CompuCell3D
CompuCell3D-based Ph.D. and Master Theses
2016
"Integrative Modeling of Microcirculatory Transport and Cell Responses in Liver and Retinal Homeostasis and Disease" - Xiao Fu, Ph.D. Indiana University, Department of Physics (May, 2017)
2014
"Modeling Tissue Polarization and Symmetry Breaking in Development and Disease" – Julio M. Belmonte, Ph.D. Indiana University, Department of Physics (December, 2014)
Simulation of electrochemical and stochastic systems using just in time compiled declarative languages – Andy Somogyi, Ph.D. Indiana University, Department of Physics (December, 2014)
Modelos Formales para la Simulación de la Epidermis Humana – Carlos Alfonso Castaneda Marroquin, Universidad Autonome de Madrid, Spain (October, 2014)
High-throughput simulation studies of angiogenesis – Margriet Palm, CWI, Amsterdam, Netherlands (September, 2014)
Mathematical Modelling of Cancer Growth and Development: Adhesion, Stem Cells and Structure – John Watson Kelly, University of Dundee, Scotland (September, 2014)
Modeling interactions between a tumor cell and its host epithelium – Eline Boghaert, Princeton University (2014)
High-throughput simulation studies of angiogenesis: Reverse engineering the role of tip cell and pericytes in vascular development. – M.M. (Margriet) Palm, Ph.D CWI and Leiden University (2014)
2013
Advances in modelling of epithelial to mesenchymal transition – T. Abdulla, Ph.D Loughborough University (June, 2013)
Modeling interactions between a tumor cell and its host epithelium – D.S. Laman Trip, Bachelor degree, Leiden University, Mathematical Institute (June, 2013)
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 (February, 2013)
Modelagem e simulação de mobilidade celular – Eduarda D. Susin, Bacharel em Física, Universidade Federal do Rio Grande do Sul, Instituto de Física (2013)
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)
2011
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)
Essential operating principles of cellular morphogenesis – Jesse Aaron Engelberg, Ph.D. University of California, San Francisco with the University of California, Berkeley (2011)
Emergent networks: A slime mold simulation – Niklas B. Semmler, Bachelor Opleiding Kunstmatige Intelligentie, University of Amsterdam, Faculty of Science (June, 2011)
2009
Cell based 3 dimensional computational model for gastrulation in chick embryos – Willemijn Magda Elly Maria Spoor, Ph.D. Dundee University, College of Life Sciences (2009)
2007
Cell positioning in the Drosophila pupal retina – David Ernfrid Larson, Ph.D. Washington University, Division of Biology and Biomedical Sciences (Dec, 2007)
Dynamic spatio-temporal interaction of morphogens, forces and growth in embryonic morphogenesis – Ying Zhang, Ph.D. Indiana University, Department of Physics (2007)
Tumour growth and response to ionizing radiation in a modified cellular Potts model – Daniel Lea, Master's Thesis, University of Surrey (2007)
2005
Empirical Evaluation of Design Patterns in Scientific Application – Kedar Aras, Master's Thesis, Univ. of Notre Dame, Dept. of Computer Science & Eng. (2005)
Computational modeling of angiogenesis: from matrix invasion to lumen formation. -Sonja E.M. Boas, Ph.D. CWI and Leiden University (2005)
2004
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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