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| 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 ( mswat@indiana.edu ) | 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 === [[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) |
For list of [[Theses|PhD and Master theses]] completed using CC3D please click [[Theses|here]] |
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| [[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) | === 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://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) | === Publications === ==== 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://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://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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| ---- === Ph.D. Theses, Master and Bachelor dissertations === [[http://etheses.nottingham.ac.uk/3139/|Integrative modelling of angiogenesis in the bovine corpus luteum]] – Sotiris Prokopiou, ''Ph.D. University of Nottingham, Centre for Mathematical Medicine and Biology, School of Mathematical Sciences'' (Feb, 2013) |
* [[http://www.nature.com/articles/srep19905|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), doi:10.1038/srep19905 |
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| [[http://www.lume.ufrgs.br/bitstream/handle/10183/87235/000910847.pdf?sequence=1|Modelagem e simulação de mobilidade celular]] – Eduarda D. Susin, ''Bacharel em Física, Universidade Federal do Rio Grande do Sul, Instituto de Física'' (2013) | * 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__'' - accepted for publication |
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| [[http://www.indiana.edu/~bioc/jglazier/docs/student_dissertations/susanhester_thesis.pdf|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) | ==== 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) |
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| [[http://www.indiana.edu/~bioc/jglazier/docs/student_dissertations/abbasshirinifard_thesis.pdf|Vascular Patterning and Its Application in Cancer and Choroidal Neovascularization]] – A. Shirinifard. ''Ph.D. Indiana University, Department of Physics'' (March, 2012) | * [[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://discovery.dundee.ac.uk/portal/en/theses/mathematical-modelling-of-cancer-cell-invasion-of-tissue(9e8221c9-120b-4167-a870-dedade5fe90e).html|Mathematical modelling of cancer cell invasion of tissue: discrete and continuum approaches to studying the central role of adhesion]] – Vivi Andasari, ''Ph.D. University of Dundee, Divison of Mathematics'' (2011) | * [[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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| [[http://bsc-slimy-networks.googlecode.com/hg-history/417c4d75ce9593d210a617dfdf22bd19a3de461a/paper/paper.pdf|Emergent networks: A slime mold simulation]] – Niklas B. Semmler,'' Bachelor Opleiding Kunstmatige Intelligentie, University of Amsterdam, Faculty of Science'' (June, 2011) | * [[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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| ---- | ==== 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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| === CompuCell3D–Based Simulations === [[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) |
* [[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 DOI: 10.1371/journal.pcbi.1003997 (2014) |
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| [[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://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://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://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://journal.frontiersin.org/Journal/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, Suzy Davies, Carolyn Muller, Yong Zhang, Robert M. Hoffman, Abbas Shirinifard, Melanie Moses, Yi Jiang, Bridget S. Wilson, __''Frontiers in Oncology''__ '''3''': 97 (2013) | * [[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, to appear in ''__Computation__'', 2014 |
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| [[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://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://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://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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| [[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://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.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.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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| [[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://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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| [[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 ] | * [[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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| [[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) | ==== 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.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.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://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://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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| [[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) | * [[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?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) | * [[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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| [[Cc3dPaper0|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://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 and Bridget S. Wilson, Frontiers in Oncology, 3:97, (2013) |
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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. Popławski, Abbas Shirinifard, Maciej Swat, James A. Glazier, ''__Mathematical biosciences and engineering__ '''''5''': 355-388'' ''(2008) | * [[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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| [[http://old.compucell3d.org/links/index.php?id=30|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://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://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) | * [[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?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, James A. Glazier, ''__Physica A__ '''''373''': 521-532 (2007) | ==== 2012 ==== * [[Multiscale Developments of the Cellular Potts Model]] – Marco Scianna, Luigi Preziosi, ''__Multiscale Model. Simul.__'' '''10'''(2):342–382. (2012) |
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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, Stuart A. Newman, __''Proc Biol Sci''__ '''271'''(1549): 1713-1722'' ''(2004) | * [[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]] ] |
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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, Stuart A. Newman, J. A. Glazier, ''__Lecture Notes in Computer Science__ '''''3305''': 543-552 (2004) | * [[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) |
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| ---- | * [[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'' , Page(s): 349 - 354,(2012) |
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| === CompuCell3D Framework === [[http://www.springerlink.com/content/r34g45202l2528l4/|Computational Modeling of Angiogenesis: Towards a Multi-Scale Understanding of Cell–Cell and Cell–Matrix Interactions]] – Sonja E. M. Boas, Margriet M. Palm, Pieter Koolwijk, Roeland M. H. Merks, ''__Mechanical and Chemical Signaling in Angiogenesis__, Studies in Mechanobiology, Tissue Engineering and Biomaterials '''''12''': 161-183 (2013) |
* [[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) |
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| [[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.nature.com/nature/journal/v491/n7425_supp/full/491S62a.html#close|Modelling: Computing cancer]] – N. Savage, ''__Nature__'' '''491''':S62–S63, (22 November 2012) |
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| [[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://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) |
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| [[http://biovis.net/year/2012/papers/visualizing-cells-and-their-connectivity-graphs-compucell3d|Visualizing Cells and their Connectivity Graphs for CompuCell3D]] – [[http://mypage.iu.edu/~heiland/|R. Heiland]], [[http://www.indiana.edu/~bioc/people/?p=staff|M. Swat]], [[http://www.indiana.edu/~bioc/people/?p=staff|J. Sluka]], [[http://www.linkedin.com/pub/benjamin-zaitlen/4/b7b/62a|B. Zaitlen]], A. Shirinifard, [[http://www.if.ufrgs.br/pos/portugues/thomas.html|G. Thomas]], [[http://osl.iu.edu/~lums/|A. Lumsdaine]], [[http://www.indiana.edu/~bioc/jglazier/|J. Glazier]], __''2nd IEEE Symposium on Biological Data Visualization''__ (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) |
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| [[http://old.compucell3d.org/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, J. A. Izaguirre, __''Computing in Science and Engineering''__ '''9''': 50-60 (2007) | * [[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) |
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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://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) |
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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, ''__J. R. Soc. Interface__ '''''2''': 237-253 (2005) | * [[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) |
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| [[http://old.compucell3d.org/links/index.php?id=23|A Cell-Centered Approach to Developmental Biology]] – Roeland M.H. Merks, James A. Glazier, ''__Physica A__ '''''352''': 113-130 (2005) | ==== 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 ] |
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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.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) |
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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.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) |
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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) | * [[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) |
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| ---- | * [[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) |
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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) |
* [[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 Swat, J. Cordero, James Glazier, Ross Cagan, PLoS Comput Biol 6, e1000841. doi:10.1371/journal.pcbi.1000841(2010) ==== 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://www3.nd.edu/~izaguirr/papers/ArCI0x.pdf|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.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
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
2016
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)
Filopodial-Tension Model of Convergent-Extension of Tissues – Julio M. Belmonte, Maciej H. Swat, James A. Glazier, PLoS Comput Biol 12: e1004952 (2016)
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), doi:10.1038/srep19905
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 - accepted for publication
2015
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)
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)
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)
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)
2014
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)
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 DOI: 10.1371/journal.pcbi.1003997 (2014)
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
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
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, to appear in Computation, 2014
Somites Without a Clock – Ana S. Dias, I. de Almeida, Julio M. Belmonte, J. A. Glazier, Claudio D. Stern, Science 343: 791-795 (2014)
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)
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)
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)
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)
A design principle underlying the paradoxical roles of E3 ubiquitin ligases - Daewon Lee, Minjin Kim & Kwang-Hyun Cho, SCIENTIFIC REPORTS 4: 5573 (2014)
2013
Agent-Based Virtual Tissue Simulations – Maciej Swat, James A. Glazier, Biomedical Computation Review, Fall 2013 p.28-29
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)
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
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)
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)
Ovarian Tumor Attachment, Invasion, and Vascularization Reflect Unique Microenvironments in the Peritoneum: Insights from Xenograft and Mathematical ModelsMara P. Steinkamp, Kimberly Kanigel Winner and Bridget S. Wilson, Frontiers in Oncology, 3:97, (2013)
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)
Vascular Networks Due to Dynamically Arrested Crystalline Ordering of Elongated Cells – Margriet M. Palm, Roeland M. H. Merks,. Phyiscal Review E 87: 012725 (2013)
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
Multiscale Developments of the Cellular Potts Model – Marco Scianna, Luigi Preziosi, Multiscale Model. Simul. 10(2):342–382. (2012)
Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study – A. Shirinifard, J. A. Glazier, M. Swat, J. S. Gens, F. Family, Y. Jiang, Hans E. Grossniklaus, PLoS Comput Biol 7(10): e1002155 (2012) [ IU press release, GSU press release ]
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)
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 , Page(s): 349 - 354,(2012)
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)
Modelling: Computing cancer – N. Savage, Nature 491:S62–S63, (22 November 2012)
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)
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)
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)
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)
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
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) [ model and a movie are available ]
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)
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)
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)
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)
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)
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
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)
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)
A Computer Simulation of Long-Range Patterning in the Drosophila Pupal Eye – David Larson , Ruth Johnson, Maciej Swat, J. Cordero, James Glazier, Ross Cagan, PLoS Comput Biol 6, e1000841. doi:10.1371/journal.pcbi.1000841(2010)
2009
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)
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
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)
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)
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)
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
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)
2005
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)
Empirical Evaluation of Design Patterns in Scientific Application – Kedar Aras, Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2005)
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)
A Cell-Centered Approach to Developmental Biology – Roeland M.H. Merks, James A. Glazier, Physica A 352: 113-130 (2005)
2004
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)
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)
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)