
22
-
-
27744570841
-
Pattern-oriented modeling of agent-based complex systems: lessons from ecology
-
Grimm V, et al: Pattern-oriented modeling of agent-based complex systems: lessons from ecology. Science. 2005, 310 (5750): 987-91. 10.1126/science.1116681.
-
(2005)
Science
, vol.310
, Issue.5750
, pp. 987-991
-
-
Grimm, V.1
-
23
-
-
0001918317
-
Mathematical analysis of hiv-1 dyamics in vivo
-
Perelson A, Nelson P: Mathematical analysis of hiv-1 dyamics in vivo. SIAM review. 1999, 41 (1): 3-44. 10.1137/S0036144598335107.
-
(1999)
SIAM review
, vol.41
, Issue.1
, pp. 3-44
-
-
Perelson, A.1
Nelson, P.2
-
24
-
-
70349454512
-
Tutorial on agent-based modeling and simulation
-
Macal C, North M: Tutorial on agent-based modeling and simulation. Journal of Simulation. 2010, 8 (2): 177-183.
-
(2010)
Journal of Simulation
, vol.8
, Issue.2
, pp. 177-183
-
-
Macal, C.1
North, M.2
-
26
-
-
33947507091
-
Computational systems biology in drug discovery and development: methods and applications
-
Materi W, Wishart DS: Computational systems biology in drug discovery and development: methods and applications. Drug Discov Today. 2007, 12 (7-8): 295-303. 10.1016/j.drudis.2007.02.013.
-
(2007)
Drug Discov Today
, vol.12
, Issue.7-8
, pp. 295-303
-
-
Materi, W.1
Wishart, D.S.2
-
27
-
-
84886745848
-
Merging concepts - coupling an agent-based model of hematopoietic stem cells with an ODE model of granulopoiesis
-
Krinner A, et al: Merging concepts - coupling an agent-based model of hematopoietic stem cells with an ODE model of granulopoiesis. BMC Syst Biol. 2013, 7: 117-10.1186/1752-0509-7-117.
-
(2013)
BMC Syst Biol
, vol.7
, pp. 117
-
-
Krinner, A.1
-
28
-
-
84918767987
-
A multiscale model of interleukin-6-mediated immune regulation in Crohn's disease and its application in drug discovery and development
-
Dwivedi G, et al: A multiscale model of interleukin-6-mediated immune regulation in Crohn's disease and its application in drug discovery and development. CPT Pharmacometrics Syst Pharmacol. 2014, 3: e89-10.1038/psp.2013.64.
-
(2014)
CPT Pharmacometrics Syst Pharmacol
, vol.3
, pp. e89
-
-
Dwivedi, G.1
-
29
-
-
85085219228
-
Multiscale Computational Modeling in Vascular Biology: From Molecular Mechanisms to Tissue-Level Structure and Function.
-
Edited by: G. Amit. Springer Berlin Heidelberg
-
Hayenga H, et al: Multiscale Computational Modeling in Vascular Biology: From Molecular Mechanisms to Tissue-Level Structure and Function. Multiscale Computer Modeling in Biomechanics and Biomedical Engineering. Edited by: G. Amit. 2013, Springer Berlin Heidelberg, 209-240. 10.1007/8415_2012_147.
-
(2013)
Multiscale Computer Modeling in Biomechanics and Biomedical Engineering.
, pp. 209-240
-
-
Hayenga, H.1
-
30
-
-
84946479380
-
Computational modeling of chemo-bio-mechanical coupling: a systems-biology approach toward wound healing
-
Buganza Tepole A, Kuhl E: Computational modeling of chemo-bio-mechanical coupling: a systems-biology approach toward wound healing. Comput Methods Biomech Biomed Engin. 2014, 1-18.
-
(2014)
Comput Methods Biomech Biomed Engin
, pp. 1-18
-
-
Buganza Tepole, A.1
Kuhl, E.2
-
31
-
-
84872511963
-
Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI
-
Sutterlin T, et al: Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. Bioinformatics. 2013, 29 (2): 223-9. 10.1093/bioinformatics/bts659.
-
(2013)
Bioinformatics
, vol.29
, Issue.2
, pp. 223-229
-
-
Sutterlin, T.1
-
32
-
-
84903153748
-
Nutrition Research and the Impact of Computational Systems Biology
-
Mc Auley MT, et al: Nutrition Research and the Impact of Computational Systems Biology. J Comput Sci Syst Biol. 2013, 6 (5): 271-285. 10.4172/jcsb.1000122.
-
(2013)
J Comput Sci Syst Biol
, vol.6
, Issue.5
, pp. 271-285
-
-
Mc Auley, M.T.1
-
33
-
-
0034861860
-
Design and implementation of an immune system simulator
-
Bernaschi M, Castiglione F: Design and implementation of an immune system simulator. Comput Biol Med. 2001, 31 (5): 303-31. 10.1016/S0010-4825(01)00011-7.
-
(2001)
Comput Biol Med
, vol.31
, Issue.5
, pp. 303-331
-
-
Bernaschi, M.1
Castiglione, F.2
-
34
-
-
0036640183
-
IMMSIM, a flexible model for in machina experiments on immune system responses
-
Puzone R, et al: IMMSIM, a flexible model for in machina experiments on immune system responses. Future Generation Computer Systems. 2002, 18 (7): 961-972. 10.1016/S0167-739X(02)00075-4.
-
(2002)
Future Generation Computer Systems
, vol.18
, Issue.7
, pp. 961-972
-
-
Puzone, R.1
-
35
-
-
33947191941
-
Cellular automata-based modeling program: synthetic immune system
-
Mata J, Cohn M: Cellular automata-based modeling program: synthetic immune system. Immunol Rev. 2007, 216: 198-212.
-
(2007)
Immunol Rev
, vol.216
, pp. 198-212
-
-
Mata, J.1
Cohn, M.2
-
36
-
-
79551555393
-
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim
-
Sneddon MW, Faeder JR, Emonet T: Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nat Methods. 2011, 8 (2): 177-83. 10.1038/nmeth.1546.
-
(2011)
Nat Methods
, vol.8
, Issue.2
, pp. 177-183
-
-
Sneddon, M.W.1
Faeder, J.R.2
Emonet, T.3
-
37
-
-
47949098283
-
The lymph node B cell immune response: Dynamic analysis in-silico
-
Swerdlin N, Cohen IR, Harel D: The lymph node B cell immune response: Dynamic analysis in-silico. Proceedings of the Ieee. 2008, 96 (8): 1421-1443.
-
(2008)
Proceedings of the Ieee
, vol.96
, Issue.8
, pp. 1421-1443
-
-
Swerdlin, N.1
Cohen, I.R.2
Harel, D.3
-
38
-
-
84944222777
-
Rhapsody: A Complete Life-Cycle Model-Based Development System.
-
Edited by: M. Butler, L. Petre, and K. Sere., Springer Berlin Heidelberg
-
Gery E, Harel H, Palachi E: Rhapsody: A Complete Life-Cycle Model-Based Development System. Integrated Formal Methods. Edited by: M. Butler, L. Petre, and K. Sere. 2002, Springer Berlin Heidelberg, 1-10. 10.1007/3-540-47884-1_1.
-
(2002)
Integrated Formal Methods.
, pp. 1-10
-
-
Gery, E.1
Harel, H.2
Palachi, E.3
-
39
-
-
34547724111
-
Agent-based Simulation Platforms: Review and Development Recommendations
-
Railsback S, Lytinen S, Jackson S: Agent-based Simulation Platforms: Review and Development Recommendations. Simulation. 2006, 82 (9): 609-623. 10.1177/0037549706073695.
-
(2006)
Simulation
, vol.82
, Issue.9
, pp. 609-623
-
-
Railsback, S.1
Lytinen, S.2
Jackson, S.3
-
40
-
-
84961618578
-
-
Swarm
-
Swarm: Available from: http://www.swarm.org
-
-
-
-
42
-
-
33646884848
-
SBMLToolbox: an SBML toolbox for MATLAB users
-
Keating SM, et al: SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics. 2006, 22 (10): 1275-1277. 10.1093/bioinformatics/btl111.
-
(2006)
Bioinformatics
, vol.22
, Issue.10
, pp. 1275-1277
-
-
Keating, S.M.1
-
45
-
-
33847626655
-
Multiscale modeling in biology - New insights into cancer illustrate how mathematical tools are enhancing the understanding of life from the smallest scale to the grandest
-
Schnell S, Grima R, Maini PK: Multiscale modeling in biology - New insights into cancer illustrate how mathematical tools are enhancing the understanding of life from the smallest scale to the grandest. American Scientist. 2007, 95 (2): 134-142. 10.1511/2007.64.134.
-
(2007)
American Scientist
, vol.95
, Issue.2
, pp. 134-142
-
-
Schnell, S.1
Grima, R.2
Maini, P.K.3
-
46
-
-
0142092630
-
In silico models for cellular and molecular immunology: successes, promises and challenges
-
Chakraborty AK, Dustin ML, Shaw AS: In silico models for cellular and molecular immunology: successes, promises and challenges. Nat Immunol. 2003, 4 (10): 933-6. 10.1038/ni1003-933.
-
(2003)
Nat Immunol
, vol.4
, Issue.10
, pp. 933-936
-
-
Chakraborty, A.K.1
Dustin, M.L.2
Shaw, A.S.3
-
47
-
-
77950361733
-
Multi-scale modelling in computational biomedicine
-
Sloot PMA, Hoekstra AG: Multi-scale modelling in computational biomedicine. Briefings in Bioinformatics. 2010, 11 (1): 142-152. 10.1093/bib/bbp038.
-
(2010)
Briefings in Bioinformatics
, vol.11
, Issue.1
, pp. 142-152
-
-
Sloot, P.M.A.1
Hoekstra, A.G.2
-
48
-
-
84866861707
-
High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENteric Immunity SImulator (ENISI).
-
Bisset K, et al: High-Performance Interaction-Based Simulation of Gut Immunopathologies with ENteric Immunity SImulator (ENISI). 2012 Ieee 26th International Parallel and Distributed Processing Symposium (Ipdps). 2012, 48-59.
-
(2012)
2012 Ieee 26th International Parallel and Distributed Processing Symposium (Ipdps)
, pp. 48-59
-
-
-
49
-
-
84909632141
-
Computational modeling of heterogeneity and function of CD4+ T cells
-
Carbo A, et al: Computational modeling of heterogeneity and function of CD4+ T cells. Front Cell Dev Biol. 2014, 2: 31-
-
(2014)
Front Cell Dev Biol
, vol.2
, pp. 31
-
-
Carbo, A.1
-
50
-
-
84867423956
-
Modeling the Role of Peroxisome Proliferator-Activated Receptor gamma and MicroRNA-146 in Mucosal Immune Responses to Clostridium difficile
-
Viladomiu M, et al: Modeling the Role of Peroxisome Proliferator-Activated Receptor gamma and MicroRNA-146 in Mucosal Immune Responses to Clostridium difficile. PLoS One. 2012, 7 (10): e47525-10.1371/journal.pone.0047525.
-
(2012)
PLoS One
, vol.7
, Issue.10
, pp. e47525
-
-
Viladomiu, M.1
-
51
-
-
77952954251
-
Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease
-
Wendelsdorf K, et al: Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease. J Theor Biol. 2010, 264 (4): 1225-39. 10.1016/j.jtbi.2010.03.027.
-
(2010)
J Theor Biol
, vol.264
, Issue.4
, pp. 1225-1239
-
-
Wendelsdorf, K.1
-
52
-
-
85020633183
-
Complex adaptive systems modeling with Repast Simphony
-
North MJ, et al: Complex adaptive systems modeling with Repast Simphony. Complex Adaptive Systems Modeling. 2013, 1: 3-10.1186/2194-3206-1-3.
-
(2013)
Complex Adaptive Systems Modeling
, vol.1
, pp. 3
-
-
North, M.J.1
-
53
-
-
84993725134
-
Introduction: The Simulation of Social Agents
-
Sallach D, Macal C: Introduction: The Simulation of Social Agents. Special Issue Social Science Computer Review. 2001, 19 (3): 245-248. 10.1177/089443930101900301.
-
(2001)
Special Issue Social Science Computer Review
, vol.19
, Issue.3
, pp. 245-248
-
-
Sallach, D.1
Macal, C.2
-
55
-
-
47949099328
-
CellDesigner 3.5: A versatile modeling tool for biochemical networks
-
Funahashi A, et al: CellDesigner 3.5: A versatile modeling tool for biochemical networks. Proceedings of the Ieee. 2008, 96 (8): 1254-1265.
-
(2008)
Proceedings of the Ieee
, vol.96
, Issue.8
, pp. 1254-1265
-
-
Funahashi, A.1
-
56
-
-
80052221036
-
A declarative model assembly infrastructure for verification and validation.
-
North MJ, et al: A declarative model assembly infrastructure for verification and validation. Advancing Social Simulation: The First World Congress. 2007, 129-140. 10.1007/978-4-431-73167-2_13.
-
(2007)
Advancing Social Simulation: The First World Congress
, pp. 129-140
-
-
North, M.J.1
-
57
-
-
84940666251
-
Suervised learning methods in modeling of CD4+ T cell heterogeneity.
-
Lu P, et al: Suervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Mining. 2015
-
(2015)
BioData Mining
-
-
Lu, P.1
-
58
-
-
84961653557
-
Supervised learning with artificial neural networks in modeling of cell differentiation processes.
-
Morgan Kaufmann: Burlignton, MA
-
Lu P, et al: Supervised learning with artificial neural networks in modeling of cell differentiation processes. Emerging Trends in Computational Biology, Bioinformatics and Systems Biology. 2015, Morgan Kaufmann: Burlignton, MA
-
(2015)
Emerging Trends in Computational Biology, Bioinformatics and Systems Biology.
-
-
Lu, P.1
-
59
-
-
84894515658
-
Neural network models for classifying immune cell subsets
-
Shangai, China
-
Mei Y, et al: Neural network models for classifying immune cell subsets. BIBM. 2013, Shangai, China
-
(2013)
BIBM
-
-
Mei, Y.1
-
60
-
-
4344591762
-
T-bet upregulation and subsequent interleukin 12 stimulation are essential for induction of Th1 mediated immunopathology in Crohn's disease
-
Matsuoka K, et al: T-bet upregulation and subsequent interleukin 12 stimulation are essential for induction of Th1 mediated immunopathology in Crohn's disease. Gut. 2004, 53 (9): 1303-8. 10.1136/gut.2003.024190.
-
(2004)
Gut
, vol.53
, Issue.9
, pp. 1303-1308
-
-
Matsuoka, K.1
-
61
-
-
33646577466
-
Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells
-
Bettelli E, et al: Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells. Nature. 2006, 441 (7090): 235-8. 10.1038/nature04753.
-
(2006)
Nature
, vol.441
, Issue.7090
, pp. 235-238
-
-
Bettelli, E.1
-
62
-
-
36248965294
-
TGF-beta and IL-6 drive the production of IL-17 and IL-10 by T cells and restrain T(H)-17 cell-mediated pathology
-
McGeachy MJ, et al: TGF-beta and IL-6 drive the production of IL-17 and IL-10 by T cells and restrain T(H)-17 cell-mediated pathology. Nat Immunol. 2007, 8 (12): 1390-7. 10.1038/ni1539.
-
(2007)
Nat Immunol
, vol.8
, Issue.12
, pp. 1390-1397
-
-
McGeachy, M.J.1
-
63
-
-
85003047735
-
Systems modeling of the role of interleukin-21 in the maintenance of effector CD4+ T cell responses during chronic Helicobacter pylori infection
-
Carbo A, et al: Systems modeling of the role of interleukin-21 in the maintenance of effector CD4+ T cell responses during chronic Helicobacter pylori infection. MBio. 2014, 5 (4): e01243-14.
-
(2014)
MBio
, vol.5
, Issue.4
, pp. e01243-e01314
-
-
Carbo, A.1
|