== CompuCell3D-based Ph.D. and Master Theses == ==== 2024 ==== * [[https://doi.org/10.57709/37395530|"Modelling Three Dimensional Morphology of Retinal Pigment Epithelium"|target=_blank]]. Akinwale Famotire, Masters Thesis, Georgia State University, 2024. doi: https://doi.org/10.57709/37395530 * [[https://hammer.purdue.edu/articles/thesis/_b_A_MULTISCALE_MODEL_TO_STUDY_ATP-INDUCED_CALCIUM_SIGNALING_IN_LARVAL_ZEBRAFISH_TAILFIN_WOUND_RESPONSE_b_/26396806|"A Multiscale Model To Study Atp-Induced Calcium Signaling In Larval Zebrafish Tailfin Wound Response"|target=_blank]]. Mothieshwar Jayaraman Krishnan. Purdue University Graduate School. Masters Thesis. doi: [[https://doi.org/10.25394/PGS.26396806.v1|10.25394/PGS.26396806.v1|target=_blank]] ==== 2023 ==== * [[https://lume.ufrgs.br/handle/10183/266301|"CompuCell3D model of cell migration reproduces chemotaxis"|target=_blank]]. Pedro Cenci Dal Castel. Masters Thesis, Instituto de Fısica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil, 2023. * [[attachment:Sharmilla_Chandrasegaran_thesis_2024.pdf|"Computational systems biology approaches to investigate cellular senescence"|&do=get]] - Sharmilla Chandrasegaran, ''Ph.D. Newcastle University'' (September 2023) * [[attachment:Juliano_Ferrari_Gianlupi_thesis_2023.pdf|"Breaking Barriers in Multiscale Agent-Based Models: Effects of Cell Individuality on Viral Infection Treatment and A Path for Cross-Platform Validation"|&do=get]] - Juliano Ferrari Gianlupi, ''Ph.D. Indiana University'' (August 2023) ==== 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) * [[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]]) * [[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) ==== 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) ==== 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) ==== 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) ==== 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)