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CompuCell3D - Based Simulations

[[links/index.php?id=35|Mathematical modeling of the capillary-like pattern generated by adrenomedullin-treated human vascular endothelial cells in vitro]] Diego Guidolin , Giovanna Albertin , Elisa Sorato , Barbara Oselladore , Alessandra Mascarin , Domenico Ribatti

[[links/index.php?id=29|Simulation of Single-Species Bacterial-Biofilm Growth Using the Glazier-Graner-Hogeweg Model and the CompuCell3D Modeling Environment]] Nikodem J. Popawski, Abbas Shirinifard, Maciej Swat, and James A. Glazier, ''Mathematical biosciences and engineering 5, 355-388 (2008)''

[[links/index.php?id=30|Discovering Novel Cancer Therapies: A Computational Modeling and Search Approach]] Mahoney A. W., Smith B. G., Flann N. S., and Podgorski G. J., ''IEEE conference on Computational Intelligence in Bioinformatics and Bioengineering, (2008)''

[[links/index.php?id=28|Adhesion Between Cells, Diffusion of Growth Factors, and Elasticity of the AER Produce the Paddle Shape of the Chick Limb]] Nikodem J. Popławski, Maciej Swat, J. Scott Gens and James A. Glazier,

''Physica A: Statistical and Theoretical Physics 373, 521-532 (2007)''

[[links/index.php?id=26|Dynamical Mechanisms For Skeletal Pattern Formation in the Vertebrate Limb]] H G E Hentschel, T Glimm, J A Glazier, S A Newman, ''Proc Biol Sci. 271, 1713–1722 (2004)''

[[links/index.php?id=27|A Hybrid Discrete-Continuum Model for 3D Skeletogenesis of the Vertebrate Limb]] R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier ''Lecture Notes in Computer Science 3305, 543-552 (2004)''

== CompuCell3D Framework ==
[[links/index.php?id=18|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]]

Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jes A. Izaguirre

Computing in Science and Engineering, 9, 50-60 (2007)

[[links/index.php?id=20|A Framework For Three-Dimensional Simulation of Morphogenesis]] Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesus A. Izaguirre, ''IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2, 273-288 (2005)''

[[links/index.php?id=22|On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis]] R. Chaturvedi, C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, T. Glimm, H. G. E. Hentschel, S. A. Newman, J. A. Glazier, M. Alber, ''Journal of The Royal Society Interface 2, 237-253 (2005)''

[[links/index.php?id=23|A Cell-Centered Approach to Developmental Biology]] Roeland M.H. Merks, and James A. Glazier, ''Physica A: Statistical Mechanics and its Applications 352, 113-130 (2005)''

[[links/index.php?id=25|Empirical Evaluation of Design Patterns in Scientific Application]] Kedar Aras, ''Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2005)''

[[links/index.php?id=21|CompuCell, a Multi-Model Framework For Simulation of Morphogenesis]] J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier, ''Bioinformatics 20, 1129-1137 (2004)''

[[links/index.php?id=24|BIOLOGO: A Domain-Specific Language For Morphogenesis]] Trevor M. Cickovski, ''Master’s Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2004)''

== Related Links ==
[[links/index.php?cat=talks|Recent Talks]][[links/index.php?cat=biological|Biological Modeling]]

 * Differential Adhesion and Cell Sorting
 * '''Limb Development '''
 * '''Tumor and Cancer '''
 * '''Angiogenesis/Vasculogenesis '''
 * '''Biofilms '''

[[links/index.php?cat=physical|Physical Modeling]]

 * Soap Foams and Liquid Foams

[[links/index.php?cat=simulations|Simulations Using GGH/CPM Approach]][[links/index.php?cat=background|General Background on Biophysical Modeling and Development]]		 This page contains selected publications which were done using CompuCell3D. While we try to keep this page updated some of the publications might be missing from it. If you want your CompuCell3D-based publication to be displayed here, please e-mail us ( jsluka@iu.edu )

'''''For list of Ph.D. and Master theses completed using CC3D please click [[Theses|here]].'''''

=== How to cite CompuCell3D ===
[[http://www.sciencedirect.com/science/article/pii/B9780123884039000138|Multi-Scale Modeling of Tissues Using CompuCell3D]] – [[http://www.indiana.edu/~bioc/people/?p=staff|M. Swat]], [[http://www.if.ufrgs.br/pos/portugues/thomas.html|Gilberto L. Thomas]], Julio M. Belmonte, A. Shirinifard, D. Hmeljak, [[http://www.indiana.edu/~bioc/jglazier/|J. A. Glazier]], ''__Computational Methods in Cell Biology__, Methods in Cell Biology '''''110''': 325-366 (2012)

=== Publications ===

==== 2021 ====

 *[[https://elifesciences.org/articles/61011|Cell-scale biophysical determinants of cell competition in epithelia]] - Daniel Gradeci, Anna Bove, Giulia Vallardi, Alan R Lowe, Shiladitya Banerjee, and Guillaume Charras. eLife. 2021; 10: e61011. Published online 2021 May 20. doi: 10.7554/eLife.61011

 *[[https://journals-biologists-com.proxyiub.uits.iu.edu/jcs/article/134/7/jcs250225/238125/Combined-heterogeneity-in-cell-size-and|Combined heterogeneity in cell size and deformability promotes cancer invasiveness]] - Asadullah, Kumar S, Saxena N, Sarkar M, Barai A, Sen S. J Cell Sci. 2021 Apr 1;134(7):jcs250225. doi: 10.1242/jcs.250225. PMID: 33602741.

 *[[https://www.biorxiv.org/content/10.1101/2021.04.29.441921v2.full|Cluster Size Distribution of Cells Disseminating from a Primary Tumor]] - Mrinmoy Mukherjee, Herbert Levine. BioRxiv. doi: https://doi.org/10.1101/2021.04.29.441921


 *[[https://www.biorxiv.org/content/10.1101/2021.02.09.430466v1.full|Supracellular organization confers directionality and mechanical potency to migrating pairs of cardiopharyngeal progenitor cells]] - Yelena Y. Bernadskaya, Haicen Yue, Calina Copos, Lionel Christiaen, Alex Mogilner. !BioRxiv. doi: https://doi.org/10.1101/2021.02.09.430466

 *[[https://www-sciencedirect-com.proxyiub.uits.iu.edu/science/article/pii/S0022519320303428|A Cellular Potts energy-based approach to analyse the influence of the surface topography on single cell motility]] - Thenard T, Catapano A, Mesnard M, Allena R. J Theor Biol. 2021 Jan 21;509:110487. doi: 10.1016/j.jtbi.2020.110487. Epub 2020 Sep 16. PMID: 32949589.

 *[[https://www.biorxiv.org/content/10.1101/2020.01.14.905711v1|Computational Modelling of Nephron Progenitor Cell Movement and Aggregation during Kidney Organogenesis]] - Pauli Tikka, Moritz Mercker, Ilya Skovorodkin, Ulla Saarela, Seppo Vainio, Veli-Pekka Ronkainen, James P. Sluka, James A. Glazier, Anna Marciniak-Czochra, Franz Schaefer. BioRxiv. doi: https://doi.org/10.1101/2020.01.14.905711

 *[[https://doi.org/10.1590/1806-9126-RBEF-2020-0400|Fenômenos estocásticos em migração celular: teoria, experimentos e simulações (Stochastic phenomena in single cell migration: theory, experiments, and simulations)]] - Rita M.C. de Almeida. Seção Especial • Rev. Bras. Ensino Fís. 43 (Suppl 1). 2021.

 *[[https://pubs.acs.org/doi/abs/10.1021/acscentsci.0c00601|Heterogeneity in 2,6-Linked Sialic Acids Potentiates Invasion of Breast Cancer Epithelia]] - Pally D, Pramanik D, Hussain S, Verma S, Srinivas A, Kumar RV, Everest-Dass A, Bhat R. ACS Cent Sci. 2021 Jan 27;7(1):110-125. doi: 10.1021/acscentsci.0c00601. Epub 2021 Jan 4. PMID: 33532574; PMCID: PMC7844859.

 *[[https://www.biorxiv.org/content/10.1101/2021.01.27.428527v1.full|The environment topography alters the transition from single-cell populations to multicellular structures in Myxococcus xanthus]] - Karla C. Hernández Ramos, Edna Rodríguez-Sánchez, Juan Antonio Arias del Angel, Alejandro V. Arzola, Mariana Benítez, Ana E. Escalante, Alessio Franci, Giovanni Volpe, Natsuko Rivera-Yoshida. !BioRxiv. doi: https://doi.org/10.1101/2021.01.27.428527

 * A useful review of methods, including CC3D: [[https://link.springer.com/article/10.1007/s11831-021-09554-1|Computational Models and Simulations of Cancer Metastasis]] - Anvari, S., Nambiar, S., Pang, J. et al. Arch Computat Methods Eng (2021). https://doi-org.proxyiub.uits.iu.edu/10.1007/s11831-021-09554-1.

 *[[https://link.springer.com/article/10.1007/s00262-020-02790-7|Run for your life: an integrated virtual tissue platform for incorporating exercise oncology into immunotherapy]] - Serrano JA, Hagar A. Cancer Immunol Immunother. 2021 Jul;70(7):1951-1964. doi: 10.1007/s00262-020-02790-7. Epub 2021 Jan 8. PMID: 33416943.

 *[[https://link.springer.com/chapter/10.1007/978-3-030-58688-1_2|Position of the Kenzan Method in the Space-Time of Tissue Engineering]] - Moldovan N.I. (2021) In: Nakayama K. (eds) Kenzan Method for Scaffold-Free Biofabrication. Springer, Cham. https://doi-org.proxyiub.uits.iu.edu/10.1007/978-3-030-58688-1_2

 *[[https://www-sciencedirect-com.proxyiub.uits.iu.edu/science/article/pii/S0022519321001557|Matrix adhesion and remodeling diversifies modes of cancer invasion across spatial scales]] - Pramanik D, Jolly MK, Bhat R. J Theor Biol. 2021 Sep 7;524:110733. doi: 10.1016/j.jtbi.2021.110733. Epub 2021 Apr 30. PMID: 33933478.

 *[[https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9451315|Physical Forces Influence the Self-organization of the Leader Cell Formation During Collective Cell Migration]] - M. Pan, Y. Yang and L. Liu. 2021 IEEE 16th International Conference on Nano/Micro Engineered and Molecular Systems (NEMS), 2021, pp. 1923-1926, doi: 10.1109/NEMS51815.2021.9451315.

 *[[https://www-sciencedirect-com.proxyiub.uits.iu.edu/science/article/pii/S2452310021000251\|Multiscale modeling in disease]] - Ashlee N. !FordVersyp. Current Opinion in Systems Biology. In press. Available online 8 May 2021. https://doi.org/10.1016/j.coisb.2021.05.001.

 *[[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009081|Multiscale modeling of tumor growth and angiogenesis: Evaluation of tumor-targeted therapy]] - Jafari Nivlouei S, Soltani M, Carvalho J, Travasso R, Salimpour MR, Shirani E. PLoS Comput Biol. 2021 Jun 23;17(6):e1009081. doi: 10.1371/journal.pcbi.1009081. PMID: 34161319.

 *[[https://doi.org/10.1016/j.isci.2021.102317|A Mechanical Model of Early Somite Segmentation]] - Adhyapok, P., Piatkowska, A.M, Norman, M.J, Clendenon, S.G, Stern, C.D, Glazier, J.A, Belmonte, J.M, ISCIENCE (2021), in press. doi: [[https://doi.org/10.1016/j.isci.2021.102317|https://doi.org/10.1016/j.isci.2021.102317]].

 * [[https://www.biorxiv.org/content/10.1101/2021.01.28.428647v1|Generating Agent-Based Multiscale Multicellular Spatiotemporal Models from Ordinary Differential Equations of Biological Systems, with Applications in Viral Infection]] - T.J. Sego, Josua Aponte-Serrano, Juliano Ferrari Gianlupi and James A. Glaizer, DOI: 10.1101/2021.01.28.428647. Jan 29, 2021. ''Preprint in bioRxiv''.


 * [[https://pubmed.ncbi.nlm.nih.gov/33498017/|Biofabrication of spheroids fusion-based tumor models: computational simulation of glucose effects]]. Bustamante DJ, Basile EJ, Hildreth BM, Browning NW, Jensen SA, Moldovan L, Petrache HI, Moldovan NI. Biofabrication. 2021 Jan 26. doi: 10.1088/1758-5090/abe025. Online ahead of print. PMID: 33498017

 * [[https://pubmed.ncbi.nlm.nih.gov/33339019/|Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D]]. Liu R, Higley KA, Swat MH, Chaplain MAJ, Powathil GG, Glazier JA. Phys Med Biol. 2021 Feb 11;66(4):045026. doi: 10.1088/1361-6560/abd4f9. PMID: 33339019


==== 2020 ====

 * [[https://pubmed.ncbi.nlm.nih.gov/32407685/|CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates]]. Fortuna I, Perrone GC, Krug MS, Susin E, Belmonte JM, Thomas GL, Glazier JA, de Almeida RMC. Biophys J. 2020 Jun 2;118(11):2801-2815. doi: 10.1016/j.bpj.2020.04.024. Epub 2020 Apr 30. PMID: 32407685

 * [[https://www.nature.com/articles/s41598-020-63506-6|Multiscale modelling of motility wave propagation in cell migration]] - Hamid Khataee, Andras Czirok, and Zoltan Neufeld, ''__Scientific Reports.__'' DOI: 10.1038/s41598-020-63506-6, (2020).

 * [[https://elifesciences.org/articles/61026|Dynamics of nevus development implicate cell cooperation in the growth arrest of transformed melanocytes]] - Ruiz-Vega, Rolando, et al., ''__Elife.__'' DOI: 10.7554/eLife.61026, (2020).

 * [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008451|A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness]] - T.J. Sego, Josua Aponte-Serrano, Juliano Ferrari Gianlupi, Sam Heaps, Kira Breithaupt, Lutz Brusch, et al., ''__PLoS Computational Biology.__'' DOI: 10.1371/journal.pcbi.1008451, (2020).

 * [[https://royalsocietypublishing.org/doi/full/10.1098/rsif.2019.0739|Mechanisms of endothelial cell coverage by pericytes: computational modelling of cell wrapping and in vitro experiments]] – Kei Sugihara, et al., ''__Journal of the Royal Society Interface.__'' DOI: 10.1098/rsif.2019.0739, (2020).


==== 2019 ====

 * [[https://aiche.onlinelibrary.wiley.com/doi/abs/10.1002/aic.16671|A hybrid discrete–continuous model of metastatic cancer cell migration through a remodeling extracellular matrix]] - Edalgo Nguyen, Yen T., Anya L. Zornes, and Ashlee N. Ford Versypt, ''__AIChE Journal.__'' DOI: 10.1002/aic.16671, (2019).

 * [[https://journals.plos.org/ploscompbiol/article?rev=2&id=10.1371/journal.pcbi.1007053|Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model]] - Mahua Roy and Stacey D. Finley, ''__PLoS Computational Biology.__'' DOI: 10.1371/journal.pcbi.1007053S, (2019).

 * [[https://www.frontiersin.org/articles/10.3389/fimmu.2019.00230/full|Model-based assessment of the Role of Uneven Partitioning of Molecular Content on Heterogeneity and Regulation of Differentiation in CD8 T-cell Immune Responses]] – Simon Girel, et al, ''__Frontiers in immunology.__'' DOI: 10.3389/fimmu.2019.00230, (2019).

 * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700745/|An Interplay Between Reaction-Diffusion and Cell-Matrix Adhesion Regulates Multiscale Invasion in Early Breast Carcinomatosis]] - Pally D, Pramanik D, Bhat R., ''__Front Physiol.__'' 2019 Aug 13;10:790. doi: 10.3389/fphys.2019.00790. eCollection 2019.

 * [[https://www.sciencedirect.com/science/article/pii/S0022519319303248?via=ihub|A multiscale in silico model of endothelial to mesenchymal transformation in a tumor microenvironment]]- Chowkwale M, Mahler GJ, Huang P, Murray BT., ''__J Theor Biol.__'' 2019 Nov 7;480:229-240. doi: 10.1016/j.jtbi.2019.08.012. Epub 2019 Aug 17.

 * [[https://link.springer.com/protocol/10.1007/978-1-4939-9224-9_1|Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche]]" - Mines R, Chen KY, Shen X., ''__Methods Mol Biol.__'' 2019;1975:3-35. doi: 10.1007/978-1-4939-9224-9_1. PMID: 31062303

 * [[https://link.springer.com/protocol/10.1007/978-1-4939-9021-4_19|Methods of Computational Analysis in Kidney Development]] - Tikka P, Schaefer F., ''__Methods Mol Biol.__'' 2019;1926:235-246. doi: 10.1007/978-1-4939-9021-4_19.

 * [[https://pubmed.ncbi.nlm.nih.gov/31456688/|An Interplay Between Reaction-Diffusion and Cell-Matrix Adhesion Regulates Multiscale Invasion in Early Breast Carcinomatosis]]. Pally D, Pramanik D, Bhat R. Front Physiol. 2019 Aug 13;10:790. doi: 10.3389/fphys.2019.00790. eCollection 2019. PMID: 31456688.

 * [[https://pubmed.ncbi.nlm.nih.gov/31430445/|A multiscale in silico model of endothelial to mesenchymal transformation in a tumor microenvironment]]. Chowkwale M, Mahler GJ, Huang P, Murray BT. J Theor Biol. 2019 Nov 7;480:229-240. doi: 10.1016/j.jtbi.2019.08.012. Epub 2019 Aug 17. PMID: 31430445

 * [[https://pubmed.ncbi.nlm.nih.gov/30742276/|Methods of Computational Analysis in Kidney Development]]. Tikka P, Schaefer F. Methods Mol Biol. 2019;1926:235-246. doi: 10.1007/978-1-4939-9021-4_19. PMID: 30742276
 

==== 2018 ====

 * [[https://www.embopress.org/doi/full/10.15252/msb.20178174|Fibroblast state switching orchestrates dermal maturation and wound healing|target=_blank]] - Emanuel Rognoni, Angela Oliveira Pisco, Toru Hiratsuka, Kalle H Sipilä, Julio M Belmonte, Seyedeh Atefeh Mobasseri, Christina Philippeos, Rui Dilão, Fiona M Watt, ''__Mol Syst Biol__'' (2018)14:e8174, https://doi.org/10.15252/msb.20178174.

 * [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006455|Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells]] - Ernest C. Y. Ho, Juan Nicolas, Abha Ahuja, Rama Singh ,Ellen Larsen, ''__PLoS Comp. Bio.__'', https://doi.org/10.1371/journal.pcbi.1006455, (2018).

 * [[https://pubs.rsc.org/en/content/articlelanding/2018/ib/c8ib00048d/|Computational model of wound healing: EGF secreted by fibroblasts promotes delayed re-epithelialization of epithelial keratinocytes]] - Vivi Andasari, Dongyuan Lü, Maciej Swat, Shiliang Feng, Fabian Spill, Li Chen, Xiangdong Luo, Muhammad Zaman, Mian Long, ''__Integrative Biology__'', DOI: 10.1039/C8IB00048D, (2018).

 * [[https://www.molbiolcell.org/doi/10.1091/mbc.E17-05-0313|Multicompartment cell-based modeling of confined migration: regulation by cell intrinsic and extrinsic factors]] - Sandeep Kumar, Alakesh Das and Shamik Sen, ''__Molecular Biology of the Cell__'', DOI:10.1091/mbc.E17-05-0313, (2018).

==== 2017 ====
 * [[http://pubs.acs.org/doi/abs/10.1021/acs.chemrestox.6b00350|Computational Model of Secondary Palate Fusion and Disruption]] - M. Shane Hutson, Maxwell C.K. Leung, Nancy Baker, Richard M. Spencer, and Thomas B. Knudsen, ''__Chemical Research in Toxicology__'', DOI: 10.1021/acs.chemrestox.6b00350, (2017).

 * [[http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.702072|Mathematical modelling of the immune response to cancer]] - Tough, Iona Kirsten. PhD Thesis, University of Dundee, (2017).

 * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536454/pdf/pcbi.1005635.pdf|Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach]] - A. Szabó and R. M. H. Merks, __''PLOS Comput Biol''__, vol. 13, no. 7, p. e1005635, Jul. 2017.

 * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283809/pdf/kccy-16-02-1241603.pdf|Shaping the cell fate]] - T. N. Sato and R. M. H. Merks, __''Cell Cycle''__, vol. 16, no. 2, pp. 149–150, Jan. 2017.

 * [[https://academic-oup-com.proxyiub.uits.iu.edu/biolreprod/article/97/3/365/4082285|Cell-based computational model of early ovarian development in mice]] - Wear HM, Eriksson A, Yao HH, Watanabe KH. Biol Reprod. 2017 Sep 1;97(3):365-377. doi: 10.1093/biolre/iox089. PMID: 29088396; PMCID: PMC6231088.

==== 2016 ====
 * [[http://aip.scitation.org/doi/pdf/10.1063/1.4952106|Multi-scale modeling of the CD8 immune response.]] - Barbarroux, L., Michel, P., Adimy, M., Crauste, F. AIP Conference Proceedings 1738, 320002 (2016); doi: http://dx.doi.org/10.1063/1.4952106.

 * [[http://www.molbiolcell.org/content/27/22/3673.full|Virtual-Tissue Computer Simulations Define the Roles of Cell Adhesion and Proliferation in the Onset of Kidney Cystic Disease]] – Julio M. Belmonte, Sherry G. Clendenon, Guilherme M. Oliveira, Maciej H. Swat, Evan V. Greene, Srividhya Jeyaraman, James A. Glazier, and Robert L. Bacallao, ''__Molecular Biology of the Cell__'' '''27''': 3673-3685 (2016).

 * [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161915|Spheroid Formation of Hepatocarcinoma Cells in Microwells: Experiments and Monte Carlo Simulations]] – Yan Wang, Myung Hee Kim, Seyed R. Tabaei, Jae Hyeok Park, Kyuhwan Na, Seok Chung, Vladimir P. Zhdanov, Nam-Joon Cho, ''__PLoS ONE__'' '''11'''(8): e0161915 (2016).

 * [[https://www.hindawi.com/journals/jdr/2016/2508381/|A Computational Model of Peripheral Photocoagulation for the Prevention of Progressive Diabetic Capillary Occlusion]] – Thomas J. Gast, Xiao Fu, John Scott Gens, James A. Glazier, ''__Journal of Diabetes Research__'' vol. 2016, Article ID 2508381, 13 pages (2016) doi:10.1155/2016/2508381.

 * [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162428|A Liver-Centric Multiscale Modeling Framework for Xenobiotics]] – James P. Sluka , Xiao Fu, Maciej Swat, Julio M. Belmonte, Alin Cosmanescu, Sherry G. Clendenon, John F. Wambaugh, James A. Glazier, ''__PLoS ONE__'' '''11''': e0162428 (2016).

 * [[https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-016-0323-y|IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8+ T cell-APC: a multiscale modeling study]] – Xuefeng Gao, Christophe Arpin, Jacqueline Marvel, Sotiris A. Prokopiou, Olivier Gandrillon, Fabien Crauste, ''__BMC Systems Biology__'' '''10''':77 (2016).

 * [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004952|Filopodial-Tension Model of Convergent-Extension of Tissues]] – Julio M. Belmonte, Maciej H. Swat, James A. Glazier, ''__PLoS Comput Biol__'' '''12''': e1004952 (2016).

 * [[http://www.nature.com/articles/ncomms11963|Memory of cell shape biases stochastic fate decision-making despite mitotic rounding]] – Takashi Akanuma, Cong Chen, Tetsuo Sato, Roeland M. H. Merks, Thomas N. Sato, ''__Nature Commun__'' '''7''': 11963 (2016).

 * [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004932|Progression of Diabetic Capillary Occlusion: A Model]] – Xiao Fu, John Scott Gens, James A. Glazier, Stephen A. Burns, Thomas J. Gast, ''__PLoS Comput Biol__'' '''12''': e1004932 (2016).

 * [[http://www.sciencedirect.com/science/article/pii/S1534580716302039|The Molecular Basis of Radial Intercalation during Tissue Spreading in Early Development]] – András Szabó, Isidoro Cobo, Sharif Omara, Sophie McLachlan, Ray Keller, Roberto Mayor, ''__Developmental Cell__'' '''37''': 213–225 (2016).

 * [[http://www.sciencedirect.com/science/article/pii/S0022519316300315|Bystander effects and their implications for clinical radiation therapy: Insights from multiscale in silico experiments]] – Gibin George Powathil, Alastair J Munro, Mark Chaplain, Maciej H. Swat, ''__Journal of Theoretical Biology__'' '''401''': 1-14 (2016).

 * [[http://cancerres.aacrjournals.org/content/76/6/1320.short|Spatial Modeling of Drug Delivery Routes for Treatment of Disseminated Ovarian Cancer]] – Kimberly R. Kanigel Winner, Mara P. Steinkamp, Rebecca J. Lee, Maciej Swat, Carolyn Y. Muller, Melanie E. Moses, Yi Jiang, Bridget S. Wilson, ''__Cancer Research__'' '''76'''(6): 1320–34 (2016).

 * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735823/|Proteolytic and non-proteolytic regulation of collective cell invasion: tuning by ECM density and organization]] – Sandeep Kumar, Aastha Kapoor, Sejal Desai, Mandar M. Inamdar, Shamik Sen, ''__Scientific Reports__'' '''6''': 19905 (2016).

 * [[http://digitalcommons.ohsu.edu/etd/3832/|Modeling the Mammalian Ovary : A Cell-based Computational Model of Early Ovarian Development in Mice and Preliminary Data for A Model of Folliculogenesis in Rhesus Monkeys]] - Wear, H.M., Masters Thesis, 2016. Oregon Health and Science University.

 * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5102492/pdf/pone.0159478.pdf|Computational Screening of Tip and Stalk Cell Behavior Proposes a Role for Apelin Signaling in Sprout Progression]] - M. M. Palm, M. G. Dallinga, E. van Dijk, I. Klaassen, R. O. Schlingemann, and R. M. H. Merks, __''PLOS ONE''__, vol. 11, no. 11, p. e0159478, Nov. 2016.

==== 2015 ====
 * [[https://link.springer.com/chapter/10.1007/978-3-319-13117-7_52|Experiences in the Use of the Compucell3d in the Career of Biomedical Engineering]] - Rosa, L., Pareja, D., Perez, F., Domech, D. & Mendez, A. in IFMBE Proceedings 49, 199–200 (2015).

 * [[http://www.nature.com/articles/ncomms7635?WT.ec_id=NCOMMS-20150415|Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation]] – A. Nakamoto, S. D. Hester, S. J. Constantinou, W. G. Blaine, A. B. Tewksbury, M. T. Matei, L. M. Nagy, T. A. Williams, ''__Nat Commun__'' '''6''': 6635 (2015).

 * [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129266|Fabrication of Biomimetic Bone Tissue Using Mesenchymal Stem Cell-Derived Three-Dimensional Constructs Incorporating Endothelial Cells]] – Jun-Ichi Sasaki, Masanori Hashimoto, Satoshi Yamaguchi, Yoshihiro Itoh, Itsumi Yoshimoto, Takuya Matsumoto, Satoshi Imazato, ''__PLoS ONE__'' '''10'''(6): e0129266 (2015).

 * [[http://pubs.rsc.org/is/content/articlelanding/2015/mb/c5mb00304k#!divAbstract|Multi-scale modeling of cell survival and death mediated by p53 network: A Systems Pharmacology Framework]] – Yuan Wang, Zihu Guo, Xuetong Chen, Wenjuan Zhang, Aiping Lu, Yonghua Wang, ''__Molecular BioSystems__'' '''11'''(6): 3011-3021 (2015).

 * [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004314|A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis]] – Alexander D. Malkin, Robert P. Sheehan, Shibin Mathew, William J. Federspiel, Heinz Redl, Gilles Clermont, ''__PLoS Comput Biol__'' '''11'''(10): e1004314 (2015).

 * [[http://journal.frontiersin.org/article/10.3389/fmicb.2015.00603/abstract|Development of cell differentiation in the transition to multicellularity: a dynamical modeling approach]] – Emilio Mora Van Cauwelaert, Juan A. Arias Del Angel, Mariana Benítez, Eugenio M. Azpeitia, ''__Front Microbiol__'' '''6''': 603 (2015).

 * [[https://www.researchgate.net/profile/Gilberto_Thomas/publication/272194313_3D_simulations_of_wet_foam_coarsening_evidence_a_self_similar_growth_regime/links/54f048680cf2432ba659a6af.pdf?origin=publication_detail|3D Simulations of Wet Foam Coarsening Evidence a Self Similar Growth Regime]] – Gilberto L. Thomas, Julio M. Belmonte, Francois Graner, James A. Glazier, Rita M.C. de Almeida, ''__Colloids and Surface A: Physicochemical and Engineering Aspects__'' '''473''':109-114 (2015).

 * [[http://www.jleukbio.org/content/98/1/119.full|Limited specificity of IRF3 and ISGF3 in the transcriptional innate-immune response to double-stranded RNA]] – Diana R. Ourthiague, Harry Birnbaum, Niklas Ortenlöf, Jesse D. Vargas, Roy Wollman, Alexander Hoffmann, ''__Journal of Leukocyte Biology__'' '''98''': 119-128 (2015).

 * [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127972|Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell Model of Tumor Evolution Using CompuCell3D]] – Maciej Swat, Gilberto Thomas, Abbas Shirinifard, Sherry Clendenon, James Glazier, ''__PLoS ONE__'' '''10'''(6): e0127972 (2015).

 * [[http://link.springer.com/protocol/10.1007/978-1-4939-1164-6_20|Large-scale parameter studies of cell-based models of tissue morphogenesis using CompuCell3D or VirtualLeaf]] – Margriet Palm, Roeland Merks, In: Nelson, C.M. (ed.), Tissue Morphogenesis. Methods in Molecular Biology , Springer-Verlag Berlin Heidelberg, ''__Methods Mol Biol__'' '''1189''': 301-22 (2015).

 * [[http://link.springer.com/chapter/10.1007/978-3-319-16480-9_37|Modeling of the Urothelium with an Agent Based Approach]] – Angelo Torelli, Fabian Siegel, Philipp Erben, Markus Gumbel, ''__Bioinformatics and Biomedical Engineering__'' '''9044''': 375-385 (2015).

 * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654812/pdf/12918_2015_Article_230.pdf|Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis]] - S. E. M. Boas and R. M. H. Merks, __''BMC Syst Biol''__, pp. 1–17, Nov. 2015.

==== 2014 ====
 * [[http://www.sciencedirect.com/science/article/pii/S1875389214002715|Physics of Cell Adhesion Failure and Human Diseases]] - Family, F. __''Phys. Procedia''__ 57, 24–28 (2014).

 * [[https://link.springer.com/chapter/10.1007/978-3-319-13117-7_52|Experiences in the Use of the Compucell3d in the Career of Biomedical Engineerin]] - La Rosa, L., Pareja, D., Pére F., Domech, G., Méndez, A. VI Latin American Congress on Biomedical Engineering CLAIB 2014, Paraná, Argentina 29, 30 & 31 October 2014 pp 199-202.

 * [[http://bioinformatics.oxfordjournals.org/content/30/16/2367.long|The Cell Behavior Ontology: Describing the intrinsic biological behaviors of real and model cells seen as active agents]] – James P. Sluka, Abbas Shirinifard, Maciej Swat, Alin Cosmanescu, Randy Heiland and James A. Glazier, ''__Bioinformatics__'' '''30'''(16): 2367-74 (2014).

 * [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003997|Lattice-Based Model of Ductal Carcinoma In Situ Suggests Rules for Breast Cancer Progression to an Invasive State]] – Eline Boghaert, Derek C. Radisky, Celeste M. Nelson, ''__PLoS Comput Biol__'' '''10'''(12): e1003997 (2014) DOI: 10.1371/journal.pcbi.1003997.

 * [[http://link.springer.com/chapter/10.1007/978-3-319-02657-2_5|Using Mathematical Modelling as a Virtual Microscope to Support Biomedical Research]] – Chiara Giverso and Luigi Preziosi, ''__Mathematical Models and Methods for Planet Earth__'' Springer INdAM Series Volume 6, 2014, pp 59-71.

 * [[http://onlinelibrary.wiley.com/doi/10.1002/wsbm.1285/epdf|Integrating multi-scale knowledge on cardiac development into a computational model of ventricular trabeculation]] – Bouke A. de Boer, Jean-François Le Garrec,Vincent M. Christoffels, Sigolène M. Meilhac and Jan M. Ruijter, ''__Wiley Interdisciplinary Reviews: Systems Biology and Medicine __''Volume 6, Issue 6, pages 389–397, November/December 2014.

 * [[http://www.mdpi.com/2079-3197/2/4/159|Multiscale modeling of the early CD8 T cell immune response in lymph nodes: an integrative study]] – SA Prokopiou, L Barbarroux, S Bernard, JMafille, Y Leverrier, C Arpin, J Marvel, O Gandrillon, F Crauste, ''__Computation__'' '''2'''(4): 159-181 (2014).

 * [[http://www.sciencemag.org/content/343/6172/791.abstract|Somites Without a Clock]] – Ana S. Dias, I. de Almeida, Julio M. Belmonte, J. A. Glazier, Claudio D. Stern, __''Science''__ '''343''': 791-795 (2014).

 * [[http://www.sciencedirect.com/science/article/pii/S0378437113010091|Dynamics of cell aggregates fusion: Experiments and simulations]] – Gilberto L. Thomas, Vladimir Mironov, Agnes Nagy-Mehez, José C. M. Mombach, ''__Physica A__ '''''395''': 247-254 (2014).

 * [[http://rsif.royalsocietypublishing.org/content/11/92/20131049.short|Synergy of cell–cell repulsion and vacuolation in a computational model of lumen formation]] – Sonja E. M. Boas, Roeland M. H. Merks, __''J. R. Soc. Interface''__ '''11'''(92): 20131049 (2014).

 * [[http://www.sciencedirect.com/science/article/pii/S0022519313005006|The effects of cell compressibility, motility and contact inhibition on the growth of tumor cell clusters using the Cellular Potts Model]] – Jonathan F. Li, John Lowengrub, ''__Journal of Theoretical Biology__'' '''343''': 79-91 (2014).

 * [[http://link.springer.com/chapter/10.1007/978-3-319-00846-2_303#page-2|Advances in Modelling of Epithelial to Mesenchymal Transition]] – R. Summers, T. Abdulla, J.-M. Schleich, __''XIII Mediterranean Conference on Medical and Biological Engineering and Computing''__ '''41''': 1225-1228 (2014).

 * [[https://www.nature.com/articles/srep05573|A design principle underlying the paradoxical roles of E3 ubiquitin ligases]] – Daewon Lee, Minjin Kim & Kwang-Hyun Cho, ''__Scientific Reports__'' '''4''': 5573 (2014).

==== 2013 ====
 * [[https://link.springer.com/chapter/10.1007/978-3-319-00846-2_303|Advances in Modelling of Epithelial to Mesenchymal Transition]] - Summers, R., Abdulla, T.,Schleich, J.-M. XIII Mediterranean Conference on Medical and Biological Engineering and Computing 2013 pp 1225-1228.

 * [[http://www.bookmetrix.com/detail/chapter/8cdaad13-6be2-4e91-961b-fe491954f083|Cellular Potts Model]] - Voß-Böhme, A., Starruß, J. & de Back, W. Encycl. Syst. Biol., Chapter 344, 386–390 (2013). doi:10.1007/978-1-4419-9863-7_298.

 * [[http://biomedicalcomputationreview.org/content/agent-based-virtual-tissue-simulations|Agent-Based Virtual Tissue Simulations]] – Maciej Swat, James A. Glazier, ''__Biomedical Computation Review__'', Fall 2013 p.28-29.

 * [[http://www.ncbi.nlm.nih.gov/pubmed/23311371|A Cellular Potts Models Simulating Cell Migration on and in Matrix Environments]] – Marco Scianna, Luigi Preziosi, Katarina Wolf, ''__Mathematical Biosciences and Engineering__'' 10(1), (2013).

 * [[http://calvino.polito.it/~preziosi/pubs/mmnp-giverso.pdf|Individual Cell-Based Model for In-Vitro Mesothelial Invasion of Ovarian Cancer]] – C. Giverso, M. Scianna, L. Preziosi, N. Lo Buono, A. Funaro, Mathematical Modelling of Natural Phenomena, DOI:http://dx.doi.org/10.1051/mmnp/20105109.

 * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836695/pdf/pcbi.1003319.pdf|Cell-Based Multi-Parametric Model of Cleft Progression during Submandibular Salivary Gland Branching Morphogenesis]] – Shayoni Ray, Daniel Yuan, Nimit Dhulekar, Basak Oztan, Bülent Yener, Melinda Larsen, ''__PLoS Comput Biol__'' '''9'''(11):e1003319 (2013).

 * [[http://dx.doi.org/10.1016/j.tcm.2012.10.002|Hyaluronan: A critical regulator of endothelial-to-mesenchymal transition during cardiac valve formation]] – Anne Karine Lagendijk, András Szabo, Roeland M.H. Merks and Jeroen Bakkers, ''__Trends in Cardiovascular Medicine__ '''''23'''(5): 135-142 (2013).

 * [[http://journal.frontiersin.org/article/10.3389/fonc.2013.00097/full|Ovarian Tumor Attachment, Invasion, and Vascularization Reflect Unique Microenvironments in the Peritoneum: Insights from Xenograft and Mathematical Models]] – Mara P. Steinkamp, Kimberly Kanigel Winner, Bridget S. Wilson, ''__Frontiers in Oncology__'' '''3''':97 (2013).

 * [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002996#pcbi-1002996-g008|A Computational Model Predicting Disruption of Blood Vessel Development]] – Nicole Kleinstreuer, David Dix, Michael Rountree, Nancy Baker, Nisha Sipes, David Reif, Richard Spencer, Thomas Knudsen, ''__PLoS Comput Biol__'' '''9'''(4): e1002996 (2013).

 * [[http://journals.aps.org/pre/abstract/10.1103/PhysRevE.87.012725|Vascular Networks Due to Dynamically Arrested Crystalline Ordering of Elongated Cells]] – Margriet M. Palm, Roeland M. H. Merks,. ''__Phyiscal Review E__'' '''87''': 012725 (2013).

 * [[http://cancerres.aacrjournals.org/content/73/5/1481.long|Acute and Fractionated Irradiation Differentially Modulate Glioma Stem Cell Division Kinetics]] – Xuefeng Gao, J. Tyson McDonald, Lynn Hlatky, Heiko Enderling, ''__Cancer Res__'' March 1, 73; 1481 (2013).

==== 2012 ====
 * [[http://dspace.lib.ntua.gr/bitstream/handle/123456789/6738/panagiotakopouloum_potts.pdf?sequence=3|The modeling of lymphangiogenesis in cancer using the Cellular Potts Model]] - Magdalini, P. 2012. (in Greek).

 * [[http://www.imeko.org/publications/wc-2012/IMEKO-WC-2012-TC13-O6.pdf|Progress On Multiscale Representation Of Cardiac Valve Morphogenesis]] - Summers, R., Abdulla, T. & Schleich, J.-M. XX IMEKO World Congr. 2–5 (2012).

 * [[Multiscale Developments of the Cellular Potts Model]] – Marco Scianna, Luigi Preziosi, ''__Multiscale Model. Simul.__'' '''10'''(2):342–382. (2012).

 * [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002440|Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study]] – A. Shirinifard, [[http://www.indiana.edu/~bioc/jglazier/|J. A. Glazier]], [[http://www.indiana.edu/~bioc/people/?p=staff|M. Swat]], [[http://www.indiana.edu/~bioc/people/?p=staff|J. S. Gens]], [[http://www.physics.emory.edu/faculty/family/|F. Family]], [[http://math.lanl.gov/~yi/|Y. Jiang]], [[http://www.eyecenter.emory.edu/faculty/grossniklaus.htm|Hans E. Grossniklaus]], ''__PLoS Comput Biol__ '''''7'''(10): e1002155 (2012) [ [[http://newsinfo.iu.edu/news/page/normal/22239.html|IU press release]], [[http://www.gsu.edu/news/60630.html|GSU press release]] ].

 * [[http://download.springer.com/static/pdf/23/chp:10.1007/978-88-470-2571-4_11.pdf?auth66=1425576897_7d893eb62674aacd4a93b56f9090ddac&ext=.pdf|Hybrid cellular Potts model for solid tumor growth]] – M. Scianna, L. Preziosi, ''in'' M. Chaplain, J. Batzel, M. Bachar, Eds., ''__New Challenges for Cancer Systems Biomedicine__'', p.205-224, Springer, (2012).

 * [[http://ieeexplore.ieee.org/Xplore/defdeny.jsp?url=http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6217251&denyReason=-134&arnumber=6217251&productsMatched=null&userType=inst|Searching a multicellular model to tame tumor-induced angiogenesis]] – Podgorski, G.J., Flann, N.S. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), ''2012 IEEE Symposium on DOI: 10.1109/CIBCB.2012.6217251'' , pp. 349-354 (2012).

 * [[http://www.sciencedirect.com/science/article/pii/S0169260713001752|Epithelial to mesenchymal transition: The roles of cell morphology, labile adhesion and junctional coupling]] – Tariq Abdulla, Luis Luna-Zurita, José Luis De La Pompa, Jean-Marc Schleich, Ron Summers, ''__Computer Methods And Programs In Biomedicine__'' '''111''':435-446 (2012).

 * [[http://www.nature.com/nature/journal/v491/n7425_supp/full/491S62a.html#close|Modelling: Computing Cancer]] – N. Savage, ''__Nature__'' '''491''':S62–S63 (2012).

 * [[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=6211560&abstractAccess=no&userType=inst|Multiscale modelling of Notch-mediated lateral induction]] – Abdulla T., Schleich, J., Summers, R., Biomedical and Health Informatics (BHI), IEEE-EMBS International Conference, p. 257 – 260 (2012).

 * [[http://www.sciencedirect.com/science/article/pii/B9780123884039000138|Multi-Scale Modeling of Tissues Using CompuCell3D]] – [[http://www.indiana.edu/~bioc/people/?p=staff|M. Swat]], [[http://www.if.ufrgs.br/pos/portugues/thomas.html|Gilberto L. Thomas]], Julio M. Belmonte, A. Shirinifard, [[http://www.indiana.edu/~iubphys/faculty/mitja.shtml|D.Hmeljak]], [[http://www.indiana.edu/~bioc/jglazier/|J. A. Glazier]], ''__Computational Methods in Cell Biology__, Methods in Cell Biology '''''110''': 325-366 (2012).

 * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033726#pone-0033726-g014|Integrating Intracellular Dynamics Using CompuCell3D and Bionetsolver: Applications to Multiscale Modelling of Cancer Cell Growth and Invasion]] – Vivi Andasari, Ryan T. Roper, Maciej H. Swat, Mark A. J. Chaplain, ''__PLoS ONE__'' '''7'''(3): e33726 (2012).

 * [[http://dl.acm.org/citation.cfm?doid=1878537.1878635|Workflows for parameter studies of multi-cell modeling]] – Randy Heiland, Maciek Swat, Benjamin Zaitlen, James A. Glazier, Andrew Lumsdaine, ''__Proceedings of the 2010 Spring Simulation Multiconference__'' p. 94 (2012).

 * [[http://biovis.net/year/2012/papers/visualizing-cells-and-their-connectivity-graphs-compucell3d|Visualizing Cells and their Connectivity Graphs for CompuCell3D]] – R. Heiland, M. Swat, J. Sluka, B. Zaitlen, A. Shirinifard, G. Thomas, A. Lumsdaine, J. Glazier, ''__2nd IEEE Symposium on Biological Data Visualization__'' (2012).

==== 2011 ====
 * [[https://hal.archives-ouvertes.fr/inserm-00745327/document|Computational modelling of epithelial to mesenchymal transition]] – T. Abdulla, R. Imms, J.-L. Dillenseger, J.-M. Schleich, R. Summers, __''IRBM''__, 32(5):306–310 (2011).

 * [[https://www.semanticscholar.org/paper/A-robust-in-silico-analogue-of-MDCK-cystogenesis-m-Engelberg-Datta/e90bb59358980c4a619261a0e079dc725c551252|A Robust in Silico Analogue of MDCK Cystogenesis Mimics Growth in Multiple Culture Conditions]] - Engelberg, J. A., Datta, A., Mostov, K. E. & Hunt, C. A. ADS ’11 Proc. 2011 Work. Agent-Directed Simul. 52–56 (2011).

 * [[https://www.academia.edu/13476031/Emergent_networks_A_slime_mold_simulation?auto|Emergent networks:A slime mold simulation]] - Semmler, N. Bachelors Thesis, June 24, 2011.

 * [[http://www.tandfonline.com/doi/pdf/10.1080/00051144.2011.11828403?needAccess=true|Progress with a Multiscale Systems Engineering Approach to Cardiac Development]] - Summers, R., Abdulla, T., Houyel, L. & Schleich, J.-M. Autom. Control. Meas. Electron. Comput. Commun. 52, 49–57 (2011).

 * [[https://link.springer.com/content/pdf/10.1007/978-3-642-23508-5_333.pdf|3D Simulation of an in vitro Epithelial to Mesenchymal Transition]] - Summers, R., Abdulla, T., Imms, R. a & Schleich, J.-M. 5th Eur. IFMBE Conf. IFMBE Proc. 37 1287–1290 (2011). doi:10.1007/978-3-642-23508-5_333.

 * [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002155|A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation]] – Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier, ''__PLoS Comput Biol__ '''''7'''(10): e1002155 (2011) [ [[Models/BelmonteHesterSomite|model]] and a [[Models/BelmonteHesterSomite|movie]] are available ].

 * [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002030|MDCK Cystogenesis Driven by Cell Stabilization within Computational Analogues]] – Jesse A. Engelberg, Anirban Datta, Keith E. Mostov, C. Anthony Hunt, ''__PLoS Comput Biol__ '''''7'''(4): e1002030 (2011).

 * [[http://www.ipcbee.com/vol5/12-X00022.pdf|A Multiscale Model for Hypoxia-induced Avascular Tumor Growth]] – Xuefeng Gao, Mark Tangney, Sabin Tabirca, __''Proceedings of 2011 International Conference on Bioscience''__, Biochemistry and Bioinformatics IPCBEE vol.5 (2011).

 * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024999|Computer Simulations of Cell Sorting Due to Differential Adhesion]] – Ying Zhang, Gilberto L. Thomas, Maciej Swat, Abbas Shirinifard, James A. Glazier, ''__PLoS ONE__'' '''6'''(10):e24999 (2011).

 * [[http://www.ncbi.nlm.nih.gov/pubmed/22254345|Towards multiscale systems modeling of endocardial to mesenchymal transition]] – Abdulla T, Imms, R., Schleich, J., Summers R., Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE, p. 449 – 452 (2011).

 * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022700|Coordination of Cell Differentiation and Migration in Mathematical Models of Caudal Embryonic Axis Extension]] – Nigel C. Harrison, Ruth Diez del Corral, Bakhtier Vasiev, ''__PLoS ONE__'' '''6'''(7):e22700 (2011).

==== 2010 ====
 * [[https://link.springer.com/protocol/10.1007/978-1-60761-842-3_19|Genetic Algorithms and Their Application to In Silico Evolution of Genetic Regulatory Networks]] - Knabe, J., Wegner, K., Nehaniv, C., Schilstra, M. Computational Biology, 2010, 673, 297-321.

 * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010571|Modeling Gastrulation in the Chick Embryo: Formation of the Primitive Streak]] – Bakhtier Vasiev, Ariel Balter, Mark Chaplain, James A. Glazier, Cornelis J. Weijer, ''__PLoS ONE__'' '''5'''(5):e10571 (2010).

 * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010641|Front Instabilities and Invasiveness of Simulated 3D Avascular Tumors]] – Nikodem J. Popławski, Abbas Shirinifard, Ubirajara Agero, J. Scott Gens, Maciej Swat, James A. Glazier, ''__PLoS ONE__'' '''5'''(5): e10641 (2010).

 * [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000841|A Computer Simulation of Long-Range Patterning in the Drosophila Pupal Eye]] – David Larson , Ruth Johnson, Maciej H. Swat, J. Cordero, James A. Glazier, Ross Cagan, ''__PLoS Comput Bio__'' '''6''': e1000841 (2010) doi:10.1371/journal.pcbi.1000841.

==== 2009 ====
 * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007190#pone-0007190-g004|3D Multi-Cell Simulation of Tumor Growth and Angiogenesis]] – Abbas Shirinifard, J. Scott Gens, Benjamin L. Zaitlen, Nikodem J. Popławski, Maciej Swat, James A. Glazier, ''__PLoS ONE__'' '''4'''(10):e7190 (2009).

 * [[http://old.compucell3d.org/links/index.php?id=35|Mathematical modeling of the capillary-like pattern generated by adrenomedullin-treated human vascular endothelial cells in vitro]] – Diego Guidolin, Giovanna Albertin, Elisa Sorato, Barbara Oselladore, Alessandra Mascarin, Domenico Ribatti, ''__Dev Dyn__'' '''238'''(8):1951-63 (2009).

==== 2008 ====
 * [[http://panmental.de/papers/FlagPottsGRNALife11.pdf|Evolution and morphogenesis of differentiated multicellular organisms: autonomously generated diffusion gradients for positional information]] – J. F. Knabe, C. L. Nehaniv, M. J. Schilstra, ''Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems, pp. 321–328. MIT Press, Cambridge ''(2008).

 * [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2547990/|Simulation of Single-Species Bacterial-Biofilm Growth Using the Glazier-Graner-Hogeweg Model and the CompuCell3D Modeling Environment]] – Nikodem J. Popławski, Abbas Shirinifard, Maciej Swat, James A. Glazier, ''__Mathematical biosciences and engineering__ '''''5''': 355-388'' ''(2008).

 * [[http://digital.cs.usu.edu/~flann/flann_CIBCB_2008.pdf|Discovering Novel Cancer Therapies: A Computational Modeling and Search Approach]] – A. W. Mahoney, B. G. Smith, N. S. Flann, G. J. Podgorski, ''__IEEE conference on Computational Intelligence in Bioinformatics and Bioengineering__'', pp. 233-240 (2008).

 * [[http://www.sciencedirect.com/science/article/pii/S0070215307810076|Coordinated Action of N-CAM, N-cadherin, EphA4, and ephrinB2 Translates Genetic Prepatterns into Structure during Somitogenesis in Chick]] – James A. Glazier, Ying Zhang, Maciej Swat, Benjamin Zaitlen, Santiago Schnell, ''__Current Topics in Developmental Biology__'' '''81''':205-247 (2008).

==== 2007 ====
 * [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695324/|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]] – Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, J. A. Izaguirre, ''__Computing in Science and Engineering__'' '''9''': 50-60 (2007).

 * [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168394/|Adhesion Between Cells, Diffusion of Growth Factors, and Elasticity of the AER Produce the Paddle Shape of the Chick Limb]] – Nikodem J. Popławski, Maciej Swat, J. Scott Gens, James A. Glazier, ''__Physica A__ '''''373''': 521-532 (2007).

 * '''A Brief History of the Glazier-Graner-Hogeweg Model.''' Glazier J.A., Balter A., Popławski N.J. (2007) Magnetization to Morphogenesis: In: Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. (eds) Single-Cell-Based Models in Biology and Medicine. Mathematics and Biosciences in Interaction. Birkhäuser Basel

 * '''The Glazier-Graner-Hogeweg Model: Extensions, Future Directions, and Opportunities for Further Study.''' Balter A., Merks R.M.H., Popławski N.J., Swat M., Glazier J.A. (2007) In: Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. (eds) Single-Cell-Based Models in Biology and Medicine. Mathematics and Biosciences in Interaction. Birkhäuser Basel.

 * '''The Cellular Potts Model and Biophysical Properties of Cells, Tissues and Morphogenesis.''' Marée A.F.M., Grieneisen V.A., Hogeweg P. (2007) In: Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. (eds) Single-Cell-Based Models in Biology and Medicine. Mathematics and Biosciences in Interaction. Birkhäuser Basel.

==== 2005 ====
 * [[http://www.ncbi.nlm.nih.gov/pubmed/17044166|A Framework For Three-Dimensional Simulation of Morphogenesis]] – Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesus A. Izaguirre, ''__IEEE/ACM Transactions on Computational Biology and Bioinformatics__ (TCBB) '''''2''': 273-288 (2005).

 * [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1629079/|On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis]] – R. Chaturvedi, C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, T. Glimm, H. G. E. Hentschel, S. A. Newman, J. A. Glazier, M. Alber, ''__J. R. Soc. Interface__ '''''2''': 237-253 (2005).

 * [[http://www.sciencedirect.com/science/article/pii/S0378437104016188|A Cell-Centered Approach to Developmental Biology]] – Roeland M.H. Merks, James A. Glazier, ''__Physica A__ '''''352''': 113-130 (2005).

==== 2004 ====
 * [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691788/|Dynamical Mechanisms For Skeletal Pattern Formation in the Vertebrate Limb]] – H. G. E. Hentschel, T. Glimm, J. A. Glazier, Stuart A. Newman, ''__Proc Biol Sci__'' '''271'''(1549): 1713-1722'' ''(2004).

 * [[http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.87.9008|A Hybrid Discrete-Continuum Model for 3D Skeletogenesis of the Vertebrate Limb]] – R. Chaturvedi, C. Huang, J. A. Izaguirre, Stuart A. Newman, J. A. Glazier, ''__Lecture Notes in Computer Science__ '''''3305''': 543-552 (2004).

 * [[http://bioinformatics.oxfordjournals.org/content/20/7/1129.full.pdf|CompuCell, a Multi-Model Framework For Simulation of Morphogenesis]] – J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier, ''__Bioinformatics__ '''''20''': 1129-1137'' ''(2004).

==== 1993 ====
 * '''Simulation of the differential adhesion driven rearrangement of biological cells.''' Glazier JA, Graner F. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Mar;'''47'''(3):2128-2154.

==== 1992 ====
 * '''Simulation of biological cell sorting using a two-dimensional extended Potts model.''' Graner F, Glazier JA. Phys Rev Lett. 1992 Sep 28;'''69'''(13):2013-2016.

This page contains selected publications which were done using CompuCell3D. While we try to keep this page updated some of the publications might be missing from it. If you want your CompuCell3D-based publication to be displayed here, please e-mail us ( jsluka@iu.edu )

For list of Ph.D. and Master theses completed using CC3D please click here.

How to cite CompuCell3D

Multi-Scale Modeling of Tissues Using CompuCell3D – M. Swat, Gilberto L. Thomas, Julio M. Belmonte, A. Shirinifard, D. Hmeljak, J. A. Glazier, Computational Methods in Cell Biology, Methods in Cell Biology 110: 325-366 (2012)

Publications

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

  • From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development – Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, J. A. Izaguirre, Computing in Science and Engineering 9: 50-60 (2007).

  • Adhesion Between Cells, Diffusion of Growth Factors, and Elasticity of the AER Produce the Paddle Shape of the Chick Limb – Nikodem J. Popławski, Maciej Swat, J. Scott Gens, James A. Glazier, Physica A 373: 521-532 (2007).

  • A Brief History of the Glazier-Graner-Hogeweg Model. Glazier J.A., Balter A., Popławski N.J. (2007) Magnetization to Morphogenesis: In: Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. (eds) Single-Cell-Based Models in Biology and Medicine. Mathematics and Biosciences in Interaction. Birkhäuser Basel

  • The Glazier-Graner-Hogeweg Model: Extensions, Future Directions, and Opportunities for Further Study. Balter A., Merks R.M.H., Popławski N.J., Swat M., Glazier J.A. (2007) In: Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. (eds) Single-Cell-Based Models in Biology and Medicine. Mathematics and Biosciences in Interaction. Birkhäuser Basel.

  • The Cellular Potts Model and Biophysical Properties of Cells, Tissues and Morphogenesis. Marée A.F.M., Grieneisen V.A., Hogeweg P. (2007) In: Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. (eds) Single-Cell-Based Models in Biology and Medicine. Mathematics and Biosciences in Interaction. Birkhäuser Basel.

2005

2004

1993

  • Simulation of the differential adhesion driven rearrangement of biological cells. Glazier JA, Graner F. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Mar;47(3):2128-2154.

1992

  • Simulation of biological cell sorting using a two-dimensional extended Potts model. Graner F, Glazier JA. Phys Rev Lett. 1992 Sep 28;69(13):2013-2016.

CompuCell3D: Publications (last edited 2026-04-20 20:26:35 by jpSluka)