Roeland Merks
Professor of Mathematical biology
- Name
- Prof.dr. R.M.H. Merks
- Telephone
- +31 71 527 7106
- merksrmh@math.leidenuniv.nl
- ORCID iD
- 0000-0002-6152-687X
PhD Candidates
News
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‘Partying is fine but we still need to protest’ -
What do maths and blood clots have to do with each other? -
Simulation of infant gut makes predictions about optimal milk -
Grant opens door to decipher the secret sensory world of plants -
How cells talk by pulling on a fibre network -
‘Building bridges between scientists: that's what we're good at’ -
Roeland Merks new director Lorentz Center -
Correcting each other’s mistakes - why cells stuck together in early evolution -
Cells ‘walk’ to firm ground -
Mathematical model helps to explain the formation of spine and ribs
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Science Groot funding for Leiden scientists -
Leiden biology appreciated with large NWO grants -
Full appointment for Roeland Merks at mathematics and biology -
New technique to study vascular growth -
Roeland Merks wint IgNobel 24/7 battle
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Appointment prof. dr. R.H.M. Merks
Former PhD candidates
Professor of Mathematical biology
- Science
- Mathematisch Instituut
- Mathematisch Instituut
Professor
- Science
- Instituut Biologie Leiden
- IBL Animal Sciences
Director Lorentz Centre
- Science
- Lorentz-Center
- Lorentz-Center
- Cheng S., Jacobs C.G., Mogollón Pérez E.A., Chen D., Sanden J.T. van de, Bretscher K.M., Verweij F., Bosman J.S., Hackmann A., Merks R.M.H., Heuvel J. van den & Zee M. van der (2024), A life-history allele of large effect shortens developmental time in a wild insect population, Nature ecology & evolution 8: 70-82.
- Vergroesen T.M., Vermeulen V. & Merks R.M.H. (2024), Falsifying computational models of angiogenesis through quantitative comparison with in vitro models. bioRxiv. [working paper].
- Vesluis D.M., Schoemaker R., Looijesteijn E., Geurts J.M.W. & Merks R.M.H. (2024), 2′-Fucosyllactose helps butyrate producers outgrow competitors in infant gut microbiota simulations, iScience 27(3): 109085.
- Versluis D.M., Wijtkamp C., Looijesteijn E., Geurts J.M.W. & Merks R.M.H. (2024), Simulations of the infant gut microbiota suggest that complex ecological interactions regulate effects of human milk oligosaccharides on microbial mucin consumption . bioRxiv. [working paper].
- Keijzer K.A.E., Tsingos E. & Merks R.M.H. (2024), How cells align to structured collagen fibrils: A hybrid cellular Potts and molecular dynamics model with dynamic mechanosensitive focal adhesions. bioRxiv. [working paper].
- Tsingos E., Bakker B.H., Keijzer K.A.E., Hupkes H.J. & Merks R.M.H. (2023), Hybrid cellular Potts and bead-spring modeling of cells in fibrous extracellular matrix, Biophysical Journal 122(13): 2609-2622.
- Steijn L. van, Wondergem A.J., Schakenraad K.K., Heinrich D.M. & Merks R.M.H. (2023), Deformability and collision-induced reorientation enhance cell topotaxis in dense microenvironments, Biophysical Journal 122(13): 2791-2807.
- Versluis D., Schoemaker R., Looijesteijn E., Geurts J.M.W. & Merks R.M.H. (2023), 2’-Fucosyllactose helps butyrate producers outgrow competitors in the infant gut. bioRxiv. [working paper].
- Jong M.A. de, Adegeest E., Bérenger-Currias N.M.L.P., Mircea M, Merks R.M.H. & Semrau S. (2023), A combination of convergent extension and differential adhesion explains the shapes of elongating gastruloids. bioRxiv. [working paper].
- Chen D., Forghany Z., Liu X., Wang H., Merks R.M.H. & Baker D.A. (2023), A new model of Notch signaling: control of Notch receptor cis-inhibition via Notch ligand dimers, PLoS Computational Biology 19(1): e1010169.
- Colizzi S.C., Dijk B. van, Merks R.M.H., Rozen D.E. & Vroomans R.M.A. (2023), Evolution of genome fragility enables microbial division of labor, Molecular Systems Biology 19(3): e11353.
- Lebovka I., Mele B.H., Zakieva A., Gursanscky N., Merks R.M.H., Großeholtz R. & Greb T. (2022), Computational modelling of cambium activity provides a regulatory framework for simulating radial plant growth. bioRxiv. Cold Spring Harbor Laboratory (bioRxiv). [working paper].
- Steijn L. van, Wortel I.M.N., Sire C., Dupré L., Theraulaz G. & Merks R.M.H. (2022), Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics, PLoS Computational Biology 18(2): e1009156.
- Antonovici C.C., Peerdeman G.Y., Wolff H.B. & Merks R.M.H. (2022), Modeling plant tissue development using VirtualLeaf. In: Lucas M. (Ed.), Plant systems biology. Methods in Molecular Biology no. 2395. New York, U.S.A.: Humana. 165-198.
- Bakker B.H., Faver T.E., Hupkes H.J., Merks R.M.H. & Voort J. van der (2022), Scaling relations for auxin waves, Journal of Mathematical Biology 85(4): 41.
- Versluis D.M., Schoemaker R., Looljesteijn E., Muysken D., Jeurink P.V., Paques M., Geurts J.M.W. & Merks R.M.H. (2022), A multiscale spatiotemporal model including a switch from aerobic to anaerobic metabolism reproduces succession in the early infant gut microbiota, mSystems 7(5): e00446-22.
- Post J.N., Loerakker S., Merks R.M.H. & Carlier A. (2022), Implementing computational modeling in tissue engineering: where disciplines meet, Tissue Engineering Part B: Reviews 28(11-12): 542-554.
- Tsingos E., Bakker B.H., Keijzer K.A.E., Hupkes H.J. & Merks R.M.H (2022), Modelling the mechanical cross-talk between cells and fibrous extracellular matrix using hybrid cellular Potts and molecular dynamics methods. bioRxiv. Cold Spring Harbor Laboratory. [working paper].
- Schakenraad K.K., Bakker B.H., Giomi L., Merks R.M.H. & Martorana G.I. (2022), Stress fibers orient traction forces on micropatterns: a hybrid cellular Potts model study. bioRxiv. Cold Spring Harbor Laboratory. [working paper].
- Hu W., Steijn L. van, Li C., Verbeek F.J., Cao L., Merks R.M.H. & Spaink H.P. (2021), A novel function of TLR2 and MyD88 in the regulation of leukocyte cell migration behavior during wounding in zebrafish larvae, Frontiers in Cell and Developmental Biology 9: 624571.
- Tessadori F., Tsingos E., Colizzi E.S., Kruse F., Brink S.C. van den, Boogaard M. van den, Christoffels V.M., Merks R.M. & Bakkers J. (2021), Twisting of the zebrafish heart tube during cardiac looping is a tbx5-dependent and tissue-intrinsic process, eLife 10: 61733.
- Hoffmann L.A., Schakenraad K.K., Merks R.M.H. & Giomi L. (2020), Chiral stresses in nematic cell monolayers, Soft Matter 16(3): 764-774.
- Schakenraad K. Ernst J. Pomp W. Danen E.H.J. Merks R.M.H. Schmidt T. Giomi L. (2020), Mechanical interplay between cell shape and actin cytoskeleton organization, Soft Matter 16(27): 6328-6343.
- Schakenraad K., Ravazzano L., Sarkar N., Wondergem J.A.J., Merks R.M.H. & Giomi L. (2020), Topotaxis of active Brownian particles, Physical Review E 101(3): 032602.
- Rens E.G., Zeegers M.T., Rabbers I., Szabó B.T. & Merks R.M.H. (2020), Autocrine inhibition of cell motility can drive epithelial branching morphogenesis in the absence of growth, Philosophical Transactions of the Royal Society B: Biological Sciences 375(1807): 20190386.
- Rens E.G. & Merks R.M.H. (2020), Cell shape and durotaxis explained from cell-extracellular matrix forces and focal adhesion dynamics, iScience 23(9): 101488.
- Colizzi E.S., Vroomans R.M.A. & Merks R.M.H. (2020), Evolution of multicellularity by collective integration of spatial information, eLife 9: e56349.
- Nelemans B.K.A., Schmitz M., Tahir H., Merks R.M.H. & Smit T.H. (2020), Somite division and new boundary formation by mechanical strain, iScience 23(4): 100976.
- Wolff H.B., Davidson L.A. & Merks R.M.H. (2019), Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf, Bulletin of Mathematical Biology 81(8): 3322-3341.
- Steijn L. van, Verbeek F.J., Spaink H.P. & Merks R.M.H. (2019), Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio, Zebrafish 16(4): 348-362.
- Alber M., Godin C., Maini P.K. & Merks R.M.H. (2019), Introduction (Special Issue "Multiscale Modelling of Tissue Growth and Shape"), Bulletin of Mathematical Biology 81(8): 3214–3218.
- Merks R.M.H. (2018), Probabilistic Cellular Automata in the Visual Arts. In: Louis P.-Y. & Nardi F.R. (Eds.), Probabilistic Cellular Automata. Emergence: Complexity and Organization: an international transdisciplinary journal of complex social systems no. 27. New York: Springer International Publishing. 31-24.
- Boas S.E.M., Jiang Y., Merks R.M.H., Prokopiou S.A. & Rens E.G. (2018), Cellular Potts Model: Applications to Vasculogenesis and Angiogenesis. In: Louis P.-Y. & Nardi F.R. (Eds.), Probabilistic Cellular Automata. Emergence: Complexity and Organization: an international transdisciplinary journal of complex social systems no. 27. New York: Springer International Publishing. 279-310.
- Boas S.E.M., Carvalho J., Broek M. van den, Weijers E.M., Goumans M.-J., Koolwijk P. & Merks R.M.H. (2018), A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants, PLoS Computational Biology 14(7): e1006239.
- Boas S.E.M., Carvalho J., Broek M. van den, Weijers E.M., Goumans M.J., Koolwijk P. & Merks R.M.H. (2018), A local uPAR-plasmin-TGF beta 1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants, PLoS Computational Biology 14(7): e1006239.
- Pomp W., Schakenraad K.K., Balcioglu H.E., Hoorn H. van der, Danen E.H.J, Merks R.M.H, Schmidt T. & Giomi L. (2018), Cytoskeletal anisotropy controls geometry and forces of adherent cells, Physical Review Letters 121(17): 178101.
- Anonymous (2017), Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: a modeling approach [Netherlands Consortium for Systems Biology] (translation: Szabó B.T. & Merks R.M.H.), PLoS Computational Biology 13(7): e1005635.
- Hoek M.J.A. van & Merks R.M.H. (2017), Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism, BMC Systems Biology 11: 56.
- Hirashima T., Rens E.G. & Merks R.M.H. (2017), Cellular potts modeling of complex multicellular behaviors in tissue morphogenesis, Development, Growth and Differentiation 55: 390.
- Rens E.G. & Merks R.M.H. (2017), Cell Contractility Facilitates Alignment of Cells and Tissues to Static Uniaxial Stretch, Biophysical Journal 112(4): 755-766.
- Cruys B., Wong B.W., Kuchnio A., Verdegem D., Cantelmo A., Conradi L.C., Vandekeere S., Bouché A., Cornelissen I., Vinckier S., Merks R.M.H., Dejana E., Gerhardt H., Dewerchin M., Bentley K. & Carmeliet P. (2016), Glycolytic regulation of cell rearrangement in angiogenesis, Nature Communications 7: 12240.
- Antonovici C.C., Boas S.E.M., Rens E.G., Tahir H. & Merks R.M.H. (2016), VERTICAL INTEGRATION: APPLICATIONS: Multiscale Analysis of Morphogenesis. In: Bradshaw R.A. & Stahl P.D (Eds.), Encyclopedia of Cell Biology. Reference Module in Biomedical Sciences no. 4: Elsevier. 122-133.
- Sato T.N. & Merks R.H.M. (2016), Shaping the cell fate, Cell Cycle 16(2): 149-150.
- Akanuma T., Chen C., Sato T., Merks R.M.H. & Sato T.N. (2016), Memory of cell shape biases stochastic fate decision-making despite mitotic rounding, Nature Communications 7: 11963.
- Rens E.G., Boas S.E.M. & Merks R.M.H. (2016), Modelling the growth of blood vessels in health and disease, ERCIM News 104: 36-37.
- Merks R.M.H. & Sagot M.F. (2016), Tackling big data in the Life Sciences : introduction to the Special Theme, ERCIM News 104(Special Theme): 16.
- Palm M.M., Dallinga M.G., Dijk E. van, Klaassen I., Schlingemann R.O. & Merks R.M.H. (2016), Computational Screening of Tip and Stalk Cell Behavior Proposes a Role for Apelin Signaling in Sprout Progression, PLoS ONE 11(11): e0159478.
- Boas S.E.M. & Merks R.M.H. (2015), Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis, BMC Systems Biology 9: 86.
- Daub J.T. & Merks R.M.H. (2015), Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit. In: Ribatti D. (Ed.), Vascular Morphogenesis. Methods in Molecular Biology no. 1214. New York: Humana Press. 67-127.
- Palachanis D., Szabó A. & Merks R.M.H. (2015), Particle-based simulation of ellipse-shaped particle aggregation as a model for vascular network formation, Computational Particle Mechanics 2(4): 371--379.
- Boas S.E.M., Navarro J.M.I., Merks R.M.H. & Blom J.G. (2015), A global sensitivity analysis approach for morphogenesis models, BMC Systems Biology 9(1): 85.
- Dallinga M.G., Boas S.E., Klaassen I., Merks R.MH., Noorden C.J. & Schlingemann R.O. (2015), Tip Cells in Angiogenesis, eLS : 1--10.
- Tahir H., Niculescu I., Bona-Casas C., Merks R.M.H. & Hoekstra A.G. (2015), An in silico study on the role of smooth muscle cell migration in neointimal formation after coronary stenting, Journal of The Royal Society Interface 12(108): 20150358.
- Merks R.M.H. (2015), Cell-Based Modeling. In: Engquist B. (Ed.), Encyclopedia of Applied and Computational Mathematics. Berlin Heidelberg: Springer. 195-201.
- Merks R.M.H. (2015), Biologie in tijden van Big Data, Eureka! 47: 24-27.
- Merks R.M.H. (2015), Cell-based modeling of cell-matrix interactions in angiogenesis, ITM Web of Conferences 5: 00015.
- Tessadori F., Noël E.S., Rens E.G., Magliozzi R., Evers-Van Gogh I.J.A., Guardavaccaro D., Merks R.M.H. & Bakkers J. (2015), Nodal Signaling Range Is Regulated by Proprotein Convertase-Mediated Maturation, Developmental Cell 32(5): 631-639.
- Palm M.M. & Merks R.M.H. (2014), Large-Scale Parameter Studies of Cell-Based Models of Tissue Morphogenesis Using CompuCell3D or VirtualLeaf. New York, NY: Springer New York. 301--322.
- Daub J.T. & Merks R.M.H. (2014), Cell-Based Computational Modeling of Vascular Morphogenesis Using Tissue Simulation Toolkit. In: Ribatti D. (Ed.), link.springer.com. New York, NY: Methods in Molecular Biology. 67--127.
- Merks R.M.H. (2014), The Next Boom of Big Data in Biology: Multicellular Datasets, ERCIM News (99): 11-22.
- Boas S.E.M. & Merks R.M.H. (2014), Synergy of cell-cell repulsion and vacuolation in a computational model of lumen formation, Journal of The Royal Society Interface 11(92): 20131049--20131049.
- Oers R.F.M., Rens E.G., LaValley D.J., Reinhart-King C.A. & Merks R.M.H. (2014), Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro, PLoS Comput. Biol. 10(8): e1003774.
- Lagendijk A.K., Szabo A., Merks R.M.H. & Bakkers J. (2013), Hyaluronan: A critical regulator of endothelial-to-mesenchymal transition during cardiac valve formation, Trends in Cardiovascular Medicine 23(5): 135-142.
- Boas S.E.M., Palm M., Koolwijk P. & Merks R.M.H. (2013), Computational modeling of angiogenesis: towards a multi-scale understanding of cell-cell and cell-matrix interactions. In: Reinhart-King C.A. (Ed.), Mechanical and Chemical Signaling in Angiogenesis 161-183.
- Merks R.M.H. & Guravage M. (2013), Building simulation models of developing plant organs using VirtualLeaf. In: De Smet I. (Ed.), Methods in Molecular Biology. Berlin Heidelberg: Springer-Verlag. 333-352.
- Szabo B.T. & Merks R.M.H. (2013), Cellular Potts modeling of tumor growth, tumor invasion, and tumor evolution, Frontiers in Oncology 3: 1-12 (87).
- Palm M.M. & Merks R.M.H. (2013), Erratum: vascular networks due to dynamically arrested crystalline ordering of elongated cells, Physical review E 87(6): 069903 (012725).
- Daub Josephine T. & Merks R.M.H. (2013), A Cell-Based Model of Extracellular-Matrix-Guided Endothelial Cell Migration During Angiogenesis, Bulletin of Mathematical Biology 75(8): 1377-1399.
- Dhondt S., Haerenborgh D. van, Cauwenbergh C. van, Merks R.M.H., Philips W., Beemster G.T.S. & Inzé D. (2012), Quantitave analysis of venation patterns of Arabidopsis leaves by supervised image analysis, The Plant Journal 69(3): 553-563.
- Merks Roeland M.H., Guravage Michael, Inze Dirk & Beemster Gerrit T.S. (2011), VirtualLeaf: An Open-Source Framework for Cell-Based Modeling of Plant Tissue Growth and Development, 155(2): 656-666.
- Van Parijs Frederik R.D., Morreel Kris, Ralph John, Boerjan Wout & Merks Roeland M.H. (2010), Modeling Lignin Polymerization. I. Simulation Model of Dehydrogenation Polymers, 153(3): 1332-1344.
- Dhondt Stijn, Coppens Frederik, De Winter Freya, Swarup Kamal, Merks Roeland M.H., Inze Dirk, Bennett Malcolm J. & Beemster Gerrit T.S. (2010), SHORT-ROOT and SCARECROW Regulate Leaf Growth in Arabidopsis by Stimulating S-Phase Progression of the Cell Cycle, 154(3): 1183-1195.
- Scianna Marco, Merks Roeland M.H., Preziosi Luigi & Medico Enzo (2009), Individual cell-based models of cell scatter of ARO and MLP-29 cells in response to hepatocyte growth factor, 260(1): 151-160.
- Merks R.M.H. & Koolwijk P. (2009), Modeling Morphogenesis in silico and in vitro: Towards Quantitative, Predictive, Cell-based Modeling, 4(4): 149-171.
- Brodsky Sergey V., Merks Roeland M.H., Mendelev Natalia, Goo Cara & Chen Jun (2007), Glycated Collagen I (GC) impairs angiogenesis in vitro - A study using an innovative chamber for cell research, Diabetes Research and Clinical Practice 76(3): 463-467.
- Merks Roeland M.H., Van de Peer Yves, Inze Dirk & Beemster Gerrit T.S. (2007), Canalization without flux sensors: a traveling-wave hypothesis, 12(9): 384-390.
- Cickovski Trevor, Aras Kedar, Alber Marks S., Izaguirre Jesus A., Swat Maciej, Glazier James A., Merks Roeland M.H., Glimm Tilmann, Hentschel H., George E. & Newman Stuart A. (2007), From genes to organisms via the cell - A problem-solving environment fir multicellular development, 9(4): 50-60.
- Merks R.M.H., Brodsky S.V., Goligorksy M.S., Newman S.A. & Glazier J.A. (2006), Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling, 289(1): 44-54.
- Merks R.M.H., Hoekstra A.G., Kaandorp J.A., Sloot P.M.A. & Hogeweg P. (2006), Problem-solving environments for biological morphogenesis, 8(1): 61-72.
- Merks R.M.H. & Glazier J.A. (2005), A cell-centered approach to developmental biology, Physica A: Statistical Mechanics and its Applications 352(1): 113-130.
- Kaandorp J.A., Sloot P.M.A., Merks R.M.H., Bak R.P.M., Vermeij M.J.A. & Maier C. (2005), Morphogenesis of the branching reef coral Madracis mirabilis, Proceedings of the Royal Society B: Biological Sciences 272(1559): 127-133.
- Merks R.M.H., Newman S.A. & Glazier J.A. (2004), Cell-oriented modeling of In Vitro capillary development, 3305: 425-434.
- Merks R.M.H., Hoekstra A.G., Kaandorp J.A. & Sloot P.M.A. (2004), Polyp oriented modelling of coral growth, 228(4): 559-576.
- Merks R.M.H., Hoekstra A.G., Kaandorp J.A. & Sloot P.M.A. (2003), Diffusion-limited aggregation in laminar flows, 14(9): 1171-1182.
- Merks R., Hoekstra A., Kaandorp J. & Sloot P. (2003), A problem solving environment for modelling stony coral morphogenesis, 2657: 639-648.
- Merks R., Hoekstra A., Kaandorp J. & Sloot P. (2003), Models of coral growth: spontaneous branching, compactification and the Laplacian growth assumption, 224(2): 153-166.
- Merks R., Hoekstra A., Kaandorp J. & Sloot P. (2002), Spontaneous branching in a polyp oriented model of stony coral growth, 2329: 88-96.
- Merks R.M.H., Hoekstra A.G. & Sloot P.M.A. (2002), The moment propagation method for advection-diffusion in the lattice Boltzmann method: Validation and Peclet number limits, 183(2): 563-576.
- Academic Editor