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= Publications, Talks, Links = 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 ( mthielme@indiana.edu )
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=== Recent Publications and Ph.D. Theses === For list of [[Theses|PhD and Master theses]] completed using CC3D please click [[Theses|here]]
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=== 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, [[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)
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[[http://biocomplexity.indiana.edu/jglazier/docs/papers/AmarieGlazierSensors2012.pdf|Label-Free Microcavity Biosensors: Steps towards Personalized Medicine]] -
[[http://biocomplexity.indiana.edu/people/?p=staff|D.Amarie]]
and [[http://biocomplexity.indiana.edu/jglazier/|J.Glazier]].
''[[http://www.mdpi.com/1424-8220/12/12/17262|Sensors]]'', 12, 17262-17294; doi:[[http://dx.doi.org/10.3390/s121217262|10.3390/s121217262]] (December, 2012)		 === Publications ===
==== 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)
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==== 2016 ====
 * [[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)
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 * [[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)
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 * [[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
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[[http://biocomplexity.indiana.edu/jglazier/docs/papers/HeilandSwatSlukaZaitlenShirinifardThomasLumsdaineGlazierBioVis2012.pdf|Visualizing Cells and their Connectivity Graphs for CompuCell3D]] -
[[http://mypage.iu.edu/%7Eheiland/|R.Heiland]],
[[http://biocomplexity.indiana.edu/people/?p=staff|M.Swat]],
[[http://biocomplexity.indiana.edu/people/?p=staff|J.Sluka]],
[[http://www.linkedin.com/pub/benjamin-zaitlen/4/b7b/62a|B.Zaitlen]],
[[http://www.linkedin.com/pub/abbas-shirinifard/6/826/a85|A.Shirinifard]],
[[http://www.if.ufrgs.br/pos/portugues/thomas.html|G.Thomas]],
[[http://osl.iu.edu/~lums/|A.Lumsdaine]],
and [[http://biocomplexity.indiana.edu/jglazier/|J.Glazier]]. ''[[http://biovis.net/year/2012/papers/visualizing-cells-and-their-connectivity-graphs-compucell3d|2nd IEEE Symposium on Biological Data Visualization]]'' (October, 2012)		  * [[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)
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 * [[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)
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[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002440|Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study]] - [[http://biocomplexity.indiana.edu/people/?p=staff|A.Shirinifard]], [[http://biocomplexity.indiana.edu/jglazier/|J.Glazier]], [[http://biocomplexity.indiana.edu/people/?p=staff|M.Swat]], [[http://biocomplexity.indiana.edu/people/?p=staff|J.S.Gens]], [[http://www.physics.emory.edu/faculty/family/|F.Family]], [[http://math.lanl.gov/~yi/|Y.Jiang]] and [[http://www.eyecenter.emory.edu/faculty/grossniklaus.htm|Hans E. Grossniklaus]]. ''PLoS Comput Biol 7(10): e1002155. doi:10.1371/journal.pcbi.1002440'' (May, 2012)
( [[http://newsinfo.iu.edu/news/page/normal/22239.html|IU press release]], [[http://www.gsu.edu/news/60630.html|GSU press release]] )		  * [[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)
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 * [[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)
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[[http://www.sciencedirect.com/science/article/pii/B9780123884039000138|Multi-Scale Modeling of Tissues Using CompuCell3D]] - [[http://biocomplexity.indiana.edu/people/?p=staff|M.Swat]], [[http://www.if.ufrgs.br/pos/portugues/thomas.html|G.Thomas]], [[http://biocomplexity.indiana.edu/people/?p=students|J.Belmonte]], [[http://biocomplexity.indiana.edu/people/?p=staff|A.Shirinifard]], [[http://www.indiana.edu/~iubphys/faculty/mitja.shtml|D.Hmeljak]] and [[http://biocomplexity.indiana.edu/jglazier/|J.Glazier]]. ''Computational Methods in Cell Biology, Methods in Cell Biology 110, 325-366'' (April, 2012)  * [[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)
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[[http://biocomplexity.indiana.edu/jglazier/cv.php?pg=2#sd|Multi-Scale Cell-Based Computational Models of Vertabrate Segmentation and Somitogenesis Illuminate Coordination of Developmental Mechanisms Across Scales]] - Susan D. Hester. ''Ph.D. Indiana University, Department of Physics'' (April, 2012)  * [[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)
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[[http://biocomplexity.indiana.edu/jglazier/cv.php?pg=2#sd|Vascular Patterning and Its Application in Cancer and Choroidal Neovascularization]] - [[http://biocomplexity.indiana.edu/people/?p=staff|A.Shirinifard]]. ''Ph.D. Indiana University, Department of Physics'' (March, 2012)
 		  * [[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)
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=== CompuCell3D - Based Simulations ===
[[http://www.nature.com/nature/journal/v491/n7425_supp/full/491S62a.html|Modelling: Computing cancer – Software models of complex tissues and disease are yielding a better understanding of cancer and suggesting potential treatments]] N.Savage, ''Nature, 491, S62-S63'' (November 2012)		  * [[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)
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[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.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'' (2011)  * [[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)
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[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.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 Computational Biology'' (2011) [The [[Models/BelmonteHesterSomite|model]] and a [[Models/BelmonteHesterSomite|movie]] are available] ==== 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)
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[[Cc3dPaper0|Evolution and morphogenesis of differentiated multicellular organisms: autonomously generated diffusion gradients for positional information.]] Knabe, J.F., Nehaniv, C.L., Schilstra, M.J. ''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://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)
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[[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  * [[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)
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[[http://old.compucell3d.org/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)''  * [[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)
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[[http://old.compucell3d.org/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)''  * [[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)
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[[http://old.compucell3d.org/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. PopÅ‚awski, Maciej Swat, J. Scott Gens and James A. Glazier, ''Physica A: Statistical and Theoretical Physics 373, 521-532 (2007)''  * [[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)
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[[http://old.compucell3d.org/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)''  * [[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)
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[[http://old.compucell3d.org/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)''  * [[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)
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=== CompuCell3D Framework ===
[[http://old.compucell3d.org/links/index.php?id=18|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]]		  * [[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)
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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  * [[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)
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Computing in Science and Engineering, 9, 50-60 (2007) ==== 2014 ====
 * [[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)
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[[http://old.compucell3d.org/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)''  * [[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
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[[http://old.compucell3d.org/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)''  * [[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
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[[http://old.compucell3d.org/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)''  * [[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
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[[http://old.compucell3d.org/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)''  * [[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)
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[[http://old.compucell3d.org/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)''  * [[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)
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[[http://old.compucell3d.org/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)''  * [[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)
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= Integration with SBW =
We have conducted a preliminary integration of CompuCell3D with		  * [[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)
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[[http://www.sys-bio.org/|Systems Biology Workbench]](SBW) to link to subcellular models. As a result users can select the level of detail in their models while working within a single integrated framework.  * [[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)
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List of Movies (Note: simulator is an ODE solver of metabolic pathways):  * [[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)
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 * Movie 1:[[http://old.compucell3d.org/OneSimulator.avi|109 Cells and one simulator]]
 * Movie 2:[[http://old.compucell3d.org/SameInitialConditions.avi|109 cells and 109 simulators (same initial conditions)]]
 * Movie 3:[[http://old.compucell3d.org/DifferentInitialConditions.avi|109 cells and 109 simulators (different initial conditions)]]		  * [[javascript:void(0);/*1458573552430*/|A design principle underlying the paradoxical roles of E3 ubiquitin ligases]] – Daewon Lee, Minjin Kim & Kwang-Hyun Cho, ''__Scientific Reports__'' '''4''': 5573 (2014)
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Movies created by [[http://sys-bio.org/sbwWiki/doku.php?id=sysbio:labmembers|Frank Bergmann]] ==== 2013 ====
 * [[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
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 * [[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)
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 * [[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
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=== Related Links ===
[[http://old.compucell3d.org/links/index.php?cat=talks|Recent Talks]]		  * [[javascript:void(0);/*1393870307162*/|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 Larse, ''__PLoS Comput Biol__'' '''9'''(11):e1003319 (2013)
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[[http://old.compucell3d.org/links/index.php?cat=biological|Biological Modeling]]  * [[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)
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 * Differential Adhesion and Cell Sorting
 * '''Limb Development '''
 * '''Tumor and Cancer '''
 * '''Angiogenesis/Vasculogenesis '''
 * '''Biofilms '''		  * [[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)
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[[http://old.compucell3d.org/links/index.php?cat=physical|Physical Modeling]]  * [[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)
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 * Soap Foams and Liquid Foams  * [[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)
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[[http://old.compucell3d.org/links/index.php?cat=simulations|Simulations Using GGH/CPM Approach]]  * [[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)
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[[http://old.compucell3d.org/links/index.php?cat=background|General Background on Biophysical Modeling and Development]] ==== 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 ====
 * [[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)

 * [[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)

 * [[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 ====
 * [[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)

==== 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)

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 ( mthielme@indiana.edu )

For list of PhD and Master theses completed using CC3D please click here

How to cite CompuCell3D

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