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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 | ==== 2014 ==== * "Modeling Tissue Polarization and Symmetry Breaking in Development and Disease", Julio M. Belmonte, Ph.D. Indiana University, Department of Physics, December, 2014 |
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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 | * [[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 |
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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) | * [[attachment:CarlosThesis.pdf|MODELOS FORMALES PARA LA SIMULACIÓN DE LA EPIDERMIS HUMANA]], Carlos Alfonso Castaneda Marroquin, ''Universidad Autonome de Madrid, Spain'' (Oct 1st 2014) |
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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) | * [[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) |
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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 | * [[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://gradworks.umi.com/36/15/3615066.html|Modeling interactions between a tumor cell and its host epithelium]], Eline Boghaert, ''Princeton University'', (2014) | * [[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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| [[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) | ==== 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) | * [[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://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://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://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://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) |
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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://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://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) | ==== 2012 ==== |
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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) | * [[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://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.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://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) | |
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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) | ==== 2011 ==== |
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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) | * [[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://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://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://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) | * [[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) |
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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) | ==== 2009 ==== |
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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://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) * [[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) * [[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
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,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 (Oct 1st 2014)
High-throughput simulation studies of angiogenesis Margriet Palm, CWI, Amsterdam, Netherlands (Sept 30th 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)
2014
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 (Feb, 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)
Empirical Evaluation of Design Patterns in Scientific Application – Kedar Aras, Master's Thesis, Univ. of Notre Dame, Dept. of Computer Science & Eng. (2005)
BIOLOGO: A Domain-Specific Language For Morphogenesis – Trevor M. Cickovski, Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2004)