Computational discrete models of tissue growth and regeneration

Briefings in Bioinformatics

Volumn 12, Issue 1, 2011, Pages 64-77

  Azuajeu, Francisco ^a  

^a LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

Author keywords

Agent based models; Angiogenesis; Cell driven models; Cellular automata; Computational discrete models; Tissue growth; Tissue regeneration

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; BLOOD VESSEL; METHODOLOGY; PHYSIOLOGY; REGENERATION; TISSUE ENGINEERING;

ALGORITHMS; BLOOD VESSELS; COMPUTATIONAL BIOLOGY; REGENERATION; TISSUE ENGINEERING;

EID: 79551647095     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbq017     Document Type: Article

References (45)

1. Cohen IR, Harel D. Explaining a complex living system: dynamics, multi-scaling and emergence. J R Soc Interface 2007;4:175-82.
2. Nuzzo R. On Simulating growth and form. Biomed Comp Rev 2008;17-23.
3. Fisher J, Henzinger TA. Executable cell biology. Nat Biotechnol 2007;25:1239-49.
4. Priami C. Algorithmic systems biology. Commun ACM 2009;52:80-88.
5. Milde F, Bergdorf M, Koumoutsakos P. A hybrid model for three-dimensional simulations of sprouting angiogenesis. Biophys J 2008;95:3146-60.
6. Schiff JL. CellularAutomata: A DiscreteView of theWorld 2008. Hoboken, NJ, USA: Wiley-Interscience, 2008.
7. Azuaje F, Devaux Y, Wagner DR. Identification of potential targets in biological signalling systems through network perturbation analysis. Biosystems 2010;100:55-64.
8. Merks RM, Glazier JA. Dynamic mechanisms of blood vessel growth. Nonlinearity 2006;19:C1-10.
9. Walker DC, Southgate J. The virtual cell-a candidate coordinator for 'middle-out' modelling of biological systems. Brief Bioinform 2009;10:450-61.
10. Mantzaris NV, Webb S, Othmer HG. Mathematical modeling of tumor-induced angiogenesis. J Math Biol 2004;49: 111-87.
11. Goldenfeld N, Kadanoff LP. Simple lessons from complexity. Science 1999;284:87-9.
12. Alber MS, Kiskowski MA, Glazier JA, et al. On cellular automaton approaches to modeling biological cells. In: Rosenthal J, Gilliam DS, (eds). Mathematical SystemsTheory in Biology Communication and Finance. New York: Springer, 2002;1-40.
13. Thorne BC, Bailey AM, Peirce SM. Combining experiments with multi-cell agent-based modeling to study biological tissue patterning. Brief Bioinform 2007;8:245-57.
14. Walker DC, Hill G, Wood SM, et al. Agent-based computational modeling of wounded epithelial cell monolayers. IEEETransNanobiosci 2004;3:153-63.
15. Abbott RG, Forrest S, Pienta KJ. Simulating the hallmarks of cancer. Artif Life 2006;12:617-34.
16. Peirce SM. Computational and mathematical modeling of angiogenesis. Microcirculation 2008;15:739-51.
17. Glazier JA, Graner F. Simulation of the differential adhesion driven rearrangement of biological cells. Phys Rev 1993;E47: 2128-54.
18. Savill NJ, Merks RMH. The cellular Potts model in biomedicine. In: Anderson ARA, et al., (eds). Single-Cell-Based Models in Biology and Medicine. Basel, Switzerland: Birkhaüser, 2007;137-150.
19. Merks RMH, Newman SA, Glazier JA. Cell-Oriented modeling of in vitro capillary development. Lecture Notes Comp Sci 2004;3305(2004):425-34.
20. Merks RMH, Koolwijk P. Modeling Morphogenesis in silico and in vitro: towards quantitative, predictive, cellbased modeling. MathModelNat Phenom 2009;4:149-71.
21. Prusinkiewicz P. Paradigms of pattern formation: towards a computational theory of morphogenesis. In: Carbone A, et al., (eds). Pattern Formation in Biology,Vision, and Dynamics. Singapore: World Scientific Publishing Company, 2002;91-5.
22. Carmeliet P. Angiogenesis in health and disease. Nat Med 2003;9:653-60.
23. Cao Y. Positive and negative modulation of angiogenesis by VEGFR1 ligands. Sci Signal 2009;2:re1.
24. Yancopoulos GD, Davis S, Gale NW, et al. Vascular-specific growth factors and blood vessel formation. Nature 2000;407: 242-8.
25. Sun S, Wheeler MF, Obeyesekere M, et al. A deterministic model of growth factor-induced angiogenesis. Bull Math Biol 2005;67:313-37.
26. Anderson ARA, Chaplain MAJ. Continuous and discrete mathematical models of tumor-induced angiogenesis. Bull Math Biol 1998;60:857-99.
27. Stokes CL, Lauffenburger DA. Analysis of the roles of microvessel endothelial cell random motility and chemotaxis in angiogenesis. JTheor Biol 1991;152:377-403.
28. Jones PF, Sleeman BD. Angiogenesis-understanding the mathematical challenge. Angiogenesis 2006;9:127-38.
29. Peirce SM, Van Gieson EJ, Skalak TC. Multicellular simulation predicts microvascular patterning and in silico tissue assembly. FASEB J 2004;18:731-3.
30. Merks RMH, Brodsky SV, Goligorksy MS, et al. Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. Dev Biol 2006;289:44-54.
31. Walker GM, Sai J, Richmond A, et al. Effects of flow and diffusion on chemotaxis studies in a microfabricated gradient generator. Lab Chip 2005;5:611-8.
32. Merks RM, Perryn ED, Shirinifard A, et al. Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth. PLoSComput Biol 2008;4:e1000163.
33. Topa P. Dynamically reorganising vascular networks modelled using cellular automata approach. Lecture Notes Comp Sci 2008;5191(2009):494-9.
34. Aittokallio T, Schwikowski B. Graph-based methods for analysing networks in cell biology. Brief Bioinform 2006;7: 243-55.
35. Goryczka S, Arodz T. Complex-network-based methodology for analysis of biomedical data. Bio-algorithms Med-systems 2006;2:19-26.
36. Gevertz JL, Torquato S. Modeling the effects of vasculature evolution on early brain tumor growth. J Theor Biol 2006; 243:517-31.
37. Richmond P, Walker D, Coakley S, et al. High performance cellular level agent-based simulation with FLAME for the GPU. Brief Bioinform 2010;11:334-347.
38. Adra S, Sun T, MacNeil S, et al. Development of a three dimensional multiscale computational model of the human epidermis. PLoS One 2010;5:e8511.
39. Hoops S, Sahle S, Gauges R, et al. Copasi-a complex pathway simulator. Bioinformatics 2006;22:3067-74.
40. Coakley S. Formal software architecture for agent-based modelling in biology. PhD thesis, Department of Computer Science, University of Sheffield, Sheffield, UK, 2007.
41. Grant MR, Mostov KE, Tlsty TD, et al. Simulating properties of in vitro epithelial cell morphogenesis. PLoS Comput Biol 2006;2:e129.
42. Galvão V, Miranda JG, Ribeiro-dos-Santos R. Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation. Bioinformatics 2008;24:2051-6.
43. Higuchi ML, Benvenuti LA, Martins-Reis M, et al. Pathophysiology of the heart in Chagas' disease: current status and new developments. Cardiovasc Res 2003;60: 96-107.
44. Ermentrout GB, Edelstein-Keshet L. Cellular automata approaches to biological modeling. J Theor Biol 1993;160: 97-133.
45. Noble D. The Music of Life: Biology Beyond the Genome. Oxford: Oxford University Press, 2006.