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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 ( mswat@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]] === 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) === Publications === ==== 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, and Eugenio M. Azpeitia, ''Front. Microbiol.'', 23 June 2015 |
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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) |
* [[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://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://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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| [[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://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://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%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://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://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://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://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://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/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://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://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/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://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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| === 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) |
==== 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%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) | * [[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.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] | * [[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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| [[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)'' | * [[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 | * [[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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| [[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://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=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://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=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)'' | * [[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?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://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=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)'' | ==== 2012 ==== * [[Multiscale Developments of the Cellular Potts Model]] – Marco Scianna, Luigi Preziosi, ''__Multiscale Model. Simul.__'' '''10'''(2):342–382. (2012) |
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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://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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| 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://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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| Computing in Science and Engineering, 9, 50-60 (2007) | * [[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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| [[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.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://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://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://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://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://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.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=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.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=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://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://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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| ==== 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://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://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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| * [[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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| == Presentations and Conferences == | * [[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) |
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| '''[[TowardThe3DVirtualCell2012|Toward the 3D Virtual Cell - UC San Diego - Atkinson Hall, December 13-14, 2012]]''' | * [[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) |
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| ==== 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) |
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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) | |
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| -------- | * [[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) |
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| == Integration with SBW == We have conducted a preliminary integration of CompuCell3D with |
==== 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) |
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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://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) |
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| List of Movies (Note: simulator is an ODE solver of metabolic pathways): | ==== 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) |
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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)]] |
* [[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) |
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| Movies created by [[http://sys-bio.org/sbwWiki/doku.php?id=sysbio:labmembers|Frank Bergmann]] | * [[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) |
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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) | |
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| ==== 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) |
|
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| -------- | * [[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) |
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| ==== 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) |
|
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| === Related Links === [[http://old.compucell3d.org/links/index.php?cat=talks|Recent Talks]] |
* [[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) |
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| [[http://old.compucell3d.org/links/index.php?cat=biological|Biological Modeling]] | * [[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) |
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| * Differential Adhesion and Cell Sorting * '''Limb Development ''' * '''Tumor and Cancer ''' * '''Angiogenesis/Vasculogenesis ''' * '''Biofilms ''' |
* [[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) |
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| [[http://old.compucell3d.org/links/index.php?cat=physical|Physical Modeling]] | ==== 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) |
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| * Soap Foams and Liquid Foams | * [[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) |
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| [[http://old.compucell3d.org/links/index.php?cat=simulations|Simulations Using GGH/CPM Approach]] [[http://old.compucell3d.org/links/index.php?cat=background|General Background on Biophysical Modeling and Development]] |
* [[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 ( mswat@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
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, and Eugenio M. Azpeitia, Front. Microbiol., 23 June 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)
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)