References
1 Piotrowska, MJ, Angus, SD. A quantitative cellular automaton model of in vitro multicellular spheroid tumour growth. J Theor Biol 2009; 258: 165–178.
2 Basanta, D, Hatzikirou, H, Deutsch, A. Studying the emergence of invasiveness in tumours using the game theory. Eur Phys J B 2008; 63: 393–397.
3 Dormann, S, Deutsch, A. Modeling of self‐organized avascular tumor growth with a hybrid cellular automaton. In Silico Biol 2002; 2: 393–406.
4 Spencer, SL, Gerety, RA, Pienta, KJ, Forrest, S. Modeling somatic evolution in tumorigenesis. PLoS Comput Biol 2006; 2: e108.
5 Enderling, H, Hlatky, L, Hahnfeldt, P. Migration rules: tumours are conglomerates of self‐metastases. Br J Cancer 2009; 100: 1917–1925.
6 Kansal, AR, Torquato, S, Chiocca, EA, Deisboeck, TS. Emergence of a subpopulation in a computational model of tumor growth. J Theor Biol 2000; 207: 431–441.
7 Zhang, L, Strouthos, CG, Wang, Z, Deisboeck, TS. Simulating brain tumor heterogeneity with multiscale agent‐based model: linking molecular signatures, phenotypes and expansion rate. Math Comp Model 2009; 49: 307–319.
8 Wcislo, R, Dzwinel, W, Yuen, DA, Dudek, AZ. A 3‐D model of tumor progression based on complex automata driven by particle dynamics. J Mol Model 2009; 15: 1517–1539.
9 Enderling, H, Anderson, ARA, Chaplain, MAJ, Beheshti, A, Hlatky, LR, Hahnfeldt, PJ. Paradoxical dependencies of tumor dormancy and progression on basic cell kinetics. Cancer Res 2009; 69: 8814–8821.
10 Stephanou, A, McDougall, SR, Anderson, ARA, Chaplain, MAJ. Mathematical modelling of flow in 2D and 3D vascular networks: applications to anti‐cancer and chemotherapeutic drug strategies. Math Comp Model 2005; 41: 1137–1156.
11 Owen, MR, Alarcon, T, Maini, PK, Byrne, HM. Angiogenesis and vascular remodelling in normal and cancerous tissues. J Math Biol 2009; 58: 689–721.
12 Anderson, ARA. %22A hybrid multiscale model of tumour invasion: evolution and the microenvironment%22. In: Anderson, A, Chaplain, M, Rejniak, KA, eds.
Single‐Cell‐Based Models in Biology and Medicine, Chapter I.1. Basel, Switzerland:
Birkhauser‐Verlag; 2007.
13 Anderson, ARA, Rejniak, KA, Gerlee, P, Quaranta, V. Microenvironment driven invasion: a multiscale model investigation. J Math Biol 2009; 58: 579–624.
14 Zhang, L, Wang, Z, Sagotsky, JA, Deisboeck, TS. Multiscale agent‐based cancer modeling. J Math Biol 2009; 58: 545–559.
15 Anderson, ARA. A hybrid mathematical model of solid tumour invasion: the importance of cell adhesion. Math Med Biol 2005; 22: 163–186.
16 Sottoriva, A, Verhoeff, JJC, Borovski, T, McWeeney, SK, Naumov, L, Medema, JP, Sloot, PMA, Vermeulen, L. Cancer stem cell tumor model reveals invasive morphology and increased phenotypical heterogeneity. Cancer Res 2010; 70: 46–56.
17 Gatenby, RA, Smallbone, K, Maini, PK, Rose, F, Averill, J, Nagle, RB, Worrall, L, Gillies, RJ. Cellular adaptations to hypoxia and acidosis during somatic evolution of breast cancer. Br J Cancer 2007; 97: 646–653.
18 Gerlee, P, Anderson, ARA. Evolution of cell motility in an individual‐based model of tumour growth. J Theor Biol 2009; 259: 67–83.
19 Silva, AS, Yunes, JA, Gilles, RJ, Gatenby, RA. The potential of systemic buffers in reducing intratumoral extracellular pH and acid‐mediated invasion. Cancer Res 2009; 69: 2677–2684.
20 Zhang, L, Chen, LL, Deisboeck, TS. Multi‐scale, multi‐resolution brain cancer modeling. Math Comput Simul 2009; 79: 2021–2035.
21 Gerlee, P, Anderson, ARA. A hybrid cellular automation model of clonal evolution in cancer: the emergence of the glycolytic phenotype. J Theor Biol 2008; 250: 705–722.
22 Smallbone, K, Gatenby, RA, Gillies, RJ, Maini, PK, Gavaghan, DJ. Metabolic changes during carcinogenesis: potential impact on invasiveness. J Theor Biol 2007; 244: 703–713.
23 Anderson, ARA, Hassanein, M, Branch, KM, Lu, J, Lobdell, NA, Maier, J, Basanta, D, Weidow, B, Narasanna, A, Arteaga, CL,
et al. Microenvironmental independence associated with tumor progression. Cancer Res 2009; 69: 8797–8806.
24 Anderson, ARA, Weaver, AM, Cummings, PT, Quaranta, V. Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment. Cell 2006; 127: 905–915.
25 Basanta, D, Strand, DW, Lukner, RB, Franco, OE, Cliffel, DE, Ayala, GE, Hayward, SW, Anderson, ARA. The role of transforming growth factor‐B–mediated tumor‐stroma interactions in prostate cancer progression: an integrative approach. Cancer Res 2009; 69: 7111–7120.
26 De Pillis, LG, Mallet, DG, Radunskaya, AE. Spatial tumor‐immune modeling. Comput Math Methods Med 2006; 7: 159–176.
27 Enderling, H, Alexander, NR, Clark, ES, Branch, KM, Estrada, L, Crooke, C, Jourquin, J, Lobdell, N, Zaman, MH, Guelcher, SA,
et al. Dependence of invadopodia function on collagen fiber spacing and cross‐linking: computational modeling and experimental evidence. Biophys J 2008; 95: 2203–2218.
28 Anderson, ARA, Quaranta, V. Integrative mathematical oncology. Nat Rev Cancer 2008; 8: 227–234.
29 Bankhead, A, Magnuson, N, Heckendorn, R. Cellular automaton simulation examining progenitor hierarchy structure effects on mammary ductal carcinoma in situ. J Theor Biol 2007; 246: 491–498.
30 Gevertz, J, Torquato, S. Growing heterogeneous tumors in silico. Phys Rev E 2009; 80: 051919.
31 Anderson, ARA, Basanta, D, Gerlee, P, Rejniak, KA. %22Evolution, regulation and disruption of homeostasis and its role in carcinogenesis%22. In: Deisboeck, TS, Stamatakos, G, eds.
Multiscale Cancer Modeling.
New York: Chapman %26 Hall; 2010.
32 Silva, AS, Gatenby, RA, Gillies, RJ, Tunes, JA. A quantitative theoretical model for development of malignancy in ductal carcinoma in situ. J Theor Biol 2010; 262: 601–613.
33 Deutsch, A. %22Lattice‐gas cellular automata modeling of developing cell systems%22. In: Anderson, A, Chaplain, M, Rejniak, KA, eds.
Single‐Cell‐Based Models in Biology and Medicine, Chapter I.2. Basel, Switzerland:
Birkhauser‐Verlag; 2007.
34 Engelberg, JA, Ropella, GEP, Hunt, CA. Essential operating principles for tumor spheroid growth. BMC SystBiol 2008; 2: 110.
35 Kim, SHJ, Debnath, J, Mostov, K, Park, S, Hunt, CA. A computational approach to resolve cell level contributions to early glandular epithelial cancer progression. BMC SystBiol 2009; 3: 122.
36 Shumate, SD, El‐Shenawee, M. Computational model of ductal carcinoma in‐situ: the effects of contact inhibition on pattern formation. IEEE Trans Biomed Eng 2009; 5: 1341–1347.
37 Aubert, M, Badoual, M, Christov, C, Grammaticos, B. A model for glioma cell migration on collagen and astrocytes. J R Soc Interface 2008; 5: 75–83.
38 Aubert, M, Badoual, M, Grammaticos, B. A model for short‐ and long‐range interactions of migrating. Tumour Cell Acta Biotheor 2008; 56: 297–314.
39 Turner, S, Sherratt, JA, Cameron, D. Tamoxifen treatment failure in cancer and the nonlinear dynamics of TGF‐beta. J Theor Biol 2004; 229: 101–111.
40 Jiang, Y, Pjesivac‐Grbovic, J, Cantrell, C, Freyer, JP. A multiscale model for avascular tumor growth. Biophys J 2005; 89: 3884–3894.
41 Maree, AFM, Grieneisen, VA, Hogweg, P. %22The cellular Potts model and biophysical properties of cells, tissues and morphogenesis%22. In: Anderson, ARA, Chaplain, MAJ, Rejniak, KAR, eds.
Single Cell Based Models in Biology and Medicine. Basel, Switzerland:
Birkhauser; 2007.
42 Rubenstein, BM, Kaufman, LJ. The role of extracellular matrix in glioma invasion: a cellular Potts model approach. Biophys J 2008; 95: 5661–5680.
43 Poplawski, NJ, Agero, U, Gens, JS, Swat, M, Glazier, JA, Anderson, ARA. Front instabilities and invasiveness of simulated avascular tumors. Bull Math Biol 2009; 71: 1189–1227.
44 Merks, RMH, Perryn, ED, Shirinifard, A, Glazier, JA. Contact‐inhibited chemotaxis in de novo and sprouting blood‐vessel growth. PLoS Comput Biol 2008; 4: e1000163.
45 Bauer, AL, Jackson, TL, Jiang, Y. Topography of extracellular matrix mediates vascular morphogenesis and migration speed in angiogenesis. PLoS Comput Boil 2009; 5: e1000445.
46 Shirinifard, A, Gens, JS, Zaitlen, BL, Poplawski, NJ, Swat, M, Glazier, JA. 3D Multi‐cell simulation of tumor growth and angiogenesis. PLoS ONE 2009; 4: e7190.
47 van Leeuwen, IMM, Mirams, GR, Walter, A, Fletcher, A, Murray, P, Osborne, J, Varma, S, Young, SJ, Cooper, J, Doyle, B,
et al.An integrative computational model for intestinal tissue renewal. Cell Prolif 2009; 42: 617–636.
48 Galle, J, Hoffmann, M, Aust, G. From single cells to tissue architecture—a bottom‐up approach to modelling the spatio‐temporal organisation of complex multi‐cellular systems. J Math Biol 2009; 58: 261–283.
49 Kim, Y, Stolarska, MA, Othmer, HG. A hybrid model for tumor spheroid growth in vitro, I: theoretical development and early results. Math Models Methods Appl Sci 2007; 17: 1773–1798.
50 Rejniak, KA. %22Modelling the development of complex tissues using individual viscoelastic cells%22. In: Anderson, A, Chaplain, M, Rejniak, KA, eds.
Single‐Cell‐Based Models in Biology and Medicine. Basel, Switzerland:
Birkhauser‐Verlag; 2007.
51 Drasdo, D, Hoehme, S. A single‐cell‐based model of tumor growth in vitro: monolayers and spheroids. Phys Biol 2005; 2: 133–147.
52 Galle, J, Sittig, D, Hanisch, I, Wobus, M, Wandel, E, Loeffler, M, Aust, G. Individual cell‐based models of tumor‐environment interactions. Multiple effects of CD97 on tumor invasion. Am J Pathol 2006; 169: 1802–1811.
53 Galle, J, Loeffler, M, Drasdo, D. Modeling the effects of deregulated proliferation and apoptosis on the growth dynamics of epithelial cell populations in vitro. Biophys J 2005; 88: 62–75.
54 Jeon, J, Quaranta, V, Cumming, PT. An off‐lattice hybrid discrete‐continuum model of tumor growth and invasion. Biophys J 2010; 98: 37–47.
55 Norton, K‐A, Wininger, M, Bhanot, G, Ganesan, S, Barnard, N, Shinbrot, T. A 2D mechanistic model of breast ductal carcinoma in situ (DCIS) morphology and progression. J Theor Biol 2010; 263: 393–406.
56 Drasdo, D, Hoehme, S, Block, M. On the role of physics in the growth and pattern formation of multi‐cellular systems: what can we learn from individual—cell based models? J Stat Phys 2007; 128: 287–345.
57 Ramis‐Conde, I, Drasdo, D, Anderson, ARA, Chaplain, MAJ. Modeling the influence of the cadherin‐b‐catenin pathway in cancer cell invasion: a multiscale approach. Biophys J 2008; 95: 155–165.
58 Ramis‐Conde, I, Chaplain, MAJ, Anderson, ARA, Drasdo, D. Multi‐scale modelling of cancer cell intravasation: the role of cadherins in metastasis. Phys Biol 2009; 6: 016008.
59 Stolarska, MA, Kim, Y, Othmer, HG. Multi‐scale models of cell and tissue dynamics. Phil Trans R Soc A 2009; 367: 3525–3553.
60 Schaller, G, Meyer‐Hermann, M. Multicellular tumor spheroid in an off‐lattice Voronoi‐Delaunay cell model. Phys Rev 2005; 71: 051910.
61 Beyer, T, Meyer‐Hermann, M. Multiscale modeling of cell mechanics and tissue organization. IEEE Eng Med Biol 2009; 28: 38–45.
62 Meineke, FA, Potten, CS, Loeffler, M. Cell migration and organization in the intestinal crypt using a lattice‐free model. Cell Prolif 2001; 34: 253.
63 Rejniak, KA. An immersed boundary framework for modelling the growth of individual cells: an application to the early tumour development. J Theor Biol 2007; 247: 186–204.
64 Dillon, RH, Owen, M, Painter, K. A single‐cell‐based model of multicellular growth using the immersed boundary method. AMS Contemp Math 2008; 466: 1–15.
65 Rejniak, KA, Dillon, RH. A single cell based model of the ductal tumour microarchitecture. Comput Math Methods Med 2007; 8: 51–69.
66 Quaranta, V, Rejniak, KA, Gerlee, P, Anderson, ARA. Invasion emerges from cancer cell adaptation to competitive microenvironments: quantitative predictions from multiscale mathematical models. Semin Cancer Biol 2008; 18: 338–348.
67 Rejniak, KA. A single‐cell approach in modeling the dynamics of tumor microregions. Math Biosci Eng 2005; 2: 643–655.
68 Rejniak, KA, Anderson, ARA. A computational study of the development of epithelial acini. I. Sufficient conditions for the formation of a hollow structure. Bull Math Biol 2008; 70: 677–712.
69 Rejniak, KA, Anderson, ARA. A computational study of the development of epithelial acini. II. Necessary conditions for structure and lumen stability. Bull Math Biol 2008; 70: 1450–1479.
70 Macklin, P, McDougall, S, Anderson, ARA, Chaplain, MAJ, Cristini, V, Lowengrub, J. Multiscale modelling and nonlinear simulation of vascular tumour growth. J Math Biol 2009; 58: 765–798.
71 Szeto, MD, Chakraborty, G, Hadley, J, Rockne, R, Muzi, M, Alvord, EC, Krohn, KA, Spence, AM, Swanson, KR. Quantitative metrics of net proliferation and invasion link biological aggressiveness assessed by MRI with hypoxia assessed by FMISO‐PET in newly diagnosed glioblastomas. Cancer Res 2009; 69: 4502–4509.
72 Stefanini, MO, Wu, FTH, Mac Gabhann, F, Popel, AS. A compartment model of VEGF distribution in blood, healthy and diseased tissues. BMC Syst Biol 2008; 2: 77.
73 Wu, FTH, Stefanini, MO, Gabhann, FM, Popel, AS. A compartment model of VEGF distribution in humans in the presence of soluble VEGF receptor‐1 acting as a ligand trap. PLoS ONE 2009; 4: e5108.
74 Fang, JS, Gillies, RD, Gatenby, RA. Adaptation to hypoxia and acidosis in carcinogenesis and tumor progression. Semin Cancer Biol 2008; 18: 330–337.
75 Vincent, TL, Gatenby, RA. An evolutionary model for initiation, promotion, and progression in carcinogenesis. Int J Oncol 2008; 32: 729–737.
76 Gatenby, RA, Frieden, BR. Application of information theory and extreme physical information to carcinogenesis. Cancer Res 2002; 62: 3675–3684.
77 Gatenby, RA. Application of competition theory to tumour growth: implications for tumour biology and treatment. Eur J Cancer 1996; 32A: 722–726.
78 Wolkenhauer, O, Auffray, Ch, Baltrusch, S, Blüthgen, N, Byrne, H, Cascante, M, Ciliberto, A, Dale, T, Drasdo, D, Fell, D,
et al. Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res 2010; 70: 12–13.
79 Wolkenhauer, O, Fell, D, De Meyts, P, Bluthgen, N, Herzel, H, Le Novere, N, Hofer, T, Schurrle, K, van Leeuwen, I. SysBioMed report: advancing systems biology for medical applications. IET Syst Biol 2009; 3: 131–136.
80 Hinow, P, Gerlee, P, McCawley, LJ, Quaranta, V, Ciobanu, M, Wang, SZ, Graham, JM, Ayati, BP, Claridge, J, Swanson, KR,
et al. A spatial model of tumor‐host interaction: application of chemotherapy. Math Biosci Eng 2009; 6: 521–546.
81 Komarova, NL, Sadovsky, AV, Wan, FYM. Selective pressures for and against genetic instability in cancer: a time‐dependent problem. J R Soc Interface 2008; 5: 105–121.