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| CompuCell3D - Based Simulations[[links/index.php?id=35|Mathematical modeling of the capillary-like pattern generated by adrenomedullin-treated human vascular endothelial cells in vitro]] Diego Guidolin , Giovanna Albertin , Elisa Sorato , Barbara Oselladore , Alessandra Mascarin , Domenico Ribatti[[links/index.php?id=29|Simulation of Single-Species Bacterial-Biofilm Growth Using the Glazier-Graner-Hogeweg Model and the CompuCell3D Modeling Environment]] Nikodem J. Popławski, Abbas Shirinifard, Maciej Swat, and James A. Glazier, ''Mathematical biosciences and engineering 5, 355-388 (2008)''[[links/index.php?id=30|Discovering Novel Cancer Therapies: A Computational Modeling and Search Approach]] Mahoney A. W., Smith B. G., Flann N. S., and Podgorski G. J., ''IEEE conference on Computational Intelligence in Bioinformatics and Bioengineering, (2008)''[[links/index.php?id=28|Adhesion Between Cells, Diffusion of Growth Factors, and Elasticity of the AER Produce the Paddle Shape of the Chick Limb]] Nikodem J. Popławski, Maciej Swat, J. Scott Gens and James A. Glazier, ''Physica A: Statistical and Theoretical Physics 373, 521-532 (2007)''[[links/index.php?id=26|Dynamical Mechanisms For Skeletal Pattern Formation in the Vertebrate Limb]] H G E Hentschel, T Glimm, J A Glazier, S A Newman, ''Proc Biol Sci. 271, 1713–1722 (2004)''[[links/index.php?id=27|A Hybrid Discrete-Continuum Model for 3D Skeletogenesis of the Vertebrate Limb]] R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier, ''Lecture Notes in Computer Science 3305, 543-552 (2004)''CompuCell3D Framework[[links/index.php?id=18|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]] Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre ''Computing in Science and Engineering, 9, 50-60 (2007)''[[links/index.php?id=20|A Framework For Three-Dimensional Simulation of Morphogenesis]] Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesus A. Izaguirre, ''IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2, 273-288 (2005)''[[links/index.php?id=22|On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis]] R. Chaturvedi, C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, T. Glimm, H. G. E. Hentschel, S. A. Newman, J. A. Glazier, M. Alber, ''Journal of The Royal Society Interface 2, 237-253 (2005)''[[links/index.php?id=23|A Cell-Centered Approach to Developmental Biology]] Roeland M.H. Merks, and James A. Glazier, ''Physica A: Statistical Mechanics and its Applications 352, 113-130 (2005) ''[[links/index.php?id=25|Empirical Evaluation of Design Patterns in Scientific Application]] Kedar Aras, ''Master’s Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2005)''[[links/index.php?id=21|CompuCell, a Multi-Model Framework For Simulation of Morphogenesis]] J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier, ''Bioinformatics 20, 1129-1137 (2004)''[[links/index.php?id=24|BIOLOGO: A Domain-Specific Language For Morphogenesis]] Trevor M. Cickovski, ''Master’s Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2004)''Related Links[[links/index.php?cat=talks|Recent Talks]][[links/index.php?cat=biological|Biological Modeling]]Differential Adhesion and Cell Sorting Limb Development Tumor and Cancer Angiogenesis/Vasculogenesis Biofilms[[links/index.php?cat=physical|Physical Modeling]]Soap Foams and Liquid Foams[[links/index.php?cat=simulations|Simulations Using GGH/CPM Approach]][[links/index.php?cat=background|General Background on Biophysical Modeling and Development]] |
=== Recent Publications and Ph.D. Theses === [[attachment:sensors_amarie_glazier.pdf|Label-Free Microcavity Biosensors: Steps towards Personalized Medicine]] - [[http://www.indiana.edu/~bioc/people/?p=staff|D.Amarie]] and [[http://www.indiana.edu/~bioc/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) [[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]], and [[http://www.indiana.edu/~bioc/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.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.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]] 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://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|G.Thomas]], [[http://www.indiana.edu/~bioc/people/?p=staff|J.Belmonte]], A.Shirinifard, [[http://www.indiana.edu/~iubphys/faculty/mitja.shtml|D.Hmeljak]] and [[http://www.indiana.edu/~bioc/jglazier/|J.Glazier]]. ''Computational Methods in Cell Biology, Methods in Cell Biology 110, 325-366'' (April, 2012) [[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) [[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) |
Recent Publications and Ph.D. Theses
Label-Free Microcavity Biosensors: Steps towards Personalized Medicine - D.Amarie and J.Glazier. Sensors, 12, 17262-17294; doi:10.3390/s121217262 (December, 2012)
Visualizing Cells and their Connectivity Graphs for CompuCell3D - R.Heiland, M.Swat, J.Sluka, B.Zaitlen, A.Shirinifard, G.Thomas, A.Lumsdaine, and J.Glazier. 2nd IEEE Symposium on Biological Data Visualization (October, 2012)
Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study - A.Shirinifard, J.Glazier, M.Swat, J.S.Gens, F.Family, Y.Jiang and Hans E. Grossniklaus. PLoS Comput Biol 7(10): e1002155. doi:10.1371/journal.pcbi.1002440 (May, 2012) ( IU press release, GSU press release )
Multi-Scale Modeling of Tissues Using CompuCell3D - M.Swat, G.Thomas, J.Belmonte, A.Shirinifard, D.Hmeljak and J.Glazier. Computational Methods in Cell Biology, Methods in Cell Biology 110, 325-366 (April, 2012)
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)
Vascular Patterning and Its Application in Cancer and Choroidal Neovascularization - A.Shirinifard. Ph.D. Indiana University, Department of Physics (March, 2012)