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| = Publications, Talks, Links = === Recent Publications and Ph.D. Theses === [[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://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://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) |
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| [[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://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) |
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| [[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://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] |
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| [[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)'' | [[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)'' |
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| [[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)'' |
[[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 |
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| [[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://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)'' |
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| [[links/index.php?id=27|A Hybrid Discrete-Continuum Model for 3D Skeletogenesis of the Vertebrate Limb]] R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier ''Lecture Notes in Computer Science 3305, 543-552 (2004)'' | [[http://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://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 and James A. Glazier, ''Physica A: Statistical and Theoretical Physics 373, 521-532 (2007)'' [[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://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)'' |
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| [[links/index.php?id=18|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]] | [[http://old.compucell3d.org/links/index.php?id=18|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]] |
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| [[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://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)'' |
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| [[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://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)'' |
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| [[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://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)'' |
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| [[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://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)'' |
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| [[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://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)'' |
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| [[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://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)'' |
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| [[links/index.php?cat=talks|Recent Talks]][[links/index.php?cat=biological|Biological Modeling]] | [[http://old.compucell3d.org/links/index.php?cat=talks|Recent Talks]] [[http://old.compucell3d.org/links/index.php?cat=biological|Biological Modeling]] |
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| [[links/index.php?cat=physical|Physical Modeling]] | [[http://old.compucell3d.org/links/index.php?cat=physical|Physical Modeling]] |
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| [[links/index.php?cat=simulations|Simulations Using GGH/CPM Approach]][[links/index.php?cat=background|General Background on Biophysical Modeling and Development]] | [[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]] |
Publications, Talks, Links
Recent Publications and Ph.D. Theses
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)
CompuCell3D - Based Simulations
Computer Simulations of Cell Sorting Due to Differential Adhesion Ying Zhang, Gilberto L. Thomas, Maciej Swat, Abbas Shirinifard, James A. Glazier. PLoS One (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 Computational Biology (2011) [The model and a movie are available]
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)
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
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)
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)
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)
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)
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
From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development
Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jes A. Izaguirre
Computing in Science and Engineering, 9, 50-60 (2007)
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)
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)
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)
Empirical Evaluation of Design Patterns in Scientific Application Kedar Aras, Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2005)
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)
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
- Differential Adhesion and Cell Sorting
Limb Development
Tumor and Cancer
Angiogenesis/Vasculogenesis
Biofilms
- Soap Foams and Liquid Foams