Principal Investigator

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Roeland Merks is a professor of Multiscale Mathematical Biology at the Mathematical Institute and the Institute for Biology of Leiden University. Merks works on a variety of topics, including plant development, cell-ECM interactions during angiogenesis, and cell-based modeling of branching growth. Roeland obtained his MSc degree in Biology from Utrecht University, with specializations in Theoretical BIology and Developmental Biology. After a nine months’ research stay at Tokyo University, Japan, he moved to  the University of Amsterdam for a PhD project on computational modeling of coral growth in the group of Prof. Dr. Peter Sloot. His postdocs were with Prof. James Glazier in the Dept. Physics and Biocomplexity Institute at Indiana University Bloomington, USA, and at the VIB Dept. Plant Systems Biology and Ghent University in Belgium, where he worked with Profs. Dirk Inzé, Gerrit Beemster, and Yves Van de Peer. He became a young group leader at VIB in 2007. In 2008 he moved to CWI in Amsterdam, the Dutch national center for mathematics and computer science,  to set up the central modeling group of the Netherlands Consortium for Systems Biology, where he received tenure in 2012. Since 2014 Roeland has been part-time full professor at Leiden University and since July 2018 he has moved to Leiden full-time. From 2015-2018 he was president of the European Society for Mathematical and Theoretical Biology. Merks is Associate Editor of PLoS Computational Biology and Academic Editor of PLoS ONE. He received a Marie Curie-Skłodowska Intra-European Fellowship in 2006, a European Reintegration Grant in 2008, an NWO Vidi grant in 2010, and an NWO Vici grant in 2018, and is co-PI of an NWO GROOT since 2020.

Postdocs

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Enrico Sandro Colizzi works on mathematical problems of scale bridging, as they arise in the study of the origins and evolutional of life. Enrico's position is funded by the Origins Center, a national, interdisciplinary collaboration for the study of origins and evolution of life, planets and the universe, funded by the Dutch Science Agenda. Enrico obtained his PhD in bioinformatics and theoretical biology from Utrecht University on 21 december 2016, where he worked with Prof. dr. P. Hogeweg on the multilevel theory of prebiotic evolution.

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Erika Tsingos wants to understand how the extracellular matrix affects cell self-organization and morphogenesis. She investigates this question in the context of angiogenesis, the formation of new blood vessels. She combines experiments in zebrafish embryos with in silico modelling to dissect how chemical and physical properties of the cellular environment regulate blood vessel formation. Erika holds a Master’s degree in Systems Biology from Heidelberg University in Germany where she also earned her PhD working on growth of the retina in medaka fish.

Research Staff

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Roxane Boyer works as a Bioinformatician at the Institute of Biology of Leiden (IBL). She assists several teams at IBL in carrying out their bioinformatic analyses and in implementing new bioinformatic tools. Roxane previously worked on the sequencing platform of Toulouse, France, where she was in charge in developing and maintaining a transfer pipeline for all data generated by Oxford Nanopore technologies sequencers. She also worked in the Prud'homme team in the Institute of Developmental Biology of Marseille, France, where she was in charge of assembling and annotating the Drosophila suzukii genome using Pacific Bioscience reads. She is co-supervised by Bastienne Vriesendorp and Roeland Merks.

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Babette de Jong works as a senior researcher in our group. With a background in Cell Biology and Advanced Microscopy she contributes to establishing and maintaining in vitro and in vivo experiments to research angiogenesis. By directly coupling endothelial cell culture and Zebrafish models to our in silico work on angiogenesis, we aim for high-speed optimization of both computational and experimental predictions. Babette holds a Master’s degree in Biomedical Sciences from the University of Amsterdam and did her PhD in Biophysics in the group of John van Noort, Leiden University. During her PhD research she explored the implementation of multiscale and multimodal approaches to study the mechanics of repetitive DNA elements, such as nucleosomes and G quadruplexes.

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Bastienne Vriesendorp works as a Facility Manager Bioinformatics at the Institute for Biology of Leiden University (IBL). She facilitates bioinformatic analyses within the institute by organizing the infrastructure and providing guidance on the implementation and execution of specific tasks. Bastienne has a background in biosystematics and bioinformatics and worked mainly with plants and industrial food bacteria. Prior to this position she worked as a bioinformatician within biotech company Corbion, mainly focusing on lactic-acid producing bacteria and fungi. She has also experience in teaching, at secondary schools and at the Marine institute of Quelimane, Mozambique, where she taught classes on phycology and biosystematics. Bastienne obtained her PhD in phylogenetics from Wageningen University and did a postdoc in Columbus, Ohio at the Dentistry Department of the Ohio State University, linking oral bacteria to diseases.

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Guayo Peerdeman is a bioinformatician interested in open source software development related to bioinformatics. Guayo likes to tackle problems by developing new methods to further the development of software techniques used during research. Right now, he works on developing a library called libCellShape. The library uses algorithms to allow lattice based and vertex based cellular modeling frameworks to share snapshots of their simulations. Guayo is supervised by Roeland Merks.

PhD students

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Daipeng Chen is a double PhD student at the Mathematical Institute of Leiden University and the School of Mathematics and Statistics of Xi’an Jiaotong University, in Xi’an City, P.R. China. Currently, he is working on an integrated study of multiscale computational modeling and biomedical data analysis on angiogenesis. He is co-supervised by Roeland Merks and by David Baker of Leiden University Medical Center and Yanni Xiao of Xi’an Jiaotong University.

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Durjay Pramanik works on simulations of endothelial cell behavior and durotaxis using a hybrid Cellular Potts Model with components of focal adhesions (FA) and the extracellular matrix (ECM) modelled by Finite Element Method (FEM). He is extending this model to get new insights into pairwise interaction and the collective behavior of endothelial cells in varying ECM environments. Durjay holds a Bachelor’s degree in Biology with a minor in Physics and a Master’s degree in Biology, both from the Indian Institute of Science (IISc, Bangalore).

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Leonie van Steijn is a PhD student at the Mathematical Institute of Leiden University, where she works on modeling (immune) cell movement and modeling zebrafish metabolism. She is co-supervised by Roeland Merks and by Herman Spaink of the Institute for Biology Leiden (IBL) and Fons Verbeek of the Leiden Institute for Advanced Computer Science (LIACS). Before starting her PhD project with us, Leonie worked as an MSc student of the master track Theoretical Biology and Bioinformatics at Utrecht University. She modelled the effects of broad- and narrow-spectrum antibiotics on the gut microbiota. She has prior experience with stochastic modelling in population dynamics. Leonie holds a Bachelor degree in Mathematics with a minor in Biology, and a Masters in Theoretical Biology and Bioinformatics.

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Tessa Vergroesen is a PhD student at the Institute for Biology of Leiden University (IBL) working on the experimental side of our research projects on angiogenesis. She investigates the effect of modifications of the extracellular matrix on the in vitro and in vivo structures of new blood vessel networks. She is supervised by Roeland Merks. Tessa holds a Bachelor's and Masters degree in Nanobiology from the Erasmus University Rotterdam and the Delft University of Technology.

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David Versluis is a PhD student at the Institute for Biology of Leiden University (IBL) on the subject of multiscale modelling of the gut microbiota of infants, in a collaborative project with FrieslandCampina. He holds a Master's degree in Artificial Intelligence and a Bachelor's degree in Biology, both from Utrecht University. David is supervised by Roeland Merks (IBL).




MSc students / BSc students / Interns

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Richard Kok works on efficient tracking of the vascular network. These updates will in turn lead to dynamic updates of the Poiseuille flow, based on the differences between consecutive graphs. Richard is a master student in Bioinformatics at Leiden University and has followed a minor in technical computer science. Previously he did an internship on machine learning techniques applied on SNP's in the plant genome. Richard is supervised by Roeland Merks.

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Clair Wijtkamp is a master student at the Mathematical Institute of Leiden. She works on the subject of the effect of mucus on the gut microbiota of infants using a multiscale modelling approach. She holds a bachelor’s degree in biomedical sciences and mathematics, both from Leiden University. Clair is supervised by David Versluis and Roeland Merks.

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We regularly host Bachelor and Masters students in Mathematics from the Mathematical Institute, Universiteit Leiden (UL) and Bachelor students in bioinformatics from the Hogeschool Leiden (HL). Students of the past years include Sebastiaan Derksen (HL Bioinformatics), Yvon Doolaard (UL Mathematics),  Jan Jansen (UL Mathematics), Diederik Laman Trip (UL Mathematics and Life Sciences and Technology, Leiden/Delft), Christiaan van der Niet (HL Bioinformatics), Jurgen Rinkel (UL Mathematics),  Bastiaan van der Roest (UL Mathematics),  Mathé Zeegers (UL Mathematics and Computer Science).

Alumni - Postdocs

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Milan van Hoek worked in our group as a postdoc on computational modeling of microbial metabolism, combining individual-based modeling with detailed modeling of intracellular metabolism. After obtaining his MSc degree in Theoretical Physics, he obtained his PhD at Utrecht University in the group of prof. P. Hogeweg, where he used this approach to study evolution of the lac operon of Escherichia coli and evolution of yeast after its whole genome duplication. At CWI he uses similar techniques to study gut microbiota metabolism. His focus was on how metabolic diversity can arise and be maintained in the gut microbiota. Milan now works as a scientific programmer at Alten PTS.

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René van Oers obtained his MSc in Biomedical Engineering at the Eindhoven University of Technology (TU/e), where he continued to do his PhD research on the topic of bone remodelling. During this work he used finite-element-based computer simulations to explain how bone cells adapt the bone structure to mechanical loads. His postdoc research in our group focused on integrating the biomechanics of the extracellular matrix within our angiogenesis models. Currently René works as a postdoctoral researcher in biomechanics at ACTA, the Amsterdam dental school.

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András Szabó has worked in our group as a postdoc on the evolutionary development of tumor growth. Using cell-based modelling, he is exploring the collective behavior of heterogeneous cell aggregates emerging from the interaction of the individual cells. In his MSc thesis (ELTE, Budapest) he presented a cell-based computational model for the spatial network formation of tissue cells. His PhD (ELTE, Budapest) is on modeling vasculogenesis and collective cell behavior with the cellular Potts model. During his PhD years he worked in close collaboration with the Kansas University Medical Center on various experimental aspects of vasculo- and embryogenesis in the quail model. András obtained a Marie Curie Intra-European Fellowship for his second postdoc in the Roberto Mayor lab at University College London. For more details, see his personal webpage.

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Hannan Tahir was a postdoc working of the group of Prof. Dr. Theo Smit at the VU University Amsterdam Medical Center. He was based in our group to develop mechanobiological models of somitogenesis using the Cellular Potts model. After that he worked as a postdoc in a public-private partnership with the Leiden-based start-up SysBioSim to work on multicellular models of kidney fibrosis.

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Séverine Urdy is interested in the morphogenetic mechanisms which can account for the patterns of morphological diversity at different spatial and temporal scales (development, populations and taxa). She received her PhD from the University of Zürich, Switzerland, where she continued as a post-doc to study the relationships between growth and form of the molluscan shells from a theoretical, experimental and comparative point of view. She is pursuing her research at the CWI to develop a cell-based modelling approach of molluscan shell growth, with a focus on the links between shell shape and the mechanical properties of the mantle, the soft thin elastic tissue which secretes the shell. Séverine currently works as a postdoc in Anthony Hunt's lab at the University of California, San Francisco. For more information, see her personal webpage.

Alumni - PhD Students

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Sonja Boas was a PhD student in our group working on cell-based, computational models of cell-ECM interactions during blood vessel growth in collaboration with Dr. P. Koolwijk at the VUMC. She has obtained her PhD degree on December 22nd, 2015 from Leiden University. Sonja received her MSc degree in Life Sciences from the University of Amsterdam, and holds a Bachelor degree in Biomedical Sciences, also from the University of Amsterdam. In addition, she completed the first year of Econometry and Operational Research at the VU University Amsterdam. Sonja currently works as consultant at Equalis Strategy & Modeling in Utrecht, The Netherlands. Her PhD thesis, entitled "Computational modeling of angiogenesis : from matrix invasion to lumen formation" is available from the Leiden University Repository.

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Margriet Palm worked in our group as a PhD student  on cell-based modeling of angiogenesis. In this research she developed models of how cell behavior  drives angiogenesis. Margriet received her MSc-degree in Biomedical Engineering from Eindhoven University of Technology. She wrote her Master's thesis on spatial and temporal modeling of chemical reaction networks inside cells at the same institute in the Biomodelling and Bioinformatics group. Margriet received her PhD from Leiden University of September 30th. She has worked as a postdoc in Joost Beltman's teeam at the Leiden Academic Centre for Drug Research (LACDR) at Leiden University, and is currently Scientific Programmer at Electric Ant Lab. Margriet's PhD thesis, entitled "High-throughput simulation studies of angiogenesis - Reverse engineering the role of tip cells and pericytes in vascular development" is available from the Leiden University Repository.

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Lisanne Rens worked in our team as a PhD student working on cell-based computational models of mechanical and chemical cell-ECM interactions during blood vessel growth. Lisanne received her MSc degree in Applied Mathematics from Delft University of Technology. As a PhD in our group Lisanne has worked on modeling mechanical cell-extracellular matrix interactions. She has received her PhD from Leiden University on June 27th 2018, and she is currently working as a postdoctoral fellow at the Mathematics Department of the University of British Columbia in Vancouver, Canada. Her PhD thesis, entitled "Multiscale mathematical biology of cell-extracellular matrix interactions during morphogenesis" is available from the Leiden University Repository.

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Koen Schakenraad was a PhD student at the Mathematical Institute (MI) and the Leiden Institute of Physics (LION) of Leiden University, where he worked on analytic models of cell shape. His supervisors were Luca Giomi (LION) and Roeland Merks (MI). Koen holds a Master's degree from Eindhoven University of Technology (TU/e) in applied physics, with a specialization in the theoretical physics of soft and biological materials. Koen has received his PhD thesis from Leiden University of May 13th 2020. His PhD thesis, entitled "Anisotropy in cell mechanics" is available from the Leiden University Repository

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Esmée Vendel was a PhD student of the Mathematical Institute of Leiden University. She has worked on the application of mathematical models to pharmacology and tumor cell competition. She was co-supervised by Vivi Rottschäfer and Roeland Merks of the Mathematical Institute, and by Liesbeth the Lange of the Leiden Academic Center for Drug Research (LACDR). Esmée received her MSc degree in biopharmaceutical sciences from Leiden University, and she received her PhD degree on December 17, 2019. Currently she works as a Consultant Pharmacometrician at LAP&P Consultants. Her PhD thesis, entitled "Prediction of spatial-temporal brain drug distribution with a novel mathematical model" is available from the Leiden University Repository.

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Claudiu Antonovici was a PhD student at the Mathematical Institute (MI) and the Institute for Biology Leiden (IBL), co-supervised by Remko Offringa (IBL) and Sander Hille (MI). Using mathematical modeling, Claudiu asks how and why stomata, the leaf's breathing openings, become evenly spaced. The spacing is due to tightly regulated, asymmetrical cell divisions, which Claudiu is modeling in a vertex-based model based on our framework VirtualLeaf. The spacing of stomata must also be such that the cells in the leaf have good access to carbon and can get rid of the oxygen during photosynthesis, while minimizing water loss. To this end, Claudiu uses transport models together with optimization approaches to get more insight into the 'why' of stomatal patterning.

Alumni - Research and Support Staff

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Michael Guravage helped establish good software engineering practices and workflow management within the group including source code release management and documentation. Michael works on VirtualLeaf, an Open Source framework for cell-based modeling of plant tissue growth and development,  is developing an on-line repository for Simulation Experiment Descriptions based on SED-ML. He currently works as IT supporter at CWI.

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Roy Masius worked in our group as senior research technician. With a background in Molecular Biology, he worked on adding experimental biology to the group. Using Endothelial Cell culture and Zebrafish modelling we aim to connect the computational models for angiogenesis to in vitro and in vivo angiogenesis. The direct feedback between the experimental and computational allows for high speed optimization of models and experimental predictions. Roy holds a Master’s degree in Life Science and Biology from Leiden University, and obtained his PhD degree from Erasmus University Rotterdam studying in the group of Prof. Dr. Vincenzo Bonifati with the Department of Clinical Genetics. During the PhD research he worked on modelling Parkinson’s disease in vitro, by generating dopaminergic neurons from patient derived iPSCs.

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Frederik Van Parijs worked in our group as a research assistant. In collaboration with Prof. Wout Boerjan of the VIB Dept. Plant Systems BIology and Ghent University, and Prof. John Ralph of the University of Wisconsin, he has developed simulation models lignin polymerization. He later moved to modeling plant development using VirtualLeaf. Frederik now works as a research assistant at the Universiteit Antwerpen.

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Harold (H.B.) Wolff worked in our group as a "pre-doc" on vertex-based models of epithelial tissues. Harold obtained his MSc degree in Systems Biology at the VU University in Amsterdam, and obtained a propedeuse degree in Medicine and a Bachelor’s degree in Bio-Medical Sciences at the VU university, including extracurricular courses in informatics and biophysics. Harold has done his MSc work in our group on analyzing and modeling cell contraction mechanisms during development of the frog Xenopus leavis, work that he continued as a research assistant at the University of Pittsburgh in the lab of Prof. Lance Davidson.

Alumni - Guests

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Takashi Akanuma

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Bert Cruys was a visiting PhD student from the group of Prof. Dr. P. Carmeliet (Vesalius Research Center; VRC) at the University of Leuven (KU Leuven). For his visit he received an EMBO Short Term Fellowship. Bert aims to integrate metabolism in our cell-based angiogenesis models in order to study the anti-angiogenic potential of altering endothelial cell metabolism. Bert received his MSc-degree in Bioscience Engineering from the KU Leuven, focusing on the metabolism of endothelial cells during his Master's thesis work at the VRC.

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Floriane Lignet has been a visiting PhD. student from the Mathematics unit of the Ecole Normale Supérieure of Lyon to work on the integration of models of tumorigenic molecular pathways with cell-based models of tumor growth. Floriane works on multi-scale modeling of tumor growth and angiogenesis, from the molecular reactions to the tissular processes. She obtained an engineer degree in Bio-Informatics and Modeling at the INSA of Lyon, and a MSc degree in Pharmacology at the University of Lyon in 2009.

Alumni - Master's students

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Cong Chen worked in our group as an MSc intern of the Computational Science program at the University of Amsterdam. He obtained his Bachelor and Masters degree in biology from the Naval University of Engineering, in Wuhan City, P.R. China. He has been extending the Cellular Potts model with a model for focal adhesions and the cytoskeleton, in collaboration with Dr. Takashi Akanuma from NAIST, Nara, Japan. He currently works as a software engineer at Sim-Industries at Sassenheim, a company specializing in flight simulators.

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Josephine Daub has done a research internship in our group as a MSc student in Computational Science at the University of Amsterdam. She worked on cell-based modeling of ECM-guided angiogenesis. She now works on human evolutionary genomics at the Swiss Institute of Bioinformatics of the Universität Bern.

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Erik van Dijk has done a research internship in our group as a MSc student in Bioinformatics at the  VU University Amsterdam. He has developed computational models of tip cell selection during sprouting angiogenesis. After doing a second research internship in the Computational Chemistry group of Daan Frenkel at the University of Cambridge, Erik now works as a PhD student with Dr. Sanne Abeln at VU University.

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Panos Firmpas was an MSc intern studying Computational Science at the University of Amsterdam. He obtained his Bachelor's degree in biology at the University of Athens, Greece. He enjoys applying computational tools to biological problems and is currently working on analysing the evolution of cancer cell groups and how collective behavior emerges from individual characteristics, using a cell-based model. He currently works as a PhD student in the Marie Curie International Training Network "Developmental and Computational Biology" at the Universidad Pablo de Olavide in Sevilla, Spain.

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Robbert Geerts is an M. Sc. student of Systems Biology at the VU University. Co-supervised by Anton Feenstra (VU) and in collaboration with Remko Offringa and Sander Hille of the Plant BioDynamics Laboratory of the Institute of Biology and the Mathematical Institute of Leiden University, Robbert worked with us on the open source framework VirtualLeaf to model the development and patterning formation of stomata in leaves.

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Daniël de Koning worked as intern in our group while he was a B.Sc. student in Bioinformatics of the Hogeschool Leiden. In a collaborative project with Gerard Muyzer of the University of Amsterdam, Daniël developed a computational framework for optimizing culture conditions of microorganisms. He has graduated as Bachelor in Bioinformatics at Hogeschool Leiden on Monday June 16, 2014 and will continue as MSc student Bioinformatics and Systems Biology at VU University Amsterdam.

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Daniël Muysken has worked with us during the academic year 2016-2017 for his Bachelor thesis in Bioinformatica from Hogeschool Leiden  He has extended our multiscale model of the gut microbiota to work with SBML model and to include interactions with the host. He is currently pursuing a Masters of Computational Science at the University of Amsterdam.

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Ioana Niculescu has done a research internship in our group as a MSc student in Computational Science at the University of Amsterdam. In collaboration with Dr. Alfons Hoekstra, Ioana has developed cell-based models of in-stent restenosis. She is now a PhD student in theoretical immunology at the Theoretical Biology group of Prof. Rob de Boer at Utrecht University.

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Christian van de Niet and Sebastiaan Derksen are students of Bioinformatics at the Hogeschool Leiden and are working on cellular Potts models of tumor cell migration in collaboration with Sylvia Ledévédec of the Leiden Academic Center for Drug Research where B.Sc. students Merve Tok and Rick Hennevelt are collecting cell migration data. Christian and Sebastaan's internal supervisor at the Hogeschool Leiden is Bo Blanckenburg.

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Kleopatra Pirpinia worked as an intern in our group while she was MSc student in Mathematics at Utrecht University. She was co-supervised by Odo Dieckmann. As intern our group she has developed an interacting particular system to describe pattern formation in cultures of elongated cells. She has graduated as a Master's of Mathematics at Utrecht University on 27th February 2014 and is now working as a PhD student at CWI and AMC in the group of Peter Bosman.

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Iraes Rabbers worked in our group as an MSc student in Biomolecular Sciences at the VU University in Amsterdam with specializations in Systems Biology and Cell Biology, and obtained a BSc degree in Biology at the VU. Iraes did her research internship in our group, working on a cell-based (3D) model on epithelial branching in the kidneys, using the CompuCell3D environment, and the analysis of this model in order to gain insight into the factors influencing branch morphology.

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Philip Rutten was working our group as an MSc student of Computational Science at the University of Amsterdam. He is developing Lagrangian methods for many-body systems, in order to study morphogenesis in multi-cellular biological systems. Philip has previous experience in the field of architecture and design, where he got acquainted with the concept of morphogenesis as a potential design strategy. He holds a Master degree in Architecture, Building, and Planning from Eindhoven University of Technology and is currently working on his PhD in Computational Science at the University of Amsterdam.

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Remi Verhoeven worked in our group as an MSc intern from Biomedical Engineering at the Eindhoven University of Technology. In our group, Remi has worked on modeling mechanical influences of strain and stress on the evolution of vascular development, for which he coupled the FEBio and CompuCell3D modeling packages. On 22 April 2013 Remi received his MSc degree in Biomedical Engineering from EIndhoven University of Technology; he is now working as an Analyst at Accenture.

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Mathé Zeegers has worked in our team as a Bachelor student in Leiden on kinetic algorithms for the Cellular Potts model, and later as a Masters student at CWI on the mathematical modeling of branching growth of epithelial organs. He has obtained Masters degrees in Mathematics and in Computer Science, and is currently a PhD student on discrete tomography at CWI in the group of Joost Batenburg.