D. A. Fletcher and R. D. Mullins, Cell mechanics and the cytoskeleton, Nature, vol.105, issue.7280, pp.485-92, 2010.
DOI : 10.1038/nature08908

U. S. Schwarz and S. A. Safran, Physics of adherent cells, Reviews of Modern Physics, vol.85, issue.3, pp.1327-1381, 2013.
DOI : 10.1103/RevModPhys.85.1327

B. Sinha, D. Köster, R. Ruez, P. Gonnord, M. Bastiani et al., Cells Respond to Mechanical Stress by Rapid Disassembly of Caveolae, Cell, vol.144, issue.3, pp.402-413, 2011.
DOI : 10.1016/j.cell.2010.12.031

URL : https://hal.archives-ouvertes.fr/hal-00821331

W. H. Goldmann, Mechanotransduction and focal adhesions, Cell Biology International, vol.103, issue.7, pp.649-652, 2012.
DOI : 10.1083/jcb.200505018

Y. Cai and M. P. Sheetz, Force propagation across cells: mechanical coherence of dynamic cytoskeletons, Current Opinion in Cell Biology, vol.21, issue.1, pp.47-50, 2009.
DOI : 10.1016/j.ceb.2009.01.020

C. S. Chen, Mechanotransduction - a field pulling together?, Journal of Cell Science, vol.121, issue.20, pp.3285-3292, 2008.
DOI : 10.1242/jcs.023507

F. Guilak, D. M. Cohen, B. T. Estes, J. M. Gimble, W. Liedtke et al., Control of Stem Cell Fate by Physical Interactions with the Extracellular Matrix, Control of Stem Cell Fate by Physical Interactions with the Extracellular Matrix, pp.17-26, 2009.
DOI : 10.1016/j.stem.2009.06.016

G. Helmlinger, P. A. Netti, H. C. Lichtenbeld, R. J. Melder, and R. K. Jain, Solid stress inhibits the growth of multicellular tumor spheroids, Nature Biotechnology, vol.14, issue.8, pp.778-83, 1997.
DOI : 10.1038/nbt0897-778

G. Cheng, J. Tse, R. K. Jain, and L. L. Munn, Micro-Environmental Mechanical Stress Controls Tumor Spheroid Size and Morphology by Suppressing Proliferation and Inducing Apoptosis in Cancer Cells, PLoS ONE, vol.321, issue.2, p.4632, 2009.
DOI : 10.1371/journal.pone.0004632.s008

M. Basan, T. Risler, J. F. Joanny, X. S. Garau, and J. Prost, Homeostatic competition drives tumor growth and metastasis nucleation, HFSP Journal, vol.3, issue.4, pp.265-272, 2009.
DOI : 10.2976/1.3086732

URL : https://hal.archives-ouvertes.fr/hal-00961019

K. Alessandri, B. R. Sarangi, V. V. Gurchenkov, B. Sinha, T. R. Kieß-ling et al., Cellular capsules as a tool for multicellular spheroid production and for investigating the mechanics of tumor progression in vitro, Proceedings of the National Academy of Sciences of the United States of America, pp.14843-14851, 2013.
DOI : 10.1073/pnas.1309482110

URL : https://hal.archives-ouvertes.fr/inserm-01356886

S. Menon and K. A. Beningo, Cancer Cell Invasion Is Enhanced by Applied Mechanical Stimulation, PLoS ONE, vol.15, issue.2, p.17277, 2011.
DOI : 10.1371/journal.pone.0017277.s005

D. C. Radisky and C. M. Nelson, Regulation of mechanical stress by mammary epithelial tissue structure controls breast cancer cell invasion, Oncotarget, vol.4, issue.4, pp.498-507, 2013.
DOI : 10.18632/oncotarget.979

J. M. Tse, G. Cheng, J. A. Tyrrell, S. A. Wilcox-adelman, Y. Boucher et al., Mechanical compression drives cancer cells toward invasive phenotype, Proceedings of the National Academy of Sciences, vol.109, issue.3, pp.911-917, 2012.
DOI : 10.1073/pnas.1118910109

X. Trepat, M. R. Wasserman, T. E. Angelini, E. Millet, D. A. Weitz et al., Physical forces during collective cell migration, Nature Physics, vol.282, issue.6, pp.426-430, 2009.
DOI : 10.1007/s00348-001-0396-1

X. Tang, P. Bajaj, R. Bashir, and T. A. Saif, How far cardiac cells can see each other mechanically, Soft Matter, vol.82, issue.13, p.6151, 2011.
DOI : 10.1039/c0sm01453b

R. B. Vernon, J. C. Angello, M. L. Iruela-arispe, T. F. Lane, and E. H. Sage, Reorganization of basement membrane matrices by cellular traction promotes the formation of cellular networks in vitro, Lab. Invest, vol.66, issue.5, p.536, 1992.

S. R. Manoussaki, R. B. Lubkin, J. D. Vemon, and . Murray, A mechanical model for the formation of vascular networks in vitro, Acta Biotheoretica, vol.147, issue.3-4, pp.271-282, 1996.
DOI : 10.1007/BF00046533

D. Manoussaki, A mechanochemical model of angiogenesis and vasculogenesis, ESAIM: Mathematical Modelling and Numerical Analysis, vol.37, issue.4, pp.581-599, 2003.
DOI : 10.1051/m2an:2003046

J. D. Murray, On the mechanochemical theory of biological pattern formation with application to vasculogenesis, Comptes Rendus Biologies, vol.326, issue.2, pp.239-252, 2003.
DOI : 10.1016/S1631-0691(03)00065-9

P. Namy, J. Ohayon, and P. Tracqui, Critical conditions for pattern formation and in vitro tubulogenesis driven by cellular traction fields, Journal of Theoretical Biology, vol.227, issue.1, pp.103-120, 2004.
DOI : 10.1016/j.jtbi.2003.10.015

URL : https://hal.archives-ouvertes.fr/hal-00846401

R. F. Van-oers, E. G. Rens, D. J. Lavalley, C. Reinhart-king, and R. M. Merks, Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro, PLoS Computational Biology, vol.258, issue.8, p.1003774, 2014.
DOI : 10.1371/journal.pcbi.1003774.s013

R. J. Pelham and Y. Wang, Cell locomotion and focal adhesions are regulated by substrate flexibility, Proceedings of the National Academy of Sciences, pp.13661-13665, 1997.
DOI : 10.1073/pnas.94.25.13661

E. Cukierman, R. Pankov, D. R. Stevens, and K. M. Yamada, Taking Cell-Matrix Adhesions to the Third Dimension, Science, vol.294, issue.5547, pp.1708-1720, 2001.
DOI : 10.1126/science.1064829

P. Wu, A. Giri, S. X. Sun, and D. Wirtz, Three-dimensional cell migration does not follow a random walk, Proceedings of the National Academy of Sciences, vol.111, issue.11, pp.3949-3954, 2014.
DOI : 10.1073/pnas.1318967111

M. H. Zaman, L. M. Trapani, A. L. Sieminski, A. Siemeski, D. Mackellar et al., Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis, Proceedings of the National Academy of Sciences, vol.103, issue.29, pp.10889-94, 2006.
DOI : 10.1073/pnas.0604460103

S. L. Spencer, S. Gaudet, J. G. Albeck, J. M. Burke, and P. K. Sorger, Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis, Nature, vol.382, issue.7245, pp.428-432, 2009.
DOI : 10.1038/nature08012

F. Bertaux, S. Stoma, D. Drasdo, and G. Batt, Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance, PLoS Computational Biology, vol.73, issue.10, p.1003893, 2014.
DOI : 10.1371/journal.pcbi.1003893.s016

URL : https://hal.archives-ouvertes.fr/hal-00942885

I. Ramis-conde, M. A. Chaplain, A. R. Anderson, and D. Drasdo, Multi-scale modelling of cancer cell intravasation: the role of cadherins in metastasis, Physical Biology, vol.6, issue.1, p.16008, 2009.
DOI : 10.1088/1478-3975/6/1/016008

S. Hoehme, M. Brulport, A. Bauer, E. Bedawy, W. Schormann et al., Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration, Proceedings of the National Academy of Sciences, vol.107, issue.23, pp.10371-10376, 2010.
DOI : 10.1073/pnas.0909374107

F. A. Meineke, C. S. Potten, and M. Loeffler, Cell migration and organization in the intestinal crypt using a lattice-free model, Cell Proliferation, vol.16, issue.4, pp.253-266, 2001.
DOI : 10.1038/333463a0

P. Buske, J. Przybilla, M. Loeffler, N. Sachs, T. Sato et al., On the biomechanics of stem cell niche formation in the gut - modelling growing organoids, FEBS Journal, vol.6, issue.Suppl. 1, pp.3475-3487, 2012.
DOI : 10.1111/j.1742-4658.2012.08646.x

J. R. Jensen, P. K. King, S. L. Maini, H. M. Waters, and . Byrne, An integrative computational model for intestinal tissue renewal, Cell proliferation, vol.42, pp.617-653, 2009.

C. Pin, A. Parker, A. P. Gunning, Y. Ohta, I. T. Johnson et al., An individual based computational model of intestinal crypt fission and its application to predicting unrestrictive growth of the intestinal epithelium, Integrative biology : quantitative biosciences from nano to macro, pp.213-241, 2015.
DOI : 10.1039/C4IB00236A

S. Hammad, S. Hoehme, A. Friebel, I. Von-recklinghausen, A. Othman et al., Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis, Archives of Toxicology, vol.56, issue.4, pp.1161-83, 2014.
DOI : 10.1007/s00204-014-1243-5

URL : https://hal.archives-ouvertes.fr/hal-01110657

D. Drasdo, S. Hoehme, and J. G. Hengstler, How predictive quantitative modelling of tissue organisation can inform liver disease pathogenesis, Journal of Hepatology, vol.61, issue.4, pp.951-956, 2014.
DOI : 10.1016/j.jhep.2014.06.013

I. Roeder and M. Loeffler, A novel dynamic model of hematopoietic stem cell organization based on the concept of within-tissue plasticity, Experimental Hematology, vol.30, issue.8, pp.853-61, 2002.
DOI : 10.1016/S0301-472X(02)00832-9

M. Eden, A Two-dimensional Growth Process, Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability, 1961.

M. Batchelor and B. Henry, Limits to Eden growth in two and three dimensions, Physics Letters A, vol.157, issue.4-5, pp.229-236, 1991.
DOI : 10.1016/0375-9601(91)90057-F

A. R. Kansal, S. Torquato, I. V. Harsh, G. , E. A. Chiocca et al., Simulated Brain Tumor Growth Dynamics Using a Three-Dimensional Cellular Automaton, Journal of Theoretical Biology, vol.203, issue.4, pp.367-382, 2000.
DOI : 10.1006/jtbi.2000.2000

D. G. Mallet and L. G. De-pillis, A cellular automata model of tumor???immune system interactions, Journal of Theoretical Biology, vol.239, issue.3, pp.334-350, 2006.
DOI : 10.1016/j.jtbi.2005.08.002

T. S. Deisboeck, Z. Wang, P. Macklin, and V. Cristini, Multiscale Cancer Modeling, Annual Review of Biomedical Engineering, vol.13, issue.1, pp.127-55, 2011.
DOI : 10.1146/annurev-bioeng-071910-124729

A. Deutsch and S. Dormann, Cellular Automaton Modeling of Biological Pattern Formation: Characterization, Applications , and Analysis (Modeling and Simulation in Science, Engineering and Technology), 2004.

D. Richardson, Random growth in a tessellation, Mathematical Proceedings of the Cambridge Philosophical Society, vol.IV, issue.03, p.515, 2008.
DOI : 10.1017/S0305004100077288

M. S. Alber, M. A. Kiskowski, J. A. Glazier, and Y. Jiang, On Cellular Automaton Approaches to Modeling Biological Cells, Mathematical Systems Theory In Biology Communications, Computation, and Finance, vol.134, pp.1-39, 2003.
DOI : 10.1007/978-0-387-21696-6_1

M. Alber, N. Chen, P. M. Lushnikov, and S. A. Newman, Continuous Macroscopic Limit of a Discrete Stochastic Model for Interaction of Living Cells, Physical Review Letters, vol.99, issue.16, 2007.
DOI : 10.1103/PhysRevLett.99.168102

P. M. Lushnikov, N. Chen, and M. Alber, Macroscopic dynamics of biological cells interacting via chemotaxis and direct contact, Physical Review E, vol.78, issue.6, 2008.
DOI : 10.1103/PhysRevE.78.061904

M. Scianna and L. Preziosi, A Hybrid Model Describing Different Morphologies of Tumor Invasion Fronts, Mathematical Modelling of Natural Phenomena, vol.7, issue.1, pp.78-104, 2012.
DOI : 10.1051/mmnp/20127105

G. D. Antonio, P. Macklin, and L. Preziosi, An agent-based model for elasto-plastic mechanical interactions between cells, basement membrane and extracellular matrix, Mathematical Biosciences and Engineering, vol.10, issue.1, pp.75-101, 2013.
DOI : 10.3934/mbe.2013.10.75

F. Graner and J. A. Glazier, Simulation of biological cell sorting using a two-dimensional extended Potts model, Physical Review Letters, vol.69, issue.13, pp.2013-2016, 1992.
DOI : 10.1103/PhysRevLett.69.2013

R. M. Merks and J. A. Glazier, A cell-centered approach to developmental biology, Physica A: Statistical Mechanics and its Applications, pp.113-130, 2005.
DOI : 10.1016/j.physa.2004.12.028

N. J. Savill and P. Hogeweg, Modelling Morphogenesis: From Single Cells to Crawling Slugs, Journal of Theoretical Biology, vol.184, issue.3, pp.229-235, 1996.
DOI : 10.1006/jtbi.1996.0237

A. F. Marée and P. Hogeweg, How amoeboids self-organize into a fruiting body: Multicellular coordination in Dictyostelium discoideum, Proceedings of the National Academy of Sciences, vol.98, issue.7, pp.3879-3883, 2001.
DOI : 10.1073/pnas.061535198

T. Alarcón, H. M. Byrne, and P. K. Maini, A cellular automaton model for tumour growth in inhomogeneous environment, Journal of Theoretical Biology, vol.225, issue.2, pp.257-274, 2003.
DOI : 10.1016/S0022-5193(03)00244-3

T. Alarcón, H. M. Byrne, and P. K. Maini, A mathematical model of the effects of hypoxia on the cell-cycle of normal and cancer cells, Journal of Theoretical Biology, vol.229, issue.3, pp.395-411, 2004.
DOI : 10.1016/j.jtbi.2004.04.016

B. Ribba, T. Alarcon, K. Marron, P. K. Maini, and Z. Agur, The Use of Hybrid Cellular Automaton Models for Improving Cancer Therapy, 2004.
DOI : 10.1007/978-3-540-30479-1_46

T. Alarcon, H. M. Byrne, and P. K. Maini, A Multiple Scale Model for Tumor Growth, Multiscale Modeling & Simulation, vol.3, issue.2, p.440, 2010.
DOI : 10.1137/040603760

D. Drasdo, R. Kree, and J. S. Mccaskill, Monte Carlo approach to tissue-cell populations, Physical Review E, vol.52, issue.6, pp.6635-6657, 1995.
DOI : 10.1103/PhysRevE.52.6635

D. Drasdo, S. Hoehme, and M. Block, On the Role of Physics in the Growth and Pattern Formation of Multi-Cellular Systems: What can we Learn from Individual-Cell Based Models?, Journal of Statistical Physics, vol.37, issue.1-2, pp.287-345, 2007.
DOI : 10.1007/s10955-007-9289-x

J. Galle, M. Loeffler, and D. Drasdo, Modeling the Effect of Deregulated Proliferation and Apoptosis on the Growth Dynamics of Epithelial Cell Populations In Vitro, Biophysical Journal, vol.88, issue.1, pp.62-75, 2005.
DOI : 10.1529/biophysj.104.041459

F. Montel, M. Delarue, J. Elgeti, D. Vignjevic, G. Cappello et al., Isotropic stress reduces cell proliferation in tumor spheroids, New Journal of Physics, vol.14, issue.5, p.55008, 2012.
DOI : 10.1088/1367-2630/14/5/055008

URL : https://hal.archives-ouvertes.fr/hal-01138975

I. Ramis-conde, D. Drasdo, A. R. Anderson, and M. A. Chaplain, Modeling the Influence of the E-Cadherin-??-Catenin Pathway in Cancer Cell Invasion: A Multiscale Approach, Biophysical Journal, vol.95, issue.1, pp.155-165, 2008.
DOI : 10.1529/biophysj.107.114678

D. K. Schluter, I. Ramis-conde, and M. A. Chaplain, Computational Modeling of Single-Cell Migration: The Leading Role of Extracellular Matrix Fibers, Biophysical Journal, vol.103, issue.6, pp.1141-1151, 2012.
DOI : 10.1016/j.bpj.2012.07.048

M. Radszuweit, M. Block, J. Hengstler, E. Schöll, and D. Drasdo, Comparing the growth kinetics of cell populations in two and three dimensions, Physical Review E, vol.79, issue.5, p.51907, 2009.
DOI : 10.1103/PhysRevE.79.051907

S. Dormann, A. Deutsch, and A. T. Lawniczak, Fourier analysis of Turing-like pattern formation in cellular automaton models, Future Generation Computer Systems, vol.17, issue.7, pp.901-909, 2001.
DOI : 10.1016/S0167-739X(00)00068-6

S. Dormann and A. Deutsch, Modeling of self-organized avascular tumor growth with a hybrid cellular automaton, In silico biology, vol.2, pp.393-406, 2002.

J. S. Lowengrub, H. B. Frieboes, F. Jin, Y. Chuang, X. Li et al., Nonlinear modelling of cancer: bridging the gap between cells and tumours, Nonlinearity, vol.23, issue.1, pp.1-9, 2010.
DOI : 10.1088/0951-7715/23/1/R01

M. Block, E. Schöll, and D. Drasdo, Classifying the Expansion Kinetics and Critical Surface Dynamics of Growing Cell Populations, Physical Review Letters, vol.99, issue.24, 2007.
DOI : 10.1103/PhysRevLett.99.248101

A. R. Anderson, M. A. Chaplain, and K. A. Rejniak, Single-Cell-Based Models in Biology and Medicine, 2007.

A. R. Anderson, A. M. Weaver, P. T. Cummings, and V. Quaranta, Tumor Morphology and Phenotypic Evolution Driven by Selective Pressure from the Microenvironment, Cell, vol.127, issue.5, 2006.
DOI : 10.1016/j.cell.2006.09.042

D. Lee, H. Rieger, and K. Bartha, Flow Correlated Percolation during Vascular Remodeling in Growing Tumors, Physical Review Letters, vol.96, issue.5, p.58104, 2006.
DOI : 10.1103/PhysRevLett.96.058104

H. Enderling and P. Hahnfeldt, Cancer stem cells in solid tumors: Is ???evading apoptosis??? a hallmark of cancer?, Progress in Biophysics and Molecular Biology, vol.106, issue.2, pp.391-399, 2011.
DOI : 10.1016/j.pbiomolbio.2011.03.007

J. C. Alfonso, N. Jagiella, L. Núñez, M. A. Herrero, and D. Drasdo, Estimating Dose Painting Effects in Radiotherapy: A Mathematical Model, PLoS ONE, vol.52, issue.5, p.89380, 2014.
DOI : 10.1371/journal.pone.0089380.s011

URL : https://hal.archives-ouvertes.fr/hal-01109675

A. Kansal, S. Torquato, G. Harsh, I. , E. Chiocca et al., Cellular automaton of idealized brain tumor growth dynamics, Biosystems, vol.55, issue.1-3, 2000.
DOI : 10.1016/S0303-2647(99)00089-1

H. Honda, Description of cellular patterns by Dirichlet domains: The two-dimensional case, Journal of Theoretical Biology, vol.72, issue.3, pp.523-543, 1978.
DOI : 10.1016/0022-5193(78)90315-6

H. Honda, Geometrical Models for Cells in Tissues, International review of cytology, vol.81, pp.191-248, 1983.
DOI : 10.1016/S0074-7696(08)62339-6

D. Jagiella, N. Mueller, B. Mueller, M. Vignon-clementel, and I. Drasdo, Inferring Growth Control Mechanisms in Growing Multi-cellular Spheroids of NSCLC Cells from Spatial-Temporal Image Data, PLOS Computational Biology, vol.76, issue.5, p.2015
DOI : 10.1371/journal.pcbi.1004412.s001

URL : https://hal.archives-ouvertes.fr/hal-01244593

D. Drasdo and S. Hoehme, : monolayers and spheroids, Physical Biology, vol.2, issue.3, pp.133-147, 2005.
DOI : 10.1088/1478-3975/2/3/001

D. Drasdo, Coarse Graining in simulated cell populations Advances in Complex Systems, pp.319-363, 2005.

S. Hoehme and D. Drasdo, Mathematical Population Studies : An International Journal of Mathematical Biomechanical and Nutrient Controls in the Growth of Mammalian Cell Populations, pp.166-187, 2010.

A. Bortz, M. Kalos, and J. Lebowitz, A new algorithm for Monte Carlo simulation of Ising spin systems, Journal of Computational Physics, vol.17, issue.1, pp.10-18, 1975.
DOI : 10.1016/0021-9991(75)90060-1

D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions, The Journal of Physical Chemistry, vol.81, issue.25, pp.2340-2361, 1977.
DOI : 10.1021/j100540a008

D. A. Beysens, G. Forgacs, and J. A. Glazier, Cell sorting is analogous to phase ordering in fluids, Proceedings of the National Academy of Sciences, vol.97, issue.17, pp.9467-9471, 2000.
DOI : 10.1073/pnas.97.17.9467

M. Kardar, G. Parisi, and Y. C. Zhang, Dynamic Scaling of Growing Interfaces, Physical Review Letters, vol.56, issue.9, pp.889-892, 1986.
DOI : 10.1103/PhysRevLett.56.889

T. Halpin-healy and Y. Zhang, Kinetic roughening phenomena, stochastic growth, directed polymers and all that. Aspects of multidisciplinary statistical mechanics, Physics Reports, vol.254, issue.4-6, pp.4-6, 1995.
DOI : 10.1016/0370-1573(94)00087-J

A. Brú, S. Albertos, J. Luis-subiza, J. L. García-asenjo, and I. Brú, The Universal Dynamics of Tumor Growth, Biophysical Journal, vol.85, issue.5, pp.2948-2961, 2003.
DOI : 10.1016/S0006-3495(03)74715-8

M. A. Huergo, M. A. Pasquale, P. H. González, A. E. Bolzán, and A. J. Arvia, Dynamics and morphology characteristics of cell colonies with radially spreading growth fronts, Physical review. E, Statistical, nonlinear, and soft matter physics, p.21917, 2011.
DOI : 10.1103/PhysRevE.84.021917

M. A. Huergo, M. A. Pasquale, P. H. González, A. E. Bolzán, and A. J. Arvia, Growth dynamics of cancer cell colonies and their comparison with noncancerous cells, Physical Review E, vol.85, issue.1, 2012.
DOI : 10.1103/PhysRevE.85.011918

C. A. Yates and R. E. Baker, Isotropic model for cluster growth on a regular lattice, Physical Review E, vol.88, issue.2, 2013.
DOI : 10.1103/PhysRevE.88.023304

N. Jagiella, Parameterization of Lattice-Based Tumor Models from Data
URL : https://hal.archives-ouvertes.fr/tel-00779981

U. Frisch, B. Hasslacher, and Y. Pomeau, Lattice-Gas Automata for the Navier-Stokes Equation, Physical Review Letters, vol.56, issue.14, pp.1505-1508, 1986.
DOI : 10.1103/PhysRevLett.56.1505

D. H. Rothman and S. Zaleski, Lattice-Gas Cellular Automata: Simple Models of Complex Hydrodynamics, 2004.
DOI : 10.1017/CBO9780511524714

N. A. Gershenfeld, The Nature of Mathematical Modeling, 1999.

K. Böttger, H. Hatzikirou, A. Chauviere, and A. Deutsch, Investigation of the Migration/Proliferation Dichotomy and its Impact on Avascular Glioma Invasion, Mathematical Modelling of Natural Phenomena, vol.7, issue.1, pp.105-135, 2012.
DOI : 10.1051/mmnp/20127106

M. Tektonidis, H. Hatzikirou, A. Chauvì-ere, M. Simon, K. Schaller et al., Identification of intrinsic in vitro cellular mechanisms for glioma invasion, Journal of Theoretical Biology, vol.287, issue.1, pp.131-147, 2011.
DOI : 10.1016/j.jtbi.2011.07.012

URL : https://hal.archives-ouvertes.fr/hal-00807370

A. G. Hoekstra, J. Kroc, and P. M. Sloot, Simulating Complex Systems by Cellular Automata, 2010.

H. Hatzikirou and A. Deutsch, Lattice-Gas Cellular Automaton Modeling of Emergent Behavior in Interacting Cell Populations, Understanding Complex Systems, vol.2010, pp.301-331, 2010.
DOI : 10.1007/978-3-642-12203-3_13

J. A. Glazier and F. Graner, Simulation of the differential adhesion driven rearrangement of biological cells, Physical Review E, vol.47, issue.3, pp.2128-2154, 1993.
DOI : 10.1103/PhysRevE.47.2128

S. Turner and J. Sherratt, Intercellular Adhesion and Cancer Invasion: A Discrete Simulation Using the Extended Potts Model, Journal of Theoretical Biology, vol.216, issue.1, pp.85-100, 2002.
DOI : 10.1006/jtbi.2001.2522

B. M. Rubenstein and L. J. Kaufman, The Role of Extracellular Matrix in Glioma Invasion: A Cellular Potts Model Approach, Biophysical Journal, vol.95, issue.12, pp.5661-5680, 2008.
DOI : 10.1529/biophysj.108.140624

A. Shirinifard, J. S. Gens, B. L. Zaitlen, N. J. Popawski, M. Swat et al., 3D Multi-Cell Simulation of Tumor Growth and Angiogenesis, PLoS ONE, vol.56, issue.10, p.7190, 2009.
DOI : 10.1371/journal.pone.0007190.s003

E. Boghaert, D. C. Radisky, and C. M. Nelson, Lattice-Based Model of Ductal Carcinoma In Situ Suggests Rules for Breast Cancer Progression to an Invasive State, PLoS Computational Biology, vol.15, issue.2, p.1003997, 2014.
DOI : 10.1371/journal.pcbi.1003997.s001

A. Szabó and R. M. Merks, Cellular Potts Modeling of Tumor Growth, Tumor Invasion, and Tumor Evolution, Frontiers in Oncology, vol.3, 2013.
DOI : 10.3389/fonc.2013.00087

J. F. Li and J. Lowengrub, The effects of cell compressibility, motility and contact inhibition on the growth of tumor cell clusters using the Cellular Potts Model, Journal of Theoretical Biology, vol.343, pp.79-91, 2014.
DOI : 10.1016/j.jtbi.2013.10.008

X. Gao, J. T. Mcdonald, L. Hlatky, and H. Enderling, Acute and Fractionated Irradiation Differentially Modulate Glioma Stem Cell Division Kinetics, Cancer Research, vol.73, issue.5, pp.1481-1490, 2013.
DOI : 10.1158/0008-5472.CAN-12-3429

R. M. Merks and J. A. Glazier, Dynamic mechanisms of blood vessel growth, Nonlinearity, vol.19, issue.1, pp.1-10, 2006.
DOI : 10.1088/0951-7715/19/1/000

R. M. Merks, E. D. Perryn, A. Shirinifard, and J. A. Glazier, Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth, PLoS Computational Biology, vol.43, issue.9, p.1000163, 2008.
DOI : 10.1371/journal.pcbi.1000163.s060

M. M. Palm and R. M. Merks, Vascular networks due to dynamically arrested crystalline ordering of elongated cells, Physical Review E, vol.87, issue.1, p.12725, 2013.
DOI : 10.1103/PhysRevE.87.012725

S. E. Boas and R. M. Merks, Synergy of cell-cell repulsion and vacuolation in a computational model of lumen formation, Journal of The Royal Society Interface, vol.10, issue.4, p.20131049, 2014.
DOI : 10.1038/ncb1705

A. L. Bauer, T. L. Jackson, and Y. Jiang, Topography of Extracellular Matrix Mediates Vascular Morphogenesis and Migration Speeds in Angiogenesis, PLoS Computational Biology, vol.181, issue.038102, p.1000445, 2009.
DOI : 10.1371/journal.pcbi.1000445.s005

A. L. Bauer, T. L. Jackson, and Y. Jiang, A Cell-Based Model Exhibiting Branching and Anastomosis during Tumor-Induced Angiogenesis, Biophysical Journal, vol.92, issue.9, pp.3105-3121, 2007.
DOI : 10.1529/biophysj.106.101501

J. T. Daub and R. M. Merks, A Cell-Based Model of Extracellular-Matrix-Guided Endothelial Cell Migration During Angiogenesis, Bulletin of Mathematical Biology, vol.109, issue.8, pp.1-23, 2013.
DOI : 10.1007/s11538-013-9826-5

N. Ouchi, J. A. Glazier, J. Rieu, A. Upadhyaya, and Y. Sawada, Improving the realism of the cellular Potts model in simulations of biological cells, Physica A: Statistical Mechanics and its Applications, vol.329, issue.3-4, pp.3-4, 2003.
DOI : 10.1016/S0378-4371(03)00574-0

R. Magno, V. A. Grieneisen, and A. F. Marée, The biophysical nature of cells: potential cell behaviours revealed by analytical and computational studies of cell surface mechanics, BMC Biophysics, vol.53, issue.4, 2015.
DOI : 10.1186/s13628-015-0022-x

P. J. Albert and U. S. Schwarz, Dynamics of Cell Shape and Forces on Micropatterned Substrates Predicted by a Cellular Potts Model, Biophysical Journal, vol.106, issue.11, pp.2340-2352, 2014.
DOI : 10.1016/j.bpj.2014.04.036

R. M. Merks, S. V. Brodsky, M. S. Goligorksy, S. A. Newman, and J. A. Glazier, Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling, Developmental Biology, vol.289, issue.1, pp.44-54, 2006.
DOI : 10.1016/j.ydbio.2005.10.003

M. Scianna and L. Preziosi, A cellular Potts model for the MMP-dependent and -independent cancer cell migration in matrix microtracks of different dimensions, Computational Mechanics, vol.103, issue.2007, pp.485-497, 2013.
DOI : 10.1007/s00466-013-0944-6

M. Scianna, L. Preziosi, and K. Wolf, A Cellular Potts model simulating cell migration on and in matrix environments, Mathematical Biosciences and Engineering, vol.10, issue.1, pp.235-261, 2013.
DOI : 10.3934/mbe.2013.10.235

A. Szabó, K. Varga, T. Garay, B. Hegedus, and A. Czirók, Invasion from a cell aggregate???the roles of active cell motion and mechanical equilibrium, Physical Biology, vol.9, issue.1, p.16010, 2012.
DOI : 10.1088/1478-3975/9/1/016010

C. A. Lemmon and L. H. Romer, A Predictive Model of Cell Traction Forces Based on Cell Geometry, Biophysical Journal, vol.99, issue.9, pp.78-80, 2010.
DOI : 10.1016/j.bpj.2010.09.024

S. E. Boas, M. I. Jimenez, R. M. Merks, and J. G. Blom, A global sensitivity analysis approach for morphogenesis models, BMC Systems Biology, vol.316, issue.8, pp.1-29, 2015.
DOI : 10.1186/s12918-015-0222-7

M. M. Palm and R. M. Merks, Large-Scale Parameter Studies of Cell-Based Models of Tissue Morphogenesis Using CompuCell3D or VirtualLeaf, Methods in Molecular Biology, vol.1189, pp.301-322, 2015.
DOI : 10.1007/978-1-4939-1164-6_20

J. Starruß, W. De-back, L. Brusch, and A. Deutsch, Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology, Bioinformatics, vol.30, issue.9, pp.1331-1332, 2014.
DOI : 10.1093/bioinformatics/btt772

M. H. Swat, G. L. Thomas, J. M. Belmonte, A. Shirinifard, D. Hmeljak et al., Multi-Scale Modeling of Tissues Using CompuCell3D, Comput, pp.325-366, 2012.
DOI : 10.1016/B978-0-12-388403-9.00013-8

G. R. Mirams, C. J. Arthurs, M. O. Bernabeu, R. Bordas, J. Cooper et al., Chaste: An Open Source C++ Library for Computational Physiology and Biology, PLoS Computational Biology, vol.38, issue.3, p.1002970, 2013.
DOI : 10.1371/journal.pcbi.1002970.s006

A. F. Marée, V. A. Grieneisen, P. Hogeweg, and A. F. Maree, The Cellular Potts Model and Biophysical Properties of Cells, Tissues and Morphogenesis, pp.107-136, 2007.
DOI : 10.1007/978-3-7643-8123-3_5

D. Drasdo and G. Forgacs, Modeling the interplay of generic and genetic mechanisms in cleavage, blastulation, and gastrulation, Developmental Dynamics, vol.219, issue.2, pp.182-191, 2000.
DOI : 10.1002/1097-0177(200010)219:2<182::AID-DVDY1040>3.3.CO;2-1

G. M. Odell, G. Oster, P. Alberch, and B. Burnside, The mechanical basis of morphogenesis, Developmental Biology, vol.85, issue.2, pp.446-462, 1981.
DOI : 10.1016/0012-1606(81)90276-1

N. Sepúlveda, L. Petitjean, O. Cochet, E. Grasland-mongrain, P. Silberzan et al., Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model, PLoS Computational Biology, vol.107, issue.Pt 5, p.1002944, 2013.
DOI : 10.1371/journal.pcbi.1002944.s014

D. Drasdo and M. Loeffler, Individual-based models to growth and folding in one-layered tissues: intestinal crypts and early development, Nonlinear Analysis: Theory, Methods & Applications, vol.47, issue.1, pp.245-256, 2001.
DOI : 10.1016/S0362-546X(01)00173-0

M. Basan, J. Prost, J. Joanny, and J. Elgeti, Dissipative particle dynamics simulations for biological tissues: rheology and competition, Physical Biology, vol.8, issue.2, p.26014, 2011.
DOI : 10.1088/1478-3975/8/2/026014

P. Pathmanathan, J. Cooper, A. Fletcher, G. Mirams, L. Montahan et al., A computational study of discrete mechanical tissue models, Physical Biology, vol.6, issue.3, p.36001, 2009.
DOI : 10.1088/1478-3975/6/3/036001

T. Odenthal, B. Smeets, P. Van-liedekerke, E. Tijskens, H. Van-oosterwyck et al., Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model, PLoS Computational Biology, vol.266, issue.(3), p.1003267, 2013.
DOI : 10.1371/journal.pcbi.1003267.s007

URL : https://hal.archives-ouvertes.fr/hal-00909485

P. Van-liedekerke, B. Smeets, T. Odenthal, E. Tijskens, and H. Ramon, Solving microscopic flow problems using Stokes equations in SPH, Computer Physics Communications, vol.184, issue.7, pp.1686-1696, 2013.
DOI : 10.1016/j.cpc.2013.02.013

URL : https://hal.archives-ouvertes.fr/hal-00802400

H. Turlier, B. Audoly, J. Prost, and J. Joanny, Furrow Constriction in Animal Cell Cytokinesis, Biophysical Journal, vol.106, issue.1, pp.114-137, 2014.
DOI : 10.1016/j.bpj.2013.11.014

G. Schaller and M. Meyer-hermann, Multicellular tumor spheroid in an off-lattice Voronoi-Delaunay cell model, Physical Review E, vol.71, issue.5, p.51910, 2005.
DOI : 10.1103/PhysRevE.71.051910

D. Drasdo and S. Hoehme, Modeling the impact of granular embedding media, and pulling versus pushing cells on growing cell clones, New Journal of Physics, vol.14, issue.5, p.55025, 2012.
DOI : 10.1088/1367-2630/14/5/055025

URL : https://hal.archives-ouvertes.fr/hal-00778129

M. Aragona, T. Panciera, A. Manfrin, S. Giulitti, F. Michielin et al., A Mechanical Checkpoint Controls Multicellular Growth through YAP/TAZ Regulation by Actin-Processing Factors, Cell, vol.154, issue.5, pp.1047-59, 2013.
DOI : 10.1016/j.cell.2013.07.042

B. C. Low, C. Q. Pan, G. V. Shivashankar, A. Bershadsky, M. Sudol et al., YAP/TAZ as mechanosensors and mechanotransducers in regulating organ size and tumor growth, FEBS Letters, vol.25, issue.16, pp.2663-70, 2014.
DOI : 10.1016/j.febslet.2014.04.012

H. Byrne and D. Drasdo, Individual-based and continuum models of growing cell populations: a comparison, Journal of Mathematical Biology, vol.14, issue.1, pp.657-680, 2009.
DOI : 10.1007/s00285-008-0212-0

J. H. Irving and J. G. Kirkwood, The Statistical Mechanical Theory of Transport Processes. IV. The Equations of Hydrodynamics, The Journal of Chemical Physics, vol.18, issue.6, p.817, 1950.
DOI : 10.1063/1.1747782

P. Ghysels, G. Samaey, B. Tijskens, P. V. Liedekerke, H. Ramon et al., Multi-scale simulation of plant tissue deformation using a model for individual cell mechanics, Physical Biology, vol.6, issue.1, p.16009, 2009.
DOI : 10.1088/1478-3975/6/1/016009

S. Hoehme and D. Drasdo, A cell-based simulation software for multi-cellular systems, Bioinformatics, vol.26, issue.20, pp.2641-2642, 2010.
DOI : 10.1093/bioinformatics/btq437

A. Friebel, J. Neitsch, T. Johann, S. Hammad, J. G. Hengstler et al., TiQuant: software for tissue analysis, quantification and surface reconstruction: Fig. 1., Bioinformatics, vol.31, issue.19, 2015.
DOI : 10.1093/bioinformatics/btv346

P. Godoy, N. Hewitt, U. Albrecht, M. Andersen, N. Ansari et al., Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME, Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME, pp.1315-1530, 2013.
DOI : 10.1007/s00204-013-1078-5

URL : https://hal.archives-ouvertes.fr/hal-00939009

J. Galle, G. Aust, G. Schaller, T. Beyer, and D. Drasdo, Individual cell-based models of the spatial-temporal organization of multicellular systems???Achievements and limitations, Cytometry Part A, vol.28, issue.7, pp.704-714, 2006.
DOI : 10.1002/cyto.a.20287

M. Delarue, F. Montel, D. Vignjevic, J. Prost, J. Joanny et al., Compressive Stress Inhibits Proliferation in Tumor Spheroids through a Volume Limitation, Biophysical Journal, vol.107, issue.8, pp.1821-1828, 2014.
DOI : 10.1016/j.bpj.2014.08.031

URL : https://hal.archives-ouvertes.fr/hal-01123922

P. Macklin, M. E. Edgerton, A. M. Thompson, and V. Cristini, Patient-calibrated agent-based modelling of ductal carcinoma in situ (DCIS): From microscopic measurements to macroscopic predictions of clinical progression, Journal of Theoretical Biology, vol.301, pp.122-162, 2012.
DOI : 10.1016/j.jtbi.2012.02.002

P. Buske, J. Galle, N. Barker, G. Aust, H. Clevers et al., A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt, PLoS Computational Biology, vol.303, issue.Pt 12, p.1001045, 2011.
DOI : 10.1371/journal.pcbi.1001045.s005

S. J. Dunn, I. S. Näthke, and J. M. Osborne, Computational Models Reveal a Passive Mechanism for Cell Migration in the Crypt, PLoS ONE, vol.1, issue.11, 2013.
DOI : 10.1371/journal.pone.0080516.s003

R. C. Van-der-wath, B. S. Gardiner, A. W. Burgess, and D. W. Smith, Cell Organisation in the Colonic Crypt: A Theoretical Comparison of the Pedigree and Niche Concepts, PLoS ONE, vol.7, issue.9, p.73204, 2013.
DOI : 10.1371/journal.pone.0073204.s007

A. G. Fletcher, C. J. Breward, and S. Chapman, Mathematical modeling of monoclonal conversion in the colonic crypt, Journal of Theoretical Biology, vol.300, pp.118-133, 2012.
DOI : 10.1016/j.jtbi.2012.01.021

S. J. Dunn, A. G. Fletcher, S. J. Chapman, D. J. Gavaghan, and J. M. Osborne, Modelling the role of the basement membrane beneath a growing epithelial monolayer, Journal of Theoretical Biology, vol.298, pp.82-91, 2012.
DOI : 10.1016/j.jtbi.2011.12.013

J. R. Jensen, P. K. King, S. L. Maini, H. M. Waters, and . Byrne, An integrative computational model for intestinal tissue renewal, Cell Proliferation, vol.42, issue.5, pp.617-636, 2009.

R. Smallwood, Computational modeling of epithelial tissues, Wiley Interdisciplinary Reviews: Systems Biology and Medicine, vol.254, issue.5, pp.191-201, 2009.
DOI : 10.1002/wsbm.18

I. M. Van-leeuwen, C. M. Edwards, M. Ilyas, and H. M. Byrne, Towards a multiscale model of colorectal cancer, World Journal of Gastroenterology, vol.13, issue.9, pp.1399-1407, 2007.
DOI : 10.3748/wjg.v13.i9.1399

M. H. Zaman, R. D. Kamm, P. Matsudaira, and D. A. Lauffenburger, Computational Model for Cell Migration in Three-Dimensional Matrices, Biophysical Journal, vol.89, issue.2, pp.1389-97, 2005.
DOI : 10.1529/biophysj.105.060723

R. Rangarajan and M. H. Zaman, Modeling cell migration in 3D, Cell Adhesion & Migration, vol.4, issue.2, pp.106-109, 2008.
DOI : 10.1007/s10439-006-9205-6

R. Rey and J. M. García-aznar, A phenomenological approach to modelling collective cell movement in 2D, Biomechanics and Modeling in Mechanobiology, vol.22, issue.19, pp.1089-100, 2013.
DOI : 10.1007/s10237-012-0465-9

F. J. Vermolen and A. Gefen, A semi-stochastic cell-based formalism to model the dynamics of migration of cells in colonies, Biomechanics and Modeling in Mechanobiology, vol.106, issue.39, pp.183-95, 2012.
DOI : 10.1007/s10237-011-0302-6

D. Harjanto and M. H. Zaman, Modeling Extracellular Matrix Reorganization in 3D Environments, PLoS ONE, vol.7, issue.4, p.52509, 2013.
DOI : 10.1371/journal.pone.0052509.t002

T. Kim, W. Hwang, H. Lee, and R. D. Kamm, Computational Analysis of Viscoelastic Properties of Crosslinked Actin Networks, PLoS Computational Biology, vol.14, issue.7, p.1000439, 2009.
DOI : 10.1371/journal.pcbi.1000439.t001

M. Basan, J. Elgeti, E. Hannezo, W. Rappel, and H. Levine, Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing, Proceedings of the National Academy of Sciences, vol.110, issue.7, pp.2452-2459, 2013.
DOI : 10.1073/pnas.1219937110

E. Palsson and H. G. Othmer, A model for individual and collective cell movement in Dictyosteliumdiscoideum, Proceedings of the National Academy of Sciences, pp.10448-10453, 2000.
DOI : 10.1073/pnas.97.19.10448

E. Palsson, A three-dimensional model of cell movement in multicellular systems, Future Generation Computer Systems, vol.17, issue.7, pp.835-852, 2001.
DOI : 10.1016/S0167-739X(00)00062-5

J. C. Dallon and H. G. Othmer, How cellular movement determines the collective force generated by the Dictyostelium discoideum slug, Journal of Theoretical Biology, vol.231, issue.2, pp.203-222, 2004.
DOI : 10.1016/j.jtbi.2004.06.015

A. Krinner, Spherical Individual Cell-Based Models : limits and applications, 2010.

H. Honda, H. Yamanaka, and M. Dan-sohkawa, A computer simulation of geometrical configurations during cell division, Journal of Theoretical Biology, vol.106, issue.3, pp.423-458, 1984.
DOI : 10.1016/0022-5193(84)90039-0

D. Drasdo and S. Höhme, Individual-based approaches to birth and death in avascu1ar tumors, Mathematical and Computer Modelling, vol.37, issue.11, pp.1163-1175, 2003.
DOI : 10.1016/S0895-7177(03)00128-6

D. Drasdo, Buckling Instabilities of One-Layered Growing Tissues, Physical Review Letters, vol.84, issue.18, pp.4244-4247, 2000.
DOI : 10.1103/PhysRevLett.84.4244

D. K. Schlüter, I. Ramis-conde, and M. A. Chaplain, Multi-scale modelling of the dynamics of cell colonies: insights into cell-adhesion forces and cancer invasion from in silico simulations, Journal of The Royal Society Interface, vol.52, issue.3, p.20141080, 2015.
DOI : 10.1016/S0006-3495(87)83236-8

H. Kempf, M. Bleicher, and M. Meyer-hermann, Spatio-temporal cell dynamics in tumour spheroid irradiation, The European Physical Journal D, vol.278, issue.1, pp.177-193, 2010.
DOI : 10.1140/epjd/e2010-00178-4

A. C. Boulanger, Agent-based model -Continuum Model in tumor growth (INRIA intership report), 2009.

F. Milde, G. Tauriello, H. Haberkern, and P. Koumoutsakos, SEM++: A particle model of cellular growth, signaling and migration, Computational Particle Mechanics, 2014.
DOI : 10.1007/s40571-014-0017-4

K. A. Rejniak, A Single-Cell Approach in Modeling the Dynamics of Tumor Microregions, Mathematical Biosciences and Engineering, vol.2, issue.3, pp.643-55, 2005.
DOI : 10.3934/mbe.2005.2.643

D. E. Discher, D. H. Boal, and S. K. Boey, Simulations of the Erythrocyte Cytoskeleton at Large Deformation. II. Micropipette Aspiration, Biophysical Journal, vol.75, issue.3, pp.1584-1597, 1998.
DOI : 10.1016/S0006-3495(98)74076-7

D. A. Fedosov, B. Caswell, and G. E. Karniadakis, Systematic coarse-graining of spectrin-level red blood cell models, Computer Methods in Applied Mechanics and Engineering, vol.199, issue.29-32, pp.1937-1948, 2010.
DOI : 10.1016/j.cma.2010.02.001

P. Van-liedekerke, E. Tijskens, H. Ramon, P. Ghysels, G. Samaey et al., Particle-based model to simulate the micromechanics of biological cells, Physical Review E, vol.81, issue.6, pp.61906-61915, 2010.
DOI : 10.1103/PhysRevE.81.061906

S. A. Sandersius and T. J. Newman, Modeling cell rheology with the Subcellular Element Model, Physical Biology, vol.5, issue.1, p.15002, 2008.
DOI : 10.1088/1478-3975/5/1/015002

D. Boal, Mechanics of the Cell, 2012.

J. C. Hansen, R. Skalak, S. Chien, and A. Hoger, An elastic network model based on the structure of the red blood cell membrane skeleton, Biophysical Journal, vol.70, issue.1, pp.146-66, 1996.
DOI : 10.1016/S0006-3495(96)79556-5

M. Buenemann and P. Lenz, Elastic properties and mechanical stability of chiral and filled viral capsids, Physical Review E, vol.78, issue.5, p.51924, 2008.
DOI : 10.1103/PhysRevE.78.051924

K. A. Rejniak, An immersed boundary framework for modelling the growth of individual cells: An application to the early tumour development, Journal of Theoretical Biology, vol.247, issue.1, pp.186-204, 2007.
DOI : 10.1016/j.jtbi.2007.02.019

K. A. Rejniak and R. H. Dillon, A Single Cell-Based Model of the Ductal Tumour Microarchitecture, Computational and Mathematical Methods in Medicine, vol.8, issue.1, pp.51-69
DOI : 10.1080/17486700701303143

R. Dillon and M. Owen, A single-cell-based model of multicellular growth using the immersed boundary method, AMS Contemporary Mathematics, vol.466, 2008.
DOI : 10.1090/conm/466/09113

K. A. Rejniak and A. R. Anderson, A Computational Study of the Development of Epithelial Acini: I.??Sufficient Conditions for the Formation of a Hollow Structure, Bulletin of Mathematical Biology, vol.95, issue.1, pp.677-712, 2008.
DOI : 10.1007/s11538-007-9274-1

J. Li, M. Dao, C. T. Lim, and S. Suresh, Spectrin-Level Modeling of the Cytoskeleton and Optical Tweezers Stretching of the Erythrocyte, Biophysical Journal, vol.88, issue.5, pp.3707-3719, 2005.
DOI : 10.1529/biophysj.104.047332

I. V. Pivkin and G. E. Karniadakisa, Accurate Coarse-Grained Modeling of Red Blood Cells, Physical Review Letters, vol.101, issue.11, p.118105, 2008.
DOI : 10.1103/PhysRevLett.101.118105

M. Hosseini and J. J. Feng, A particle-based model for the transport of erythrocytes in capillaries, Chemical Engineering Science, vol.64, issue.22, pp.4488-4497, 2009.
DOI : 10.1016/j.ces.2008.11.028

D. Fedosov, B. Caswell, S. Suresh, and G. E. Karniadakis, Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation, Proceedings of the National Academy of Sciences, vol.108, issue.1, pp.35-44, 2011.
DOI : 10.1073/pnas.1009492108

Z. Peng, X. Li, I. V. Pivkin, M. Dao, G. E. Karniadakis et al., Lipid bilayer and cytoskeletal interactions in a red blood cell, Proceedings of the National Academy of Sciences, 2013.
DOI : 10.1073/pnas.1311827110

D. E. Ingber, Tensegrity I. Cell structure and hierarchical systems biology, Journal of Cell Science, vol.116, issue.7, pp.1157-1173, 2003.
DOI : 10.1242/jcs.00359

S. A. Sandersius, C. J. Weijer, and T. J. Newman, Emergent cell and tissue dynamics from subcellular modeling of active biomechanical processes, Physical Biology, vol.8, issue.4, p.45007, 2011.
DOI : 10.1088/1478-3975/8/4/045007

Y. Jamali, M. Azimi, and M. R. Mofrad, A Sub-Cellular Viscoelastic Model for Cell Population Mechanics, PLoS ONE, vol.1, issue.8, p.12097, 2010.
DOI : 10.1371/journal.pone.0012097.t002

P. Van-liedekerke, D. Roose, H. Ramon, P. Ghysels, E. Tijskens et al., Mechanisms of soft cellular tissue bruising. A particle based simulation approach, Soft Matter, vol.6, issue.7, p.3580, 2011.
DOI : 10.1039/c0sm01261k

K. Tamura, S. Komura, and T. Kato, Adhesion induced buckling of spherical shells, Journal of Physics: Condensed Matter, vol.16, issue.39, pp.421-428, 2004.
DOI : 10.1088/0953-8984/16/39/L01

M. P. Murrell, R. Voituriez, J. Joanny, P. Nassoy, C. Sykes et al., Liposome adhesion generates traction stress, Nature Physics, vol.18, issue.2, pp.163-169, 2014.
DOI : 10.1007/s12195-010-0102-6

URL : https://hal.archives-ouvertes.fr/hal-00989037

M. Kim, D. M. Neal, R. D. Kamm, and H. H. Asada, Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries, PLoS Computational Biology, vol.10, issue.2, p.1002926, 2013.
DOI : 10.1371/journal.pcbi.1002926.s015

M. Tozluolu, A. L. Tournier, R. P. Jenkins, S. Hooper, P. A. Bates et al., Matrix geometry determines optimal cancer cell migration strategy and modulates response to interventions, Nature Cell Biology, vol.115, issue.7, pp.751-762, 2013.
DOI : 10.1038/sj.bjc.6602255

K. Bentley, G. Mariggi, H. Gerhardt, and P. A. Bates, Tipping the Balance: Robustness of Tip Cell Selection, Migration and Fusion in Angiogenesis, PLoS Computational Biology, vol.134, issue.10, p.1000549, 2009.
DOI : 10.1371/journal.pcbi.1000549.s016

T. Nagai and H. Honda, A dynamic cell model for the formation of epithelial tissues, Philosophical Magazine Part B, vol.23, issue.7, pp.699-719, 2001.
DOI : 10.1083/jcb.90.2.507

T. Nagai and H. Honda, Computer simulation of wound closure in epithelial tissues: Cell???basal-lamina adhesion, Physical Review E, vol.80, issue.6, p.61903, 2009.
DOI : 10.1103/PhysRevE.80.061903

R. Farhadifar, J. Röper, B. Aigouy, S. Eaton, and F. Jülicher, The Influence of Cell Mechanics, Cell-Cell Interactions, and Proliferation on Epithelial Packing, Current Biology, vol.17, issue.24, pp.2095-104, 2007.
DOI : 10.1016/j.cub.2007.11.049

S. Hilgenfeldt, S. Erisken, and R. W. Carthew, Physical modeling of cell geometric order in an epithelial tissue, Proceedings of the National Academy of Sciences of the United States of America, pp.907-918, 2008.
DOI : 10.1073/pnas.0711077105

M. L. Manning, R. A. Foty, M. S. Steinberg, and E. Schoetz, Coaction of intercellular adhesion and cortical tension specifies tissue surface tension, Proceedings of the National Academy of Sciences, 2010.
DOI : 10.1073/pnas.1003743107

T. Rudge and J. Haseloff, Advances in Artificial Life, Lecture Notes in Computer Science, vol.3630, 2005.

A. G. Fletcher, J. M. Osborne, P. K. Maini, and D. J. Gavaghan, Implementing vertex dynamics models of cell populations in biology within a consistent computational framework, Progress in biophysics and molecular biology, pp.299-326, 2013.
DOI : 10.1016/j.pbiomolbio.2013.09.003

C. T. Lim, E. H. Zhou, and S. T. Quek, Mechanical models for living cells???a review, Journal of Biomechanics, vol.39, issue.2, pp.195-216, 2006.
DOI : 10.1016/j.jbiomech.2004.12.008

E. H. Zhou, F. Xu, S. T. Quek, and C. T. Lim, A power-law rheology-based finite element model for single cell deformation, Biomechanics and Modeling in Mechanobiology, vol.9, issue.2, pp.1075-84, 2012.
DOI : 10.1007/s10237-012-0374-y

X. Trepat, G. Lenormand, and J. J. Fredberg, Universality in cell mechanics, Soft Matter, vol.30, issue.9, p.1750, 2008.
DOI : 10.1039/b804866e

F. Wottawah, S. Schinkinger, B. Lincoln, R. Ananthakrishnan, M. Romeyke et al., Optical Rheology of Biological Cells, Physical Review Letters, vol.94, issue.9, p.98103, 2005.
DOI : 10.1103/PhysRevLett.94.098103

T. Roose, S. J. Chapman, and P. K. Maini, Mathematical Models of Avascular Tumor Growth, SIAM Review, vol.49, issue.2, pp.179-208, 2007.
DOI : 10.1137/S0036144504446291

H. M. Byrne, T. Alarcon, M. R. Owen, S. D. Webb, and P. K. Maini, Modelling aspects of cancer dynamics: a review, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.4, issue.1, pp.1563-78, 2006.
DOI : 10.1016/j.jns.2003.06.001

T. Roose, P. A. Netti, L. L. Munn, Y. Boucher, and R. K. Jain, Solid stress generated by spheroid growth estimated using a linear poroelasticity model???, Microvascular research, pp.204-216, 2003.
DOI : 10.1016/S0026-2862(03)00057-8

D. Ambrosi and L. Preziosi, Cell adhesion mechanisms and stress relaxation in the mechanics of tumours, Biomechanics and Modeling in Mechanobiology, vol.2, issue.5, pp.397-413, 2009.
DOI : 10.1007/s10237-008-0145-y

L. Preziosi and A. Tosin, Multiphase modelling of tumour growth and extracellular matrix interaction: mathematical tools and applications, Journal of Mathematical Biology, vol.114, issue.4, pp.625-56, 2009.
DOI : 10.1007/s00285-008-0218-7

L. Preziosi, D. Ambrosi, and C. Verdier, An elasto-visco-plastic model of cell aggregates, Journal of Theoretical Biology, vol.262, issue.1, pp.35-47, 2010.
DOI : 10.1016/j.jtbi.2009.08.023

URL : https://hal.archives-ouvertes.fr/hal-00554642

G. Sciumè, R. Santagiuliana, M. Ferrari, P. Decuzzi, and B. A. Schrefler, A tumor growth model with deformable ECM, Physical Biology, vol.11, issue.6, p.65004, 2014.
DOI : 10.1088/1478-3975/11/6/065004

M. Alber, N. Chen, T. Glimm, and P. M. Lushnikov, Multiscale dynamics of biological cells with chemotactic interactions: From a discrete stochastic model to a continuous description, Physical Review E, vol.73, issue.5, 2006.
DOI : 10.1103/PhysRevE.73.051901

A. De-masi, S. Luckhaus, and E. Presutti, Two scales hydrodynamic limit for a model of malignant tumor cells, Annales de l'institut Henri Poincare (B) Probability and Statistics, pp.257-297, 2007.

A. Stevens, The Derivation of Chemotaxis Equations as Limit Dynamics of Moderately Interacting Stochastic Many- Particle Systems, 2000.

A. Chauviere, H. Hatzikirou, I. G. Kevrekidis, J. S. Lowengrub, and V. Cristini, Dynamic density functional theory of solid tumor growth: Preliminary models, AIP Advances, vol.2, issue.1, p.11210, 2012.
DOI : 10.1063/1.3699065

L. A. D-'alessandro, S. Hoehme, A. Henney, D. Drasdo, and U. Klingmüller, Unraveling liver complexity from molecular to organ level: Challenges and perspectives, Progress in biophysics and molecular biology, pp.78-86, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01257160

J. Galle, L. Preziosi, and A. Tosin, Contact inhibition of growth described using a multiphase model and an individual cell based model, Applied Mathematics Letters, vol.22, issue.10, pp.1483-1490, 2009.
DOI : 10.1016/j.aml.2008.06.051

P. Murray, C. Edwards, M. Tindall, and P. Maini, From a discrete to a continuum model of cell dynamics in one dimension, Physical Review E, vol.80, issue.3, p.31912, 2009.
DOI : 10.1103/PhysRevE.80.031912

H. B. Frieboes, F. Jin, Y. Chuang, S. M. Wise, J. S. Lowengrub et al., Three-dimensional multispecies nonlinear tumor growth???II: Tumor invasion and angiogenesis, Journal of Theoretical Biology, vol.264, issue.4, pp.1254-78, 2010.
DOI : 10.1016/j.jtbi.2010.02.036

B. H. Osborne, J. M. Walter, A. Kershaw, S. K. Mirams, G. R. Fletcher et al., A hybrid approach to multi-scale modelling of cancer, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.67, issue.2, pp.5013-5028, 2010.
DOI : 10.1016/j.bulm.2004.08.001

Y. Kim, M. A. Stolarska, and H. G. Othemer, I: THEORETICAL DEVELOPMENT AND EARLY RESULTS, Mathematical Models and Methods in Applied Sciences, vol.17, issue.supp01, pp.1773-1798, 2007.
DOI : 10.1142/S0218202507002479

J. C. Dallon, J. A. Sherratt, and P. K. Maini, Mathematical Modelling of Extracellular Matrix Dynamics using Discrete Cells: Fiber Orientation and Tissue Regeneration, Journal of Theoretical Biology, vol.199, issue.4, pp.449-71, 1999.
DOI : 10.1006/jtbi.1999.0971

B. D. Cumming, D. L. Mcelwain, and Z. Upton, A mathematical model of wound healing and subsequent scarring, Journal of The Royal Society Interface, vol.154, issue.1, pp.19-34, 2010.
DOI : 10.1016/S0022-5193(05)80715-5

L. Yang, T. M. Witten, and R. M. Pidaparti, A biomechanical model of wound contraction and scar formation, Journal of Theoretical Biology, vol.332, pp.228-276, 2013.
DOI : 10.1016/j.jtbi.2013.03.013

F. Milde, M. Bergdorf, and P. Koumoutsakos, A Hybrid Model for Three-Dimensional Simulations of Sprouting Angiogenesis, Biophysical Journal, vol.95, issue.7, pp.3146-60, 2008.
DOI : 10.1529/biophysj.107.124511

J. Monaghan, Smoothed Particle Hydrodynamics and Its Diverse Applications, Annual Review of Fluid Mechanics, vol.44, issue.1, pp.323-346, 2012.
DOI : 10.1146/annurev-fluid-120710-101220

B. Gholami, A. Comerford, and M. Ellero, A multiscale SPH particle model of the near-wall dynamics of leukocytes in flow, International Journal for Numerical Methods in Biomedical Engineering, vol.34, issue.1, pp.83-102, 2013.
DOI : 10.1002/cnm.2591

N. Tanaka and T. Takano, MICROSCOPIC-SCALE SIMULATION OF BLOOD FLOW USING SPH METHOD, International Journal of Computational Methods, vol.02, issue.04, pp.555-568, 2005.
DOI : 10.1142/S021987620500065X

B. R. Angermann, F. Klauschen, A. D. Garcia, T. Prustel, F. Zhang et al., Computational modeling of cellular signaling processes embedded into dynamic spatial contexts, Nature Methods, vol.7, issue.3, pp.283-289, 2012.
DOI : 10.1016/j.jcp.2007.05.025

G. P. Figueredo, T. V. Joshi, J. M. Osborne, H. M. Byrne, and M. R. Owen, On-lattice agent-based simulation of populations of cells within the open-source Chaste framework, Interface Focus, vol.51, issue.8, p.20120081, 2013.
DOI : 10.1158/0008-5472.CAN-10-2834

T. Sütterlin, C. Kolb, H. Dickhaus, D. Jäger, and N. Grabe, Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI, Bioinformatics, vol.29, issue.2, pp.223-232, 2013.
DOI : 10.1093/bioinformatics/bts659

M. Cytowski and Z. Szymanska, Large-Scale Parallel Simulations of 3D Cell Colony Dynamics, Computing in Science & Engineering, vol.16, issue.5, pp.86-95, 2014.
DOI : 10.1109/MCSE.2014.2

M. Cytowski and Z. Szymanska, Large Scale Parallel Simulations of 3-D Cell Colony Dynamics. II. Coupling with continuous description of cellular environment, Comput. Sci. Eng, issue.99, pp.1-6, 2015.

S. Kang, S. Kahan, J. Mcdermott, N. Flann, and I. Shmulevich, Biocellion: accelerating computer simulation of multicellular biological system models, Bioinformatics, vol.30, issue.21, pp.3101-3109, 2014.
DOI : 10.1093/bioinformatics/btu498

R. M. Merks, M. Guravage, D. Inzé, and G. T. Beemster, VirtualLeaf: An Open-Source Framework for Cell-Based Modeling of Plant Tissue Growth and Development, PLANT PHYSIOLOGY, vol.155, issue.2, pp.656-666, 2011.
DOI : 10.1104/pp.110.167619

S. Tanaka, D. Sichau, and D. Iber, LBIBCell: a cell-based simulation environment for morphogenetic problems, Bioinformatics, vol.31, issue.14, 2015.
DOI : 10.1093/bioinformatics/btv147

M. Hucka, H. M. Finney, H. Sauro, J. C. Bolouri, H. Doyle et al., The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003.
DOI : 10.1093/bioinformatics/btg015

V. Andasari, R. T. Roper, M. H. Swat, and M. A. Chaplain, Integrating Intracellular Dynamics Using CompuCell3D and Bionetsolver: Applications to Multiscale Modelling of Cancer Cell Growth and Invasion, PLoS ONE, vol.22, issue.3, p.33726, 2012.
DOI : 10.1371/journal.pone.0033726.s001

S. Hoops, R. Gauges, C. Lee, J. Pahle, N. Simus et al., COPASI--a COmplex PAthway SImulator, Bioinformatics, vol.22, issue.24, pp.3067-3074, 2006.
DOI : 10.1093/bioinformatics/btl485

G. Marsaglia, Choosing a Point from the Surface of a Sphere, The Annals of Mathematical Statistics, vol.43, issue.2, pp.645-646, 1972.
DOI : 10.1214/aoms/1177692644

T. Iskratsch, H. Wolfenson, and M. P. Sheetz, Appreciating force and shape ??? the rise of mechanotransduction in cell biology, Nature Reviews Molecular Cell Biology, vol.323, issue.12, pp.825-833, 2014.
DOI : 10.1038/nrm3903

M. Kardar, G. Parisi, and Y. C. Zhang, Dynamic Scaling of Growing Interfaces, Physical Review Letters, vol.56, issue.9, pp.889-892, 1986.
DOI : 10.1103/PhysRevLett.56.889

P. Marmottant, A. Mgharbel, J. Käfer, B. Audren, J. Rieu et al., The role of fluctuations and stress on the effective viscosity of cell aggregates, Proceedings of the National Academy of Sciences, vol.106, issue.41, pp.17271-17276, 2009.
DOI : 10.1073/pnas.0902085106

URL : https://hal.archives-ouvertes.fr/inserm-00524596

A. R. Kansal, S. Torquato, I. V. Harsh, G. , E. A. Chiocca et al., Simulated Brain Tumor Growth Dynamics Using a Three-Dimensional Cellular Automaton, Journal of Theoretical Biology, vol.203, issue.4, pp.367-382, 2000.
DOI : 10.1006/jtbi.2000.2000

G. Sciumè, S. Shelton, W. Gray, C. Miller, F. Hussain et al., A multiphase model for three-dimensional tumor growth, New Journal of Physics, vol.15, issue.1, p.15005, 2013.
DOI : 10.1088/1367-2630/15/1/015005

A. K. Subramaniyan and C. Sun, Continuum interpretation of virial stress in molecular simulations, International Journal of Solids and Structures, vol.45, issue.14-15, pp.4340-4346, 2008.
DOI : 10.1016/j.ijsolstr.2008.03.016

D. G. Harvey, A. G. Fletcher, J. M. Osborne, and J. Pitt-francis, A parallel implementation of an off-lattice individual-based model of multicellular populations, Computer Physics Communications, vol.192, pp.130-137, 2015.
DOI : 10.1016/j.cpc.2015.03.005

T. Bittig, O. Wartlick, A. Kicheva, M. González-gaitárr, and F. Jülicher, Dynamics of anisotropic tissue growth, New Journal of Physics, vol.10, issue.6, 2008.
DOI : 10.1088/1367-2630/10/6/063001

M. A. Huergo, M. A. Pasquale, P. H. González, A. E. Bolzán, and A. J. Arvia, Growth dynamics of cancer cell colonies and their comparison with noncancerous cells, Physical Review E, vol.85, issue.1, 2012.
DOI : 10.1103/PhysRevE.85.011918

H. Hatzikirou, L. Brusch, and A. Deutsch, Form Cellular Automaton rules to a macroscopic mean-field description, Acta Physica Polonica Series B, 2014.

M. Scianna and L. Preziosi, A cellular Potts model for the MMP-dependent and -independent cancer cell migration in matrix microtracks of different dimensions, Computational Mechanics, vol.103, issue.2007, 2013.
DOI : 10.1007/s00466-013-0944-6

D. G. Mallet and L. G. De-pillis, A cellular automata model of tumor???immune system interactions, Journal of Theoretical Biology, vol.239, issue.3, pp.334-350, 2006.
DOI : 10.1016/j.jtbi.2005.08.002

Y. Jamali, M. Azimi, and M. R. Mofrad, A Sub-Cellular Viscoelastic Model for Cell Population Mechanics, PLoS ONE, vol.1, issue.8, p.12097, 2010.
DOI : 10.1371/journal.pone.0012097.t002

N. J. Savill and P. Hogeweg, Modelling Morphogenesis: From Single Cells to Crawling Slugs, Journal of Theoretical Biology, vol.184, issue.3, pp.229-235, 1997.
DOI : 10.1006/jtbi.1996.0237

M. Yao, B. T. Goult, H. Chen, P. Cong, M. P. Sheetz et al., Mechanical activation of vinculin binding to talin locks talin in an unfolded conformation, Scientific reports, p.4610, 2014.
DOI : 10.1038/srep04610

A. Brú, J. Pastor, I. Fernaud, I. Brú, S. Melle et al., Super-Rough Dynamics on Tumor Growth, Physical Review Letters, vol.81, issue.18, pp.4008-4011, 1998.
DOI : 10.1103/PhysRevLett.81.4008

T. Eissing, L. Kuepfer, C. Becker, M. Block, K. Coboeken et al., A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks, Frontiers in Physiology, vol.2, p.4, 2011.
DOI : 10.3389/fphys.2011.00004