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| ==== 2021 ==== * [[attachment:Josua Oscar Aponte-Serrano_thesis_2021.pdf|"Multicellular Multiscale Spatial Modeling of The Immune Response to Pathogens And Cancer"|&do=get]] - Josua Oscar Aponte-Serrano, ''Ph.D. Indiana University'' (December 2021) |
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| "Modeling Tissue Polarization and Symmetry Breaking in Development and Disease", Julio M. Belmonte, Ph.D. Indiana University, Department of Physics, December, 2014 | * [[attachment:EngstlerElena_Thesis2021.pdf|"Developing a multi scale cellular automata simulation model of a vascularised brain tumour environment to predict angiogenic potential of brain endothelial cells"|&do=get]] - Elena Sophie Engstler, ''MSc in Neuroscience King's College London, University of London'' (September 2021) (and a [[attachment:EngstlerElena_Poster2021.pdf|poster|&do=get]]) |
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| [[attachment:andy_thesis.pdf|Simulation of electrochemical and stochastic systems using just in time compiled declarative languages]], Andy Somogyi,Indiana University, Department of Physics, December, 2014 | * [[https://doi.org/10.11588/heidok.00029457|"Modelling of Cell Movements and Aggregations During Early Nephrogenesis"]] - Pauli Tikka, ''Ph.D. University of Heidelberg'' (April 2021) |
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| [[attachment:CarlosThesis.pdf|MODELOS FORMALES PARA LA SIMULACIÓN DE LA EPIDERMIS HUMANA]], Carlos Alfonso Castaneda Marroquin, ''Universidad Autonome de Madrid, Spain'' (Oct 1st 2014) | ==== 2020 ==== * [[https://www.proquest.com/openview/1ac8883b621902b85ae7e5f4fbca2401/1.pdf?cbl=51922&diss=y&loginDisplay=true&loginDisplay=true&pq-origsite=gscholar|"Modeling Cell Mediated Interactions in Epithelial Tissue Organization and Repair"]] Priyom Adhyapok, ''Ph.D. Indiana University, Department of Physics'' (August 2020) |
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| [[http://biomodel.project.cwi.nl/news/phd-thesis-margriet-palm-printed| High-throughput simulation studies of angiogenesis]] Margriet Palm, ''CWI, Amsterdam, Netherlands'' (Sept 30th 2014) | ==== 2018 ==== * [[https://shareok.org/handle/11244/317617|"Computational Modeling Of Metastatic Cancer Migration Through A Remodeling Extracellular Matrix"]] Yen T. Nguyen ''Master of Science'' Chemical Engineering Oklahoma State University Stillwater, Oklahoma (July 2018) |
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| [[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 | ==== 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) |
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| [[http://gradworks.umi.com/36/15/3615066.html|Modeling interactions between a tumor cell and its host epithelium]], Eline Boghaert, ''Princeton University'', (2014) | ==== 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) |
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| [[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) | * [[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) |
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| [[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) | * [[attachment:Publications/CarlosThesis.pdf|Modelos Formales para la Simulación de la Epidermis Humana]] – Carlos Alfonso Castaneda Marroquin, ''Universidad Autonome de Madrid, Spain'' (October, 2014) |
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| [[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'' (Feb, 2013) | * [[http://biomodel.project.cwi.nl/news/phd-thesis-margriet-palm-printed|High-throughput simulation studies of angiogenesis]] – Margriet Palm, ''CWI, Amsterdam, Netherlands'' (September, 2014) |
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| [[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) | * [[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) |
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| [[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://gradworks.umi.com/36/15/3615066.html|Modeling interactions between a tumor cell and its host epithelium]] – Eline Boghaert, ''Princeton University'' (2014) |
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| [[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) | * [[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) |
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| [[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) | ==== 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) |
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| [[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://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) |
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| [[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) | * [[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) |
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| [[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) | * [[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) |
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| [[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) | ==== 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) |
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| [[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.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) |
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| [[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) | ==== 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) |
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| [[http://old.compucell3d.org/links/index.php?id=25|Empirical Evaluation of Design Patterns in Scientific Application]] – Kedar Aras, ''Master's Thesis, Univ. of Notre Dame, Dept. of Computer Science & Eng.'' (2005) | * [[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) |
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| [[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) | * [[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
"Multicellular Multiscale Spatial Modeling of The Immune Response to Pathogens And Cancer" - Josua Oscar Aponte-Serrano, Ph.D. Indiana University (December 2021)
"Developing a multi scale cellular automata simulation model of a vascularised brain tumour environment to predict angiogenic potential of brain endothelial cells" - Elena Sophie Engstler, MSc in Neuroscience King's College London, University of London (September 2021) (and a poster)
"Modelling of Cell Movements and Aggregations During Early Nephrogenesis" - Pauli Tikka, Ph.D. University of Heidelberg (April 2021)
2020
"Modeling Cell Mediated Interactions in Epithelial Tissue Organization and Repair" Priyom Adhyapok, Ph.D. Indiana University, Department of Physics (August 2020)
2018
"Computational Modeling Of Metastatic Cancer Migration Through A Remodeling Extracellular Matrix" Yen T. Nguyen Master of Science Chemical Engineering Oklahoma State University Stillwater, Oklahoma (July 2018)
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)