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| ==== 2025 ==== * [[https://libraetd.lib.virginia.edu/public_view/kh04dr33b|Multicellular Agent-Based Computational Modeling Approaches to Investigate Cell- and Tissue Scale Effectors of Collective Migration Within an In Vivo Context|target=_blank]]. Tien Comlekoglu, PhD, Biomedical Engineering - School of Engineering and Applied Science, University of Virginia; 2025. * [[https://webthesis.biblio.polito.it/34724/|A Cellular Potts Model to describe tumor infiltration in confined in vivo tissues|target=_blank]]. Sofia Giordano, Masters Thesis, Politecnico di Torino, 2025. * [[https://www.repository.cam.ac.uk/items/cd26a194-3786-409a-a7c9-d66746f4f3e5|Clonal Dynamics in Barrett's Oesophagus and Oesophageal Adenocarcinoma|target=_blank]]. E Black. Ph.D. Thesis, 2025. doi.org/10.17863/CAM.115012 * [[https://repositorioinstitucional.buap.mx/items/eeded8f2-b6cb-4a57-a93b-66bf5cb83aba|A cellular model for the mechanistic simulation of biological response to radiation damage|target=_blank]]. OR García. Ph.D. Thesis, 2025 (spanish) |
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* [[https://www.proquest.com/docview/3067599500?fromopenview=true&pq-origsite=gscholar&sourcetype=Dissertations%20&%20Theses|Modeling the Spatio -Temporal Effect of 2,3, 7,8 Tetrachlorodibenzo-P-Dioxin on Hepatic Gene Expression|target=_blank]] Marri, Daniel Kwabena. Michigan State University PhD Dissertation. !ProQuest Dissertations & Theses, 2024. * [[https://www.repository.cam.ac.uk/items/cd26a194-3786-409a-a7c9-d66746f4f3e5|Clonal Dynamics in Barrett’s Oesophagus and Oesophageal Adenocarcinoma|target=_blank]]Emily Black, PhD Thesis Emmanuel College University of Cambridge (2024). https://doi.org/10.17863/CAM.115012 |
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| * [[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]] |
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| * [[https://lume.ufrgs.br/handle/10183/266301|"CompuCell3D model of cell migration reproduces chemotaxis"|target=_blank]]. Pedro Cenci Dal Castel. Masters Thesis, Instituto de F´ısica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil, 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. |
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==== 2019 ==== * [[https://pure.uva.nl/ws/files/36020905/Thesis.pdf|"The Emergence of Biofilms: Computational and Experimental Studies"|tarfget=_blank]]. Sheraton Muniraj, V. ''PhD Thesis, University of Amsterdam'' (June 2019) |
CompuCell3D-based Ph.D. and Master Theses
2025
Multicellular Agent-Based Computational Modeling Approaches to Investigate Cell- and Tissue Scale Effectors of Collective Migration Within an In Vivo Context. Tien Comlekoglu, PhD, Biomedical Engineering - School of Engineering and Applied Science, University of Virginia; 2025.
A Cellular Potts Model to describe tumor infiltration in confined in vivo tissues. Sofia Giordano, Masters Thesis, Politecnico di Torino, 2025.
Clonal Dynamics in Barrett's Oesophagus and Oesophageal Adenocarcinoma. E Black. Ph.D. Thesis, 2025. doi.org/10.17863/CAM.115012
A cellular model for the mechanistic simulation of biological response to radiation damage. OR García. Ph.D. Thesis, 2025 (spanish)
2024
Modeling the Spatio -Temporal Effect of 2,3, 7,8 Tetrachlorodibenzo-P-Dioxin on Hepatic Gene Expression Marri, Daniel Kwabena. Michigan State University PhD Dissertation. ProQuest Dissertations & Theses, 2024.
Clonal Dynamics in Barrett’s Oesophagus and Oesophageal AdenocarcinomaEmily Black, PhD Thesis Emmanuel College University of Cambridge (2024). https://doi.org/10.17863/CAM.115012
"Modelling Three Dimensional Morphology of Retinal Pigment Epithelium". Akinwale Famotire, Masters Thesis, Georgia State University, 2024. doi: https://doi.org/10.57709/37395530
"A Multiscale Model To Study Atp-Induced Calcium Signaling In Larval Zebrafish Tailfin Wound Response". Mothieshwar Jayaraman Krishnan. Purdue University Graduate School. Masters Thesis. doi: 10.25394/PGS.26396806.v1
2023
"CompuCell3D model of cell migration reproduces chemotaxis". Pedro Cenci Dal Castel. Masters Thesis, Instituto de Fısica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil, 2023.
"Computational systems biology approaches to investigate cellular senescence" - Sharmilla Chandrasegaran, Ph.D. Newcastle University (September 2023)
"Breaking Barriers in Multiscale Agent-Based Models: Effects of Cell Individuality on Viral Infection Treatment and A Path for Cross-Platform Validation" - Juliano Ferrari Gianlupi, Ph.D. Indiana University (August 2023)
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)
2019
"The Emergence of Biofilms: Computational and Experimental Studies". Sheraton Muniraj, V. PhD Thesis, University of Amsterdam (June 2019)
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)
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)