-
1
-
-
20244373849
-
On cellular automaton approaches to modeling biological cells
-
J. Rosenthal D.S. Gilliam (eds). Springer-Verlag New York
-
Alber, M. S., M. A. Kiskowski, J. A. Glazier, and Y. Jiang. On cellular automaton approaches to modeling biological cells. In: Mathematical Systems Theory in Biology, Communications, Computation, and Finance, edited by J. Rosenthal, and D. S. Gilliam. New York: Springer-Verlag, 2003, pp. 1-40.
-
(2003)
Mathematical Systems Theory in Biology, Communications, Computation, and Finance
, pp. 1-40
-
-
Alber, M.S.1
Kiskowski, M.A.2
Glazier, J.A.3
Jiang, Y.4
-
2
-
-
33749059757
-
An agent based model for real-time signaling induced in osteocytic networks by mechanical stimuli
-
BJ Ausk TS Gross S Srinivasan 2006 An agent based model for real-time signaling induced in osteocytic networks by mechanical stimuli J. Theor. Biol 39 2638 2646
-
(2006)
J. Theor. Biol
, vol.39
, pp. 2638-2646
-
-
Ausk, B.J.1
Gross, T.S.2
Srinivasan, S.3
-
3
-
-
61449164943
-
Agent-based model of therapeutic adipose-derived stromal cell trafficking during ischemia predicts ability to roll on P-selectin
-
10.1371/journal.pcbi.1000294
-
AM Bailey MB Lawrence H Shang AJ Katz SM Peirce 2009 Agent-based model of therapeutic adipose-derived stromal cell trafficking during ischemia predicts ability to roll on P-selectin PLoS Comput. Biol 5 e1000294 10.1371/journal.pcbi. 1000294
-
(2009)
PLoS Comput. Biol
, vol.5
, pp. 1000294
-
-
Bailey, A.M.1
Lawrence, M.B.2
Shang, H.3
Katz, A.J.4
Peirce, S.M.5
-
4
-
-
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, Systems Biology, Bioinformatics, and Computational Biology
-
AM Bailey BC Thorne SM Peirce 2007 Multi-cell agent-based simulation of the microvasculature to study the dynamics of circulating inflammatory cell trafficking Ann. BioMed Eng 35 916 936 10.1007/s10439-007-9266-1 (Pubitemid 46828704)
-
(2007)
Annals of Biomedical Engineering
, vol.35
, Issue.6
, pp. 916-936
-
-
Bailey, A.M.1
Thorne, B.C.2
Peirce, S.M.3
-
5
-
-
33746260079
-
Vascular network remodeling via vessel cooption, regression and growth in tumors
-
2266760
-
K Bartha H Rieger 2006 Vascular network remodeling via vessel cooption, regression and growth in tumors J. Theor. Biol 241 903 918 2266760
-
(2006)
J. Theor. Biol
, vol.241
, pp. 903-918
-
-
Bartha, K.1
Rieger, H.2
-
7
-
-
58349117422
-
Individual-based and continuum models of growing cell populations: A comparison
-
10.1007/s00285-008-0212-0 2471306
-
H Byrne D Drasdo 2009 Individual-based and continuum models of growing cell populations: a comparison J. Math. Biol 58 657 687 10.1007/s00285-008-0212- 0 2471306
-
(2009)
J. Math. Biol
, vol.58
, pp. 657-687
-
-
Byrne, H.1
Drasdo, D.2
-
8
-
-
56249123996
-
Characterizing emergent properties of immunological systems with multi-cellular rule-based computational modeling
-
10.1016/j.it.2008.08.006
-
AK Chavali EP Gianchandani KS Tung MB Lawrence SM Peirce JA Papin 2008 Characterizing emergent properties of immunological systems with multi-cellular rule-based computational modeling Trends Immunol. 29 589 599 10.1016/j.it.2008.08.006
-
(2008)
Trends Immunol
, vol.29
, pp. 589-599
-
-
Chavali, A.K.1
Gianchandani, E.P.2
Tung, K.S.3
Lawrence, M.B.4
Peirce, S.M.5
Papin, J.A.6
-
9
-
-
57349105663
-
A mechanobiological model for tissue differentiation that includes angiogenesis: A lattice-based modeling approach
-
10.1007/s10439-008-9594-9
-
S Checa PJ Prendergast 2009 A mechanobiological model for tissue differentiation that includes angiogenesis: a lattice-based modeling approach Ann. BioMed Eng 37 129 145 10.1007/s10439-008-9594-9
-
(2009)
Ann. BioMed Eng
, vol.37
, pp. 129-145
-
-
Checa, S.1
Prendergast, P.J.2
-
10
-
-
33646198731
-
Cell population dynamics modulate the rates of tissue growth processes
-
10.1529/biophysj.105.063701
-
G Cheng BB Youssef P Markenscoff K Zygourakis 2006 Cell population dynamics modulate the rates of tissue growth processes Biophys. J. 90 713 724 10.1529/biophysj.105.063701
-
(2006)
Biophys. J.
, vol.90
, pp. 713-724
-
-
Cheng, G.1
Youssef, B.B.2
Markenscoff, P.3
Zygourakis, K.4
-
12
-
-
1542344734
-
Modeling self-organized avascular tumor growth with a hybrid cellular automaton
-
S Dormann A Deutsch 2002 Modeling self-organized avascular tumor growth with a hybrid cellular automaton In Silico Biol 2 0035
-
(2002)
In Silico Biol
, vol.2
, pp. 0035
-
-
Dormann, S.1
Deutsch, A.2
-
13
-
-
2542516200
-
Agent-based modeling in the social and behavioral sciences
-
E Elliott LD Kiel 2004 Agent-based modeling in the social and behavioral sciences Nonlinear Dynam., Psych., Life Sci. 8 121 130
-
(2004)
Nonlinear Dynam., Psych., Life Sci
, vol.8
, pp. 121-130
-
-
Elliott, E.1
Kiel, L.D.2
-
14
-
-
64949187961
-
Essential operating principles for tumor spheroid growth
-
10.1186/1752-0509-2-110
-
JA Engelberg GEP Ropella CA Hunt 2008 Essential operating principles for tumor spheroid growth BMC Syst. Biol 2 110 10.1186/1752-0509-2-110
-
(2008)
BMC Syst. Biol
, vol.2
, pp. 110
-
-
Engelberg, J.A.1
Ropella, G.E.P.2
Hunt, C.A.3
-
15
-
-
0027415226
-
Cellular automata approaches to biological modeling
-
10.1006/jtbi.1993.1007
-
GB Ermentrout L Edelstein-Keshet 1993 Cellular automata approaches to biological modeling J. Theor. Biol 160 97 133 10.1006/jtbi.1993.1007
-
(1993)
J. Theor. Biol
, vol.160
, pp. 97-133
-
-
Ermentrout, G.B.1
Edelstein-Keshet, L.2
-
16
-
-
41349093099
-
Reaction-diffusion model for the growth of avascular tumor
-
10.1103/PhysRevE.65.021907 1908293
-
SC Ferreira Jr ML Martins MJ Vilela 2002 Reaction-diffusion model for the growth of avascular tumor Phys. Rev. E 65 021907 10.1103/PhysRevE.65.021907 1908293
-
(2002)
Phys. Rev. e
, vol.65
, pp. 021907
-
-
Ferreira Jr, S.C.1
Martins, M.L.2
Vilela, M.J.3
-
17
-
-
35949016104
-
Lattice-gas automata for the Navier-Stokes equation
-
10.1103/PhysRevLett.56.1505
-
U Frisch B Hasslacher Y Pomeau 1986 Lattice-gas automata for the Navier-Stokes equation Phys. Rev. Lett. 56 1505 1508 10.1103/PhysRevLett.56.1505
-
(1986)
Phys. Rev. Lett
, vol.56
, pp. 1505-1508
-
-
Frisch, U.1
Hasslacher, B.2
Pomeau, Y.3
-
18
-
-
62849098260
-
From single cells to tissue architecture-a bottom-up approach to modelling the spatio-temporal organisation of complex multi-cellular systems
-
1161.92021 10.1007/s00285-008-0172-4 2448431
-
J Galle M Hoffmann G Aust 2009 From single cells to tissue architecture-a bottom-up approach to modelling the spatio-temporal organisation of complex multi-cellular systems J. Math. Biol 58 261 283 1161.92021 10.1007/s00285-008- 0172-4 2448431
-
(2009)
J. Math. Biol
, vol.58
, pp. 261-283
-
-
Galle, J.1
Hoffmann, M.2
Aust, G.3
-
19
-
-
11244250625
-
Modeling the effect of deregulated proliferation and apoptosis on the growth dynamics of epithelial cell populations in vitro
-
DOI 10.1529/biophysj.104.041459
-
J Galle M Loeffler D Drasdo 2005 Modeling the effect of deregulated proliferation and apoptosis on the growth dynamics of epithelial cell populations in vitro Biophys. J. 88 62 75 10.1529/biophysj.104.041459 (Pubitemid 40070658)
-
(2005)
Biophysical Journal
, vol.88
, Issue.1
, pp. 62-75
-
-
Galle, J.1
Loeffler, M.2
Drasdo, D.3
-
20
-
-
51749108892
-
Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation
-
10.1093/bioinformatics/btn362
-
V Galvão JGV Miranda R Ribeiro-dos-Santos 2008 Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation Bioinformatics 24 2051 2056 10.1093/bioinformatics/btn362
-
(2008)
Bioinformatics
, vol.24
, pp. 2051-2056
-
-
Galvão, V.1
Miranda, J.G.V.2
Ribeiro-Dos-Santos, R.3
-
21
-
-
70349549737
-
Fluid flow-agent based hybrid model for the simulation of virtual prairies
-
to appear
-
Garbey, M., C. Mony, and M. Smaoui. Fluid flow-agent based hybrid model for the simulation of virtual prairies. Proceedings of the Conference of Parallell CFD, Lyon, 2008, to appear.
-
(2008)
Proceedings of the Conference of Parallell CFD, Lyon
-
-
Garbey, M.1
Mony, C.2
Smaoui, M.3
-
22
-
-
0000870032
-
Mathematical games: The fantastic combinations of John Conway's new solitaire game "life"
-
M Gardner 1970 Mathematical games: the fantastic combinations of John Conway's new solitaire game "Life" Sci. Am. 223 120 123
-
(1970)
Sci. Am
, vol.223
, pp. 120-123
-
-
Gardner, M.1
-
23
-
-
34248216634
-
An evolutionary hybrid cellular automaton model of solid tumour growth
-
DOI 10.1016/j.jtbi.2007.01.027, PII S0022519307000549
-
P Gerlee ARA Anderson 2007 An evolutionary hybrid cellular automaton model of solid tumour growth J. Theor. Biol 246 583 603 10.1016/j.jtbi.2007.01. 027 2306906 (Pubitemid 46719261)
-
(2007)
Journal of Theoretical Biology
, vol.246
, Issue.4
, pp. 583-603
-
-
Gerlee, P.1
Anderson, A.R.A.2
-
24
-
-
38649099056
-
A hybrid cellular automaton model of clonal evolution in cancer: The emergence of the glycolytic phenotype
-
10.1016/j.jtbi.2007.10.038
-
P Gerlee ARA Anderson 2008 A hybrid cellular automaton model of clonal evolution in cancer: the emergence of the glycolytic phenotype J. Theor. Biol 250 705 722 10.1016/j.jtbi.2007.10.038
-
(2008)
J. Theor. Biol
, vol.250
, pp. 705-722
-
-
Gerlee, P.1
Anderson, A.R.A.2
-
25
-
-
33750715064
-
Modeling the effects of vasculature evolution on early brain tumor growth
-
DOI 10.1016/j.jtbi.2006.07.002, PII S0022519306002918
-
JL Gevertz S Torquato 2006 Modeling the effects of vasculature evolution on early brain tumor growth J. Theor. Biol 243 517 531 10.1016/j.jtbi.2006.07. 002 2306342 (Pubitemid 44708219)
-
(2006)
Journal of Theoretical Biology
, vol.243
, Issue.4
, pp. 517-531
-
-
Gevertz, J.L.1
Torquato, S.2
-
26
-
-
41349083584
-
-
Sage Publications Los Angeles
-
Gilbert, N. Agent-Based Models. Los Angeles: Sage Publications, 2008.
-
(2008)
Agent-Based Models
-
-
Gilbert, N.1
-
27
-
-
24144487070
-
2+ flow
-
DOI 10.1093/bioinformatics/bti585
-
2+ flow Bioinformatics 21 3541 3547 10.1093/bioinformatics/bti585 (Pubitemid 41235999)
-
(2005)
Bioinformatics
, vol.21
, Issue.17
, pp. 3541-3547
-
-
Grabe, N.1
Neuber, K.2
-
28
-
-
33750439801
-
Simulating properties of in vitro epithelial cell morphogenesis
-
DOI 10.1371/journal.pcbi.0020129
-
MR Grant KE Mostov TD Tisty CA Hunt 2006 Simulating properties of in vitro epithelial cell morphogenesis PLoS Comput. Biol 2 e129 10.1371/journal.pcbi.0020129 (Pubitemid 44656514)
-
(2006)
PLoS Computational Biology
, vol.2
, Issue.10
, pp. 1193-1209
-
-
Grant, M.R.1
Mostov, K.E.2
Tlsty, T.D.3
Hunt, C.A.4
-
30
-
-
54249142981
-
A hybrid agent-based approach for modeling microbiological systems
-
10.1016/j.jtbi.2008.08.008
-
Z Guo PMA Sloot JC Tay 2008 A hybrid agent-based approach for modeling microbiological systems J. Theor. Biol 255 163 175 10.1016/j.jtbi.2008.08.008
-
(2008)
J. Theor. Biol
, vol.255
, pp. 163-175
-
-
Guo, Z.1
Sloot, P.M.A.2
Tay, J.C.3
-
31
-
-
0038169275
-
Hidden Order, How Adaptation Builds Complexity
-
Holland, J. H. Hidden Order, How Adaptation Builds Complexity. Helix Books, 1995.
-
(1995)
Helix Books
-
-
Holland, J.H.1
-
32
-
-
28444483647
-
A multiscale model for avascular tumor growth
-
DOI 10.1529/biophysj.105.060640
-
Y Jiang J Pjesivac-Grbovic C Cantrell JP Freyer 2005 A multiscale model for avascular tumor growth Biophys. J. 89 3884 3894 10.1529/biophysj.105.060640 (Pubitemid 41725610)
-
(2005)
Biophysical Journal
, vol.89
, Issue.6
, pp. 3884-3894
-
-
Jiang, Y.1
Pjesivac-Grbovic, J.2
Cantrell, C.3
Freyer, J.P.4
-
34
-
-
38649099394
-
Investigation of cellular movement in the prostate epithelium using an agent-based model
-
10.1016/j.jtbi.2007.11.001
-
BJ Lao DT Kamei 2008 Investigation of cellular movement in the prostate epithelium using an agent-based model J. Theor. Biol 250 642 654 10.1016/j.jtbi.2007.11.001
-
(2008)
J. Theor. Biol
, vol.250
, pp. 642-654
-
-
Lao, B.J.1
Kamei, D.T.2
-
35
-
-
33644890522
-
A cellular automata model of tumor-immune system interactions
-
10.1016/j.jtbi.2005.08.002
-
DG Mallet LG De Pillis 2006 A cellular automata model of tumor-immune system interactions J. Theor. Biol 239 334 350 10.1016/j.jtbi.2005.08.002
-
(2006)
J. Theor. Biol
, vol.239
, pp. 334-350
-
-
Mallet, D.G.1
De Pillis, L.G.2
-
36
-
-
0142124428
-
The impact of "search precision" in an agent-based tumor model
-
DOI 10.1016/S0022-5193(03)00169-3
-
Y Mansury TS Deisboeck 2003 The impact of "search precision" in an agent-based tumor model J. Theor. Biol 224 325 337 10.1016/S0022-5193(03) 00169-3 2067241 (Pubitemid 37297429)
-
(2003)
Journal of Theoretical Biology
, vol.224
, Issue.3
, pp. 325-337
-
-
Mansury, Y.1
Deisboeck, T.S.2
-
37
-
-
34848830242
-
Agent-based model of inflammation and wound healing: Insights into diabetic foot ulcer pathology and the role of transforming growth factor-β1
-
DOI 10.1111/j.1524-475X.2007.00271.x
-
Q Mi B Rivière G Clermont DL Steed Y Vodovotz 2007 Agent-based model of inflammation and wound healing: insights into diabetic foot ulcer pathology and the role of transforming growth factor-β1 Wound Repair Regen. 15 671 682 10.1111/j.1524-475X.2007.00271.x (Pubitemid 47493883)
-
(2007)
Wound Repair and Regeneration
, vol.15
, Issue.5
, pp. 671-682
-
-
Mi, Q.1
Riviere, B.2
Clermont, G.3
Steed, D.L.4
Vodovotz, Y.5
-
38
-
-
0141530984
-
Computational modeling of cell adhesion and movement using a continuum-kinetics approach
-
10.1016/S0006-3495(03)74652-9
-
NA N'Dri W Shyy R Tran-Son-Tay 2003 Computational modeling of cell adhesion and movement using a continuum-kinetics approach Biophys. J. 85 2273 2286 10.1016/S0006-3495(03)74652-9
-
(2003)
Biophys. J.
, vol.85
, pp. 2273-2286
-
-
N'Dri, N.A.1
Shyy, W.2
Tran-Son-Tay, R.3
-
40
-
-
0034794986
-
Graph-cellular automata: A generalised discrete urban and regional model
-
DOI 10.1068/b2707
-
D O'Sullivan 2001 Graph-cellular automata: a generalised discrete urban and regional model Environ. Plann. B 28 687 705 10.1068/b2707 (Pubitemid 32901650)
-
(2001)
Environment and Planning B: Planning and Design
, vol.28
, Issue.5
, pp. 687-705
-
-
O'Sullivan, D.1
-
41
-
-
49049087690
-
A 3-D model used to explore how cell adhesion and stiffness affect cell sorting and movement in multicellular systems
-
10.1016/j.jtbi.2008.05.004 2043156
-
E Palsson 2008 A 3-D model used to explore how cell adhesion and stiffness affect cell sorting and movement in multicellular systems J. Theor. Biol 254 1 13 10.1016/j.jtbi.2008.05.004 2043156
-
(2008)
J. Theor. Biol
, vol.254
, pp. 1-13
-
-
Palsson, E.1
-
42
-
-
34250894953
-
Random-walk models of cell dispersal included in mechanobiological simulations of tissue differentiation
-
10.1016/j.jBiomech2006.10.020
-
MA Pérez PJ Prendergast 2007 Random-walk models of cell dispersal included in mechanobiological simulations of tissue differentiation J. Biomech 40 2244 2253 10.1016/j.jBiomech2006.10.020
-
(2007)
J. Biomech
, vol.40
, pp. 2244-2253
-
-
Pérez, M.A.1
Prendergast, P.J.2
-
43
-
-
64749102223
-
A quantitative cellular automaton model of in vitro multicellular spheroid tumour growth
-
10.1016/j.jtbi.2009.02.008
-
MJ Piotrowska SD Angus 2009 A quantitative cellular automaton model of in vitro multicellular spheroid tumour growth J. Theor. Biol 258 165 178 10.1016/j.jtbi.2009.02.008
-
(2009)
J. Theor. Biol
, vol.258
, pp. 165-178
-
-
Piotrowska, M.J.1
Angus, S.D.2
-
44
-
-
65449162276
-
Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting
-
10.1186/1752-0509-3-13
-
AA Qutub AS Popel 2009 Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting BMC Syst. Biol 3 13 10.1186/1752-0509-3-13
-
(2009)
BMC Syst. Biol
, vol.3
, pp. 13
-
-
Qutub, A.A.1
Popel, A.S.2
-
45
-
-
38049172599
-
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior
-
10.1186/1752-0509-1-46
-
SH Robertson CK Smith AL Langhans SE McLinden MA Oberhardt KR Jakab B Dzamba DW DeSimone JA Papin SM Peirce 2007 Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior BMC Syst. Biol 1 46 10.1186/1752-0509-1-46
-
(2007)
BMC Syst. Biol
, vol.1
, pp. 46
-
-
Robertson, S.H.1
Smith, C.K.2
Langhans, A.L.3
McLinden, S.E.4
Oberhardt, M.A.5
Jakab, K.R.6
Dzamba, B.7
Desimone, D.W.8
Papin, J.A.9
Peirce, S.M.10
-
46
-
-
34250624475
-
A modelling approach towards epidermal homoeostasis control
-
DOI 10.1016/j.jtbi.2007.03.023, PII S0022519307001397
-
G Schaller M Meyer-Hermann 2007 A modelling approach towards epidermal homoeostasis control J. Theor. Biol 247 554 573 10.1016/j.jtbi.2007.03.023 2317878 (Pubitemid 46935216)
-
(2007)
Journal of Theoretical Biology
, vol.247
, Issue.3
, pp. 554-573
-
-
Schaller, G.1
Meyer-Hermann, M.2
-
50
-
-
34548342938
-
Combining experiments with multi-cell agent-based modeling to study biological tissue patterning
-
DOI 10.1093/bib/bbm024, Integrative Biology
-
BC Thorne AM Bailey SM Peirce 2007 Combining experiments with multi-cell agent-based modeling to study biological tissue patterning Brief Bioinform. 8 245 257 10.1093/bib/bbm024 (Pubitemid 47335455)
-
(2007)
Briefings in Bioinformatics
, vol.8
, Issue.4
, pp. 245-257
-
-
Thorne, B.C.1
Bailey, A.M.2
Peirce, S.M.3
-
52
-
-
4444350085
-
The epitheliome: Agent-based modelling of the social behaviour of cells
-
DOI 10.1016/j.biosystems.2004.05.025, PII S030326470400070X
-
DC Walker J Southgate G Hill M Holcombe DR Hose SM Wood S Mac Neil RH Smallwood 2004 The epitheliome: agent-based modelling of the social behaviour of cells BioSystems 76 89 100 10.1016/j.biosystems.2004.05.025 (Pubitemid 39207439)
-
(2004)
BioSystems
, vol.76
, Issue.1-3
, pp. 89-100
-
-
Walker, D.C.1
Southgate, J.2
Hill, G.3
Holcombe, M.4
Hose, D.R.5
Wood, S.M.6
Mac Neil, S.7
Smallwood, R.H.8
-
54
-
-
33750974791
-
Development of a three-dimensional multiscale agent-based tumor model: Simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer
-
DOI 10.1016/j.jtbi.2006.06.034, PII S0022519306002785
-
L Zhang CA Athale TS Deisboeck 2007 Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer J. Theor. Biol 244 96 107 10.1016/j.jtbi.2006.06.034 2280486 (Pubitemid 44751755)
-
(2007)
Journal of Theoretical Biology
, vol.244
, Issue.1
, pp. 96-107
-
-
Zhang, L.1
Athale, C.A.2
Deisboeck, T.S.3
-
55
-
-
58349094920
-
Multiscale agent-based cancer modeling
-
10.1007/s00285-008-0211-1 2471302
-
L Zhang Z Wang JA Sagotsky TS Deisboeck 2009 Multiscale agent-based cancer modeling J. Math. Biol 58 545 559 10.1007/s00285-008-0211-1 2471302
-
(2009)
J. Math. Biol
, vol.58
, pp. 545-559
-
-
Zhang, L.1
Wang, Z.2
Sagotsky, J.A.3
Deisboeck, T.S.4
-
56
-
-
70349520999
-
Dynamic behavior of heterogeneous cell populations growing under mass transport limitations
-
10.1016/j.bpj.2008.12.1587
-
K Zygourakis G Cheng P Markenscoff 2009 Dynamic behavior of heterogeneous cell populations growing under mass transport limitations Biophys. J. 96 317a 10.1016/j.bpj.2008.12.1587
-
(2009)
Biophys. J.
, vol.96
-
-
Zygourakis, K.1
Cheng, G.2
Markenscoff, P.3
|