Publications, Talks, Links

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)

CompuCell3D - Based Simulations

Vascular Networks Due to Dynamically Arrested Crystalline Ordering of Elongated Cells Palm, Margriet M, and Roeland M H Merks, Phyiscal Review E, 87 (2013), 012725

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)

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

Computational Modeling of Angiogenesis: Towards a Multi-Scale Understanding of Cell–Cell and Cell–Matrix Interactions Boas, Sonja E M, Margriet M Palm, Pieter Koolwijk, and Roeland M H Merks, Mechanical and Chemical Signaling in Angiogenesis (Springer, 2012), pp. 161–183

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)

Presentations and Conferences

Toward the 3D Virtual Cell - UC San Diego - Atkinson Hall, December 13-14, 2012

Integration with SBW

We have conducted a preliminary integration of CompuCell3D with

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.

List of Movies (Note: simulator is an ODE solver of metabolic pathways):

• Movie 1:109 Cells and one simulator

• Movie 2:109 cells and 109 simulators (same initial conditions)

• Movie 3:109 cells and 109 simulators (different initial conditions)

Movies created by Frank Bergmann

Related Links

Recent Talks

Biological Modeling

• Differential Adhesion and Cell Sorting

• Limb Development

• Tumor and Cancer

• Angiogenesis/Vasculogenesis

• Biofilms

Physical Modeling

• Soap Foams and Liquid Foams

Simulations Using GGH/CPM Approach

General Background on Biophysical Modeling and Development