메뉴 건너뛰기




Volumn 1214, Issue , 2015, Pages 67-127

Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit

Author keywords

Agent based modeling; Angiogenesis; Cell based model; Cellular Potts model; Glazier Graner Hogeweg model; Parameter study; Quantification; Tissue Simulation Toolkit

Indexed keywords

ANGIOGENESIS; ARTICLE; CELL ADHESION; CELL ELONGATION; CELL FUNCTION; CHEMOTAXIS; COMPUTER MODEL; SIMULATION; TISSUE SIMULATION TOOLKIT; VASCULAR MORPHOGENESIS; BIOLOGICAL MODEL; BLOOD VESSEL; COMPUTER PROGRAM; COMPUTER SIMULATION; CYTOLOGY; EXTRACELLULAR MATRIX; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MORPHOGENESIS; PHYSIOLOGY;

EID: 84955401289     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1462-3_6     Document Type: Article
Times cited : (21)

References (51)
  • 1
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano H (2002) Systems biology: A brief overview. Science 295:1662-1664
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 2
    • 0019133502 scopus 로고
    • Angiogenesis in vitro
    • Folkman J, Hauenschild C (1980) Angiogenesis in vitro. Nature 288:551-556
    • (1980) Nature , vol.288 , pp. 551-556
    • Folkman, J.1    Hauenschild, C.2
  • 3
    • 70449502236 scopus 로고    scopus 로고
    • A balance of substrate mechanics and matrix chemistry regulates endothelial cell network assembly
    • Califano J, Reinhart-King C (2008) A balance of substrate mechanics and matrix chemistry regulates endothelial cell network assembly. Cell Mol Bioeng 1:122-132. doi:10.1007/s12195-008-0022-x
    • (2008) Cell Mol Bioeng , vol.1 , pp. 122-132
    • Califano, J.1    Reinhart-King, C.2
  • 5
    • 0030292469 scopus 로고    scopus 로고
    • A mechanical model for the formation of vascular networks in vitro
    • Manoussaki D, Lubkin S, Vernon R, Murray J (1996) A mechanical model for the formation of vascular networks in vitro. Acta Biotheor 44:271-282
    • (1996) Acta Biotheor , vol.44 , pp. 271-282
    • Manoussaki, D.1    Lubkin, S.2    Vernon, R.3    Murray, J.4
  • 6
    • 0345492033 scopus 로고    scopus 로고
    • A mechanochemical model of angiogenesis and vasculogenesis
    • Manoussaki D (2003) A mechanochemical model of angiogenesis and vasculogenesis. ESAIM: Math Model Num 37:581-599. doi:10.1051/m2an:2003046
    • (2003) ESAIM: Math Model Num , vol.37 , pp. 581-599
    • Manoussaki, D.1
  • 7
    • 0038528528 scopus 로고    scopus 로고
    • Percolation, morphogenesis, and Burgers dynamics in blood vessels formation
    • 118101
    • Gamba A, Ambrosi D, Coniglio A, de Candia A, Di Talia S et al (2003) Percolation, morphogenesis, and Burgers dynamics in blood vessels formation. Phys Rev Lett 90:118101. doi:10.1103/PhysRevLett.90.118101
    • (2003) Phys Rev Lett , vol.90
    • Gamba, A.1    Ambrosi, D.2    Coniglio, A.3    De Candia, A.4    Di Talia, S.5
  • 8
    • 0345373937 scopus 로고    scopus 로고
    • Modeling the early stages of vascular network assembly
    • Serini G, Ambrosi D, Giraudo E, Gamba A, Preziosi L et al (2003) Modeling the early stages of vascular network assembly. EMBO J 22:1771-1779. doi:10.1093/emboj/cdg176
    • (2003) EMBO J , vol.22 , pp. 1771-1779
    • Serini, G.1    Ambrosi, D.2    Giraudo, E.3    Gamba, A.4    Preziosi, L.5
  • 9
    • 7444221201 scopus 로고    scopus 로고
    • Cell directional and chemotaxis in vascular morphogenesis
    • Ambrosi D, Gamba A, Serini G (2004) Cell directional and chemotaxis in vascular morphogenesis. B Math Biol 66:1851-1873. doi:10.1016/j.blum.2004.04.004
    • (2004) B Math Biol , vol.66 , pp. 1851-1873
    • Ambrosi, D.1    Gamba, A.2    Serini, G.3
  • 10
    • 0014748565 scopus 로고
    • Initiation of slime mold aggregation viewed as an instability
    • Keller E (1970) Initiation of slime mold aggregation viewed as an instability. J Theor Biol 26:399-415
    • (1970) J Theor Biol , vol.26 , pp. 399-415
    • Keller, E.1
  • 11
    • 17844408690 scopus 로고    scopus 로고
    • A cell-centered approach to developmental biology
    • Merks RMH, Glazier JA (2005) A cell-centered approach to developmental biology. Physica A 352:113-130. doi:10.1016/j.physa.2004.12.028
    • (2005) Physica A , vol.352 , pp. 113-130
    • Merks, R.M.H.1    Glazier, J.A.2
  • 12
    • 0000135489 scopus 로고
    • Simulation of biological cell sorting using a two-dimensional extended Potts model
    • Graner F, Glazier JA (1992) Simulation of biological cell sorting using a two-dimensional extended Potts model. Phys Rev Lett 69:2013-2016
    • (1992) Phys Rev Lett , vol.69 , pp. 2013-2016
    • Graner, F.1    Glazier, J.A.2
  • 13
    • 29144462629 scopus 로고    scopus 로고
    • Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling
    • Merks RMH, Brodsky SV, Goligorksy MS, Newman SA, Glazier JA (2006) Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. Dev Biol 289:44-54. doi:10.1016/j.ydbio.2005.10.003
    • (2006) Dev Biol , vol.289 , pp. 44-54
    • Merks, R.M.H.1    Brodsky, S.V.2    Goligorksy, M.S.3    Newman, S.A.4    Glazier, J.A.5
  • 14
    • 84873668027 scopus 로고    scopus 로고
    • Vascular networks due to dynamically arrested crystalline ordering of elongated cells
    • Palm MM, Merks RMH (2013) Vascular networks due to dynamically arrested crystalline ordering of elongated cells. Phys Rev E 87:012725. doi:10.1103/PhysRevE.87.012725
    • (2013) Phys Rev E , vol.12725 , pp. 87
    • Palm, M.M.1    Merks, R.M.H.2
  • 15
    • 52949146011 scopus 로고    scopus 로고
    • Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth
    • e1000163
    • Merks RMH, Perryn ED, Shirinifard A, Glazier JA (2008) Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth. PLoS Comp Biol 4:e1000163. doi:10.1371/journal.pcbi.1000163
    • (2008) PLoS Comp Biol , vol.4
    • Merks, R.M.H.1    Perryn, E.D.2    Shirinifard, A.3    Glazier, J.A.4
  • 16
    • 55549111246 scopus 로고    scopus 로고
    • Multicellular sprouting in vitro
    • Szabó A, Mehes E, Kosa E, Czirok A (2008) Multicellular sprouting in vitro. Biophys J 95:2702-2710. doi:10.1529/biophysj.108.129668
    • (2008) Biophys J , vol.95 , pp. 2702-2710
    • Szabó, A.1    Mehes, E.2    Kosa, E.3    Czirok, A.4
  • 17
    • 80052891631 scopus 로고    scopus 로고
    • Early embryonic vascular patterning by matrix-mediated paracrine signalling: A mathematical model study
    • Köhn-Luque A, De Back W, Starruß J, Mattiotti A, Deutsch A et al (2011) Early embryonic vascular patterning by matrix-mediated paracrine signalling: A mathematical model study. PLoS One 6:e24175. doi:10.1371/journal.pone.0024175.t001
    • (2011) PLoS One , vol.6 , pp. e24175
    • Köhn-Luque, A.1    De Back, W.2    Starruß, J.3    Mattiotti, A.4    Deutsch, A.5
  • 18
    • 84891381516 scopus 로고    scopus 로고
    • Dynamics of VEGF matrix-retention in vascular network patterning
    • 066007
    • Köhn-Luque A, de Back W, Yamaguchi Y, Yoshimura K, Herrero MA et al (2013) Dynamics of VEGF matrix-retention in vascular network patterning. Phys Biol 10:066007. doi:10.1088/1478-3975/10/6/066007
    • (2013) Phys Biol , vol.10
    • Köhn-Luque, A.1    De Back, W.2    Yamaguchi, Y.3    Yoshimura, K.4    Herrero, M.A.5
  • 19
    • 84881368916 scopus 로고    scopus 로고
    • A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis
    • Daub JT, Merks RMH (2013) A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis. B Math Biol 75:1377-1399. doi:10.1007/s11538-013-9826-5
    • (2013) B Math Biol , vol.75 , pp. 1377-1399
    • Daub, J.T.1    Merks, R.M.H.2
  • 20
    • 80051671525 scopus 로고    scopus 로고
    • A multiscale hybrid approach for vasculogenesis and related potential blocking therapies
    • Scianna M, Munaron L, Preziosi L (2011) A multiscale hybrid approach for vasculogenesis and related potential blocking therapies. Prog Biophys Mol Biol 106:450-462. doi:10.1016/j.pbiomolbio.2011.01.004
    • (2011) Prog Biophys Mol Biol , vol.106 , pp. 450-462
    • Scianna, M.1    Munaron, L.2    Preziosi, L.3
  • 21
    • 84893126486 scopus 로고    scopus 로고
    • Synergy of cell-cell repulsion and vacuolation in a computational model of lumen formation
    • 20131049
    • Boas SEM, Merks RMH (2014) Synergy of cell-cell repulsion and vacuolation in a computational model of lumen formation. J R Soc Interface 11:20131049. doi:10.1038/ncb1705
    • (2014) J R Soc Interface , vol.11
    • Boas, S.E.M.1    Merks, R.M.H.2
  • 22
    • 70449397345 scopus 로고    scopus 로고
    • 3D multi-cell simulation of tumor growth and angiogenesis
    • Shirinifard A, Gens JS, Zaitlen BL, Popławski NJ, Swat M et al (2009) 3D multi-cell simulation of tumor growth and angiogenesis. PLoS One 4:e7190. doi:10.1371/journal.pone.0007190
    • (2009) PLoS One , vol.4 , pp. e7190
    • Hirinifard, A.1    Gens, J.S.2    Zaitlen, B.L.3    Popławski, N.J.4    Swat, M.5
  • 23
    • 84863667691 scopus 로고    scopus 로고
    • Adhesion failures determine the pattern of choroidal neovascularization in the eye: A computer simulation study
    • e1002440
    • Shirinifard A, Glazier JA, Swat M, Gens JS, Family F et al (2012) Adhesion failures determine the pattern of choroidal neovascularization in the eye: A computer simulation study. PLoS Comput Biol 8:e1002440. doi:10.1371/journal.pcbi.1002440.s022
    • (2012) PLoS Comput Biol , vol.8
    • Shirinifard, A.1    Glazier, J.A.2    Swat, M.3    Gens, J.S.4    Family, F.5
  • 24
    • 84876922933 scopus 로고    scopus 로고
    • A computational model predicting disruption of blood vessel development
    • e1002996
    • Kleinstreuer N, Dix D, Rountree M, Baker N, Sipes N et al (2013) A computational model predicting disruption of blood vessel development. PLoS Comput Biol 9:e1002996. doi:10.1371/journal.pcbi.1002996.s011
    • (2013) PLoS Comput Biol , vol.9
    • Kleinstreuer, N.1    Dix, D.2    Rountree, M.3    Baker, N.4    Sipes, N.5
  • 25
    • 34247569970 scopus 로고    scopus 로고
    • A cell-based model exhibiting branching and anastomosis during tumor-induced angiogenesis
    • Bauer AL, Jackson TL, Jiang Y (2007) A cell-based model exhibiting branching and anastomosis during tumor-induced angiogenesis. Biophys J 92:3105-3121. doi:10.1529/biophysj.106.101501
    • (2007) Biophys J , vol.92 , pp. 3105-3121
    • Bauer, A.L.1    Jackson, T.L.2    Jiang, Y.3
  • 26
    • 68249103288 scopus 로고    scopus 로고
    • Topography of extracellular matrix mediates vascular morphogenesis and migration speeds in angiogenesis
    • e1000445
    • Bauer AL, Jackson TL, Jiang Y (2009) Topography of extracellular matrix mediates vascular morphogenesis and migration speeds in angiogenesis. PLoS Comput Biol 5:e1000445. doi:10.1371/journal.pcbi.1000445
    • (2009) PLoS Comput Biol , vol.5
    • Bauer, A.L.1    Jackson, T.L.2    Jiang, Y.3
  • 27
    • 84880699962 scopus 로고    scopus 로고
    • A review of mathematical models for the formation of vascular networks
    • Scianna M, Bell CG, Preziosi L (2013) A review of mathematical models for the formation of vascular networks. J Theor Biol 333:174-209. doi:10.1016/j.jtbi.2013.04.037
    • (2013) J Theor Biol , vol.333 , pp. 174-209
    • Scianna, M.1    Bell, C.G.2    Preziosi, L.3
  • 28
    • 84881639246 scopus 로고    scopus 로고
    • Endothelial cell motility, coordination and pattern formation during vasculogenesis
    • Czirok A (2013) Endothelial cell motility, coordination and pattern formation during vasculogenesis. Wiley Interdiscip Rev Syst Biol Med 5:587-602. doi:10.1002/wsbm.1233
    • (2013) Wiley Interdiscip Rev Syst Biol Med , vol.5 , pp. 587-602
    • Czirok, A.1
  • 29
    • 82555176570 scopus 로고    scopus 로고
    • Endothelial development taking shape
    • Wacker A, Gerhardt H (2011) Endothelial development taking shape. Curr Opin Cell Biol 23:676-685
    • (2011) Curr Opin Cell Biol , vol.23 , pp. 676-685
    • Wacker, A.1    Gerhardt, H.2
  • 31
    • 84856972051 scopus 로고    scopus 로고
    • Invasion from a cell aggregate the roles of active cell motion and mechanical equilibrium
    • 016010
    • Szabó A, Varga K, Garay T, Hegedűs B, Czirok A (2012) Invasion from a cell aggregate the roles of active cell motion and mechanical equilibrium. Phys Biol 9:016010. doi:10.1088/1478-3975/9/1/016010
    • (2012) Phys Biol , vol.9
    • Szabó, A.1    Varga, K.2    Garay, T.3    Hegedűs, B.4    Czirok, A.5
  • 32
    • 37849046926 scopus 로고    scopus 로고
    • A unified theory for osteonal and hemi-osteonal remodeling
    • van Oers RFM, Ruimerman R, Tanck E, Hilbers PAJ, Huiskes R (2008) A unified theory for osteonal and hemi-osteonal remodeling. Bone 42:250-259. doi:10.1016/j.bone.2007.10.009
    • (2008) Bone , vol.42 , pp. 250-259
    • Van Oers, R.F.M.1    Ruimerman, R.2    Tanck, E.3    Hilbers, P.A.J.4    Huiskes, R.5
  • 33
    • 84893596337 scopus 로고    scopus 로고
    • Morpheus: A user-friendly modeling environment for multiscale and multicellular systems biology
    • Starruß J, De Back W, Brusch L, Deutsch A (2014) Morpheus: A user-friendly modeling environment for multiscale and multicellular systems biology. Bioinformatics 30:1331-1332. doi:10.1093/bioinformatics/btt772
    • (2014) Bioinformatics , vol.30 , pp. 1331-1332
    • Starruß, J.1    De Back, W.2    Brusch, L.3    Deutsch, A.4
  • 34
    • 70350588995 scopus 로고    scopus 로고
    • Chaste: A test-driven approach to software development for biological modelling
    • Pitt-Francis J, Pathmanathan P, Bernabeu MO, Bordas R, Cooper J et al (2009) Chaste: A test-driven approach to software development for biological modelling. Comput Phys Commun 180:2452-2471. doi:10.1016/j.cpc.2009.07.019
    • (2009) Comput Phys Commun , vol.180 , pp. 2452-2471
    • Pitt-Francis, J.1    Pathmanathan, P.2    Bernabeu, M.O.3    Bordas, R.4    Cooper, J.5
  • 35
    • 79551713682 scopus 로고    scopus 로고
    • VirtualLeaf: An open-source framework for cell-based modeling of plant tissue growth and development
    • Merks RMH, Guravage M, Inze D, Beemster GTS (2011) VirtualLeaf: An open-source framework for cell-based modeling of plant tissue growth and development. Plant Physiol 155:656-666. doi:10.1104/pp.110.167619
    • (2011) Plant Physiol , vol.155 , pp. 656-666
    • Merks, R.M.H.1    Guravage, M.2    Inze, D.3    Beemster, G.T.S.4
  • 36
    • 84855248431 scopus 로고    scopus 로고
    • Modelling complex biological systems using an agent-based approach
    • Holcombe M, Adra S, Bicak M, Chin S, Coakley S et al (2012) Modelling complex biological systems using an agent-based approach. Integr Biol 4:53-64
    • (2012) Integr Biol , vol.4 , pp. 53-64
    • Holcombe, M.1    Adra, S.2    Bicak, M.3    Chin, S.4    Coakley, S.5
  • 37
    • 0000825469 scopus 로고
    • Simulation of the differential adhesion driven rearrangement of biological cells
    • Glazier JA, Graner F (1993) Simulation of the differential adhesion driven rearrangement of biological cells. Phys Rev E 47:2128-2154
    • (1993) Phys Rev E , vol.47 , pp. 2128-2154
    • Glazier, J.A.1    Graner, F.2
  • 38
    • 0031557195 scopus 로고    scopus 로고
    • Modelling morphogenesis: From single cells to crawling slugs
    • Savill NJ, Hogeweg P (1997) Modelling morphogenesis: From single cells to crawling slugs. J Theor Biol 184:229-235
    • (1997) J Theor Biol , vol.184 , pp. 229-235
    • Savill, N.J.1    Hogeweg, P.2
  • 40
    • 29144487147 scopus 로고    scopus 로고
    • Dynamic mechanisms of blood vessel growth
    • Merks RMH, Glazier JA (2006) Dynamic mechanisms of blood vessel growth. Nonlinearity 19:C1-C10. doi:10.1088/0951-7715/19/1/000
    • (2006) Nonlinearity , vol.19 , pp. C1-C10
    • Merks, R.M.H.1    Glazier, J.A.2
  • 41
    • 33947732977 scopus 로고    scopus 로고
    • Angiogenesis: An organizing principle for drug discovery?
    • Folkman J (2007) Angiogenesis: An organizing principle for drug discovery? Nat Rev Drug Discov 6:273-286. doi:10.1038/nrd2115
    • (2007) Nat Rev Drug Discov , vol.6 , pp. 273-286
    • Folkman, J.1
  • 42
    • 0035721955 scopus 로고    scopus 로고
    • Role of the matrix metalloproteinase and plasminogen activator-plasmin systems in angiogenesis
    • Pepper MS (2001) Role of the matrix metalloproteinase and plasminogen activator-plasmin systems in angiogenesis. Arterioscler Thromb Vasc Biol 21:1104-1117
    • (2001) Arterioscler Thromb Vasc Biol , vol.21 , pp. 1104-1117
    • Pepper, M.S.1
  • 43
    • 42349114587 scopus 로고    scopus 로고
    • Endothelial sprouting and angiogenesis: Matrix metalloproteinases in the lead
    • van Hinsbergh VWM, Koolwijk P (2008) Endothelial sprouting and angiogenesis: Matrix metalloproteinases in the lead. Cardiovasc Res 78:203-212. doi:10.1093/cvr/cvm102
    • (2008) Cardiovasc Res , vol.78 , pp. 203-212
    • Van Hinsbergh, V.W.M.1    Koolwijk, P.2
  • 44
    • 0242405617 scopus 로고    scopus 로고
    • Endothelial-pericyte interactions in angiogenesis
    • Gerhardt H, Betsholtz C (2003) Endothelial-pericyte interactions in angiogenesis. Cell Tissue Res 314:15-23. doi:10.1007/s00441-003-0745-x
    • (2003) Cell Tissue Res , vol.314 , pp. 15-23
    • Gerhardt, H.1    Betsholtz, C.2
  • 45
    • 57349200481 scopus 로고    scopus 로고
    • VEGF and endothelial guidance in angiogenic sprouting
    • Gerhardt H (2008) VEGF and endothelial guidance in angiogenic sprouting. Organogenesis 4:241-246
    • (2008) Organogenesis , vol.4 , pp. 241-246
    • Gerhardt, H.1
  • 46
    • 0036142782 scopus 로고    scopus 로고
    • The and integrins provide critical support for vascular endothelial growth factor signaling, endothelial cell migration, and tumor angiogenesis
    • Senger DR, Perruzzi CA, Streit M, Koteliansky VE, de Fougerolles AR et al (2002) The and integrins provide critical support for vascular endothelial growth factor signaling, endothelial cell migration, and tumor angiogenesis. Am J Pathol 160:195-204
    • (2002) Am J Pathol , vol.160 , pp. 195-204
    • Senger, D.R.1    Perruzzi, C.A.2    Streit, M.3    Koteliansky, V.E.4    De Fougerolles, A.R.5
  • 47
    • 34147171490 scopus 로고    scopus 로고
    • Endothelial cell migration during angiogenesis
    • Lamalice L, Le Boeuf F, Huot J (2007) Endothelial cell migration during angiogenesis. Circ Res 100:782-794. doi:10.1161/01.RES.0000259593.07661.1e
    • (2007) Circ Res , vol.100 , pp. 782-794
    • Lamalice, L.1    Le Boeuf, F.2    Huot, J.3
  • 48
    • 0027227425 scopus 로고
    • Maximal migration of human smooth muscle cells on fibronectin and type IV collagen occurs at an intermediate attachment strength
    • DiMilla PA, Stone JA, Quinn JA, Albelda SM, Lauffenburger DA (1993) Maximal migration of human smooth muscle cells on fibronectin and type IV collagen occurs at an intermediate attachment strength. J Cell Biol 122:729-737
    • (1993) J Cell Biol , vol.122 , pp. 729-737
    • Dimilla, P.A.1    Stone, J.A.2    Quinn, J.A.3    Albelda, S.M.4    Lauffenburger, D.A.5
  • 49
    • 0035152391 scopus 로고    scopus 로고
    • Integrin-mediated adhesion regulates cell polarity and membrane protrusion through the Rho family of GTPases
    • Cox E, Sastry S, Huttenlocher A (2001) Integrin-mediated adhesion regulates cell polarity and membrane protrusion through the Rho family of GTPases. Mol Biol Cell 12:265-277
    • (2001) Mol Biol Cell , vol.12 , pp. 265-277
    • Cox, E.1    Sastry, S.2    Huttenlocher, A.3
  • 50
    • 0025269797 scopus 로고
    • In vitro endothelial wound repair. Interaction of cell migration and proliferation
    • Coomber BL, Gotlieb AI (1990) In vitro endothelial wound repair. Interaction of cell migration and proliferation. Arteriosclerosis 10:215-222
    • (1990) Arteriosclerosis , vol.10 , pp. 215-222
    • Coomber, B.L.1    Gotlieb, A.I.2
  • 51
    • 0015011285 scopus 로고
    • Model for chemotaxis
    • Keller EF, Segel LA (1971) Model for chemotaxis. J Theor Biol 30:225-234. doi:10.1016/0022-5193(71)90050-6
    • (1971) J Theor Biol , vol.30 , pp. 225-234
    • Keller, E.F.1    Segel, L.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.