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| ==== 2021 ==== * [[|""]] - Pauli Tikka, ''Ph.D. University of Heidelberg'' (April 2021) ==== 2016 ==== * [[https://search.proquest.com/pqdtglobal/docview/1899473208/21288DDEE6DB40CEPQ/1?accountid=11620|"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 ==== * [[attachment:Belmonte_thesis.pdf|"Modeling Tissue Polarization and Symmetry Breaking in Development and Disease"|&do=get]] – Julio M. Belmonte,'' Ph.D. Indiana University, Department of Physics'' (December, 2014) * [[attachment:Publications/andy_thesis.pdf|Simulation of electrochemical and stochastic systems using just in time compiled declarative languages]] – Andy Somogyi, ''Ph.D. Indiana University, Department of Physics'' (December, 2014) * [[attachment:Publications/CarlosThesis.pdf|Modelos Formales para la Simulación de la Epidermis Humana]] – Carlos Alfonso Castaneda Marroquin, ''Universidad Autonome de Madrid, Spain'' (October, 2014) * [[http://biomodel.project.cwi.nl/news/phd-thesis-margriet-palm-printed|High-throughput simulation studies of angiogenesis]] – Margriet Palm, ''CWI, Amsterdam, Netherlands'' (September, 2014) * [[http://discovery.dundee.ac.uk/portal/files/6142930/THESIS_FINAL_JOHN_KELLY.pdf|Mathematical Modelling of Cancer Growth and Development: Adhesion, Stem Cells and Structure]] – John Watson Kelly, ''University of Dundee, Scotland'' (September, 2014) * [[http://gradworks.umi.com/36/15/3615066.html|Modeling interactions between a tumor cell and its host epithelium]] – Eline Boghaert, ''Princeton University'' (2014) * [[javascript:void(0);/*1510950005222*/|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 ==== * [[https://dspace.lboro.ac.uk/dspace-jspui/handle/2134/12744|Advances in modelling of epithelial to mesenchymal transition]] – T. Abdulla, ''Ph.D Loughborough University'' (June, 2013) * [[http://www.math.leidenuniv.nl/en/theses/369/|Modeling interactions between a tumor cell and its host epithelium]] – D.S. Laman Trip, ''Bachelor degree, Leiden University, Mathematical Institute'' (June, 2013) * [[http://etheses.nottingham.ac.uk/3139/|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) * [[http://www.lume.ufrgs.br/bitstream/handle/10183/87235/000910847.pdf?sequence=1|Modelagem e simulação de mobilidade celular]] – Eduarda D. Susin, ''Bacharel em Física, Universidade Federal do Rio Grande do Sul, Instituto de Física'' (2013) ==== 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) ==== 2011 ==== * [[http://discovery.dundee.ac.uk/portal/en/theses/mathematical-modelling-of-cancer-cell-invasion-of-tissue(9e8221c9-120b-4167-a870-dedade5fe90e).html|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) * [[http://pqdtopen.proquest.com/pqdtopen/doc/863480555.html?FMT=ABS|Essential operating principles of cellular morphogenesis]] – Jesse Aaron Engelberg, ''Ph.D. University of California, San Francisco with the University of California, Berkeley'' (2011) * [[http://bsc-slimy-networks.googlecode.com/hg-history/417c4d75ce9593d210a617dfdf22bd19a3de461a/paper/paper.pdf|Emergent networks: A slime mold simulation]] – Niklas B. Semmler,'' Bachelor Opleiding Kunstmatige Intelligentie, University of Amsterdam, Faculty of Science'' (June, 2011) ==== 2009 ==== * [[http://www.findaphd.com/search/ProjectDetails.aspx?PJID=39242|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 ==== * [[http://search.proquest.com/docview/304800235|Cell positioning in the Drosophila pupal retina]] – David Ernfrid Larson, ''Ph.D. Washington University, Division of Biology and Biomedical Sciences'' (Dec, 2007) * [[http://www.indiana.edu/~bioc/jglazier/docs/student_dissertations/ying_thesis.pdf|Dynamic spatio-temporal interaction of morphogens, forces and growth in embryonic morphogenesis]] – Ying Zhang, ''Ph.D. Indiana University, Department of Physics'' (2007) * [[http://www.mendeley.com/download/public/1324/280554252/1a384fd69b656e0922e40d00ec1fa49971e71ea5/dl.pdf|Tumour growth and response to ionizing radiation in a modified cellular Potts model]] – Daniel Lea,'' Master's Thesis, University of Surrey ''(2007) ==== 2005 ==== * [[http://www3.nd.edu/~izaguirr/papers/ArCI0x.pdf|Empirical Evaluation of Design Patterns in Scientific Application]] – Kedar Aras, ''Master's Thesis, Univ. of Notre Dame, Dept. of Computer Science & Eng.'' (2005) * [[https://www.universiteitleiden.nl/onderzoek/onderzoeksoutput/wiskunde-en-natuurwetenschappen/computational-modeling-of-angiogenesis-from-matrix-invasion-to-lumen-formation|Computational modeling of angiogenesis: from matrix invasion to lumen formation.]] -Sonja E.M. Boas, Ph.D. ''CWI and Leiden University ''(2005) ==== 2004 ==== * [[http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=pdf&doi=10.1.1.226.67|BIOLOGO: A Domain-Specific Language For Morphogenesis]] – Trevor M. Cickovski, ''Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame ''(2004) |||||| | |
CompuCell3D-based Ph.D. and Master Theses
2021
[[|""]] - Pauli Tikka, Ph.D. University of Heidelberg (April 2021)
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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