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The Biomodeling and Biosystems Analysis Group

Group members

 

Team leader

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 M.Sc. 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. 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.


Postdocs

Enrico Sandro Collizi will work in our team at U Leiden and CWI 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 Ph.D 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.

Ph.D students

Claudiu Antonovici is a PhD student at the Mathematical Institute (MI) and the Institute for Biology Leiden (IBL), and is 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.


Koen Schakenraad is a Ph.D student at the Mathematical Institute and the Leiden Institute of Physics of Leiden University, where he works on analytic models of cell shape. His supervisors are Luca Giomi (LION) and Roeland Merks (MI). Koen hold a Master's degree in theoretical physics from Technical University Eindhoven (TU/e). 

Leonie van Steijn
is a Ph.D student at the Mathematical Institute of Leiden University, where she works on modeling of the wasting syndrome in the zebrafish. 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 Ph.D project with us, Leonie worked as an M.Sc. 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.


Esmée Vendel
is a PhD student of the Mathematical Institute of Leiden University and is working on the application of mathematical models to pharmacology and tumor cell competition. She is co-supervised by Vivi Rottschäfer, Arjen Doelman and Roeland Merks of the Mathematical Institute, and by Liesbeth the Lange of the Leiden Academic Center for Drug Research (LACDR). Esmée received her M.Sc. degree in biopharmaceutical sciences from Leiden University

 

M.Sc. students / B.Sc. students / Stagiers

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

Sonja Boas was a Ph.D 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 Ph.D degree on December 22nd, 2015 from Leiden University. Sonja received her M.Sc. 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 is currently working as a consultant at Equalis Strategy & Modeling in Utrecht, The Netherlands. 

Cong Chen
worked in our group as an M.Sc. 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.

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). Bert aims to integrate metabolism in our cell-based angiogenesis models in order to study the anti-angiogenic potential of altering endothelial cell metabolism. This already successful and intense collaboration will be maintained in the future. Bert received his M.Sc.-degree in Bioscience Engineering from the KU Leuven, focusing on the metabolism of endothelial cells during his master thesis work at the VRC.

Josephine Daub has done a research internship in our group as a M.Sc. 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.

Erik van Dijk has done a research internship in our group as a M.Sc. 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.

Panos Firmpas was an M.Sc. 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.

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.

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 M.Sc 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.

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 is IT supporter at CWI and in this role still regularly interacts with our group.

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 M.Sc. student Bioinformatics and Systems Biology at VU University Amsterdam.

Floriane Lignet has been a visiting Ph.D. 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 M.Sc degree in Pharmacology at the University of Lyon in 2009.

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. Her is currently pursuing a Masters of Computational Science at the University of Amsterdam.

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.

Ioana Niculescu has done a research internship in our group as a M.Sc. 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 Ph.D student in theoretical immunology at the Theoretical Biology group of Prof. Rob de Boer at Utrecht University.

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.

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 M.Sc.-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 is currently a postdoc in Dirk Drasdo's team at INRIA Rocquencourt in France.

Kleopatra Pirpinia worked as an intern in our group while she was M.Sc. 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.

Iraes Rabbers is 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.

Philip Rutten
was working our group as an M.Sc. 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.


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.

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.

Lisanne Rens is a Ph.D student working on cell-based computational models of mechanical and chemical cell-ECM interactions during blood vessel growth. Lisanne received her M.Sc. degree in Applied Mathematics from Delft University of Technology. During her master studies she gained some experience in mathematical biology, such as population dynamics and cell migration models.

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 Ph.D 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.

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.

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 M.Sc degree in Biomedical Engineering from EIndhoven University of Technology; he is now working as an Analyst at Accenture.

Harold (H.B.) Wolff worked in our group as a "pre-doc" on vertex-based models of epithelial tissues. Harold obtained his M.Sc. 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 M.Sc. 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.

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.