Publications Quantitative Developmental Biology

Latest Publications

  • W.K. Spoelstra, Shedding light on dynamic processes in the intestinal epithelium, Delft University of Technology, 2026-01-23

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  • B. Demirbas, O. Filina, T. Louisse, A. Natarajan, Y.J. Goos, M.A. Sánchez-Romero, M. Olmedo and J.S. van Zon, Body-wide synchronization of insulin-signaling dependent DAF-16/FOXO nuclear translocation pulses correlated with C. elegans growth, Nat. Commun. 16, (1), 11273: 1-16 (2025)

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  • D. Wang, S. Lim, W.J. van de Wetering, C. Lopez-Iglesias, Y. Okura, Y. Teranishi-Ikawa, A. Mizoroki, W.K. Spoelstra, T. Dayton, G.J.F. van Son, A. Pronk, N. Smakman, G.B.C. Gonera-de Jong, S. Withoff, I.H. Jonkers, J.S. van Zon, S.J. Tans, P.J. Peters, J.H. van Es and H. Clevers, Human gut M cells resemble dendritic cells and present gluten antigen, Nature, (2025)

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  • M.A. Betjes, R.N.U. Kok, S.J. Tans and J.S. van Zon, Cell tracking with accurate error prediction, Nature Meth. 22, 2400-2410 (2025)

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  • D. Krueger, W.K. Spoelstra, D.J. Mastebroek, R.N.U. Kok, S. WU, M. Nikolaev, M. Bannier-Hélaouët, N. Gjorevski, M. Lutolf, J.H. van Es, J.S. van Zon, S.J. Tans and H. Clevers, Epithelial tension controls intestinal cell extrusion, Science 389, (6764), eadr8753: 1-16 (2025)

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  • J.R. Buissant des Amorie, M.A. Betjes, J.H. Bernink, J.H. Hageman, V.E. Geurts, H. Begthel, D. Laskaris, M.C. Heinz, I. Jordens, T. Vinck, R.M. Houtekamer, I. Verlaan-Klink, S.R. Brunner, J. van Rheenen, M. Gloerich, H. Clevers, S.J. Tans, J.S. van Zon and H.J.G. Snippert, Intestinal tuft cell subtypes represent successive stages of maturation driven by crypt-villus signaling gradients, Nat. Commun. 16, (1), 6765 : 1-18 (2025)

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  • B. Demirbas, Stress-induced protein dynamics and growth arrest in C. elegans during development, Leiden University, 2025-05-16

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  • R.N.U. Kok, W.K. Spoelstra, M.A. Betjes, J.S. van Zon and S.J. Tans, Label-free cell imaging and tracking in 3D organoids, Cell Rep. Phys. Sci. 6, (4), 102522: 1-12 (2025)

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  • D. Wang, W.K. Spoelstra, L. Lin, N. Akkerman, D. Krueger, T. Dayton, J.S. van Zon, S.J. Tans, J.H. van Es and H. Clevers, Interferon-responsive intestinal BEST4/CA7+ cells are targets of bacterial diarrheal toxins, Cell Stem Cell 32, (4), 598-612.e5 (2025)

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  • N.T.B. Nguyen, S. Gevers, R.N.U. Kok, L.M. Burgering, H. Neikes, N. Akkerman, M.A. Betjes, M.C. Ludikhuize, C. Gulersonmez, E.C.A. Stigter, Y. Vercoulen, J. Drost, H. Clevers, M. Vermeulen, J.S. van Zon, S.J. Tans, B.M.T. Burgering and M.J. Rodríguez Colman, Lactate controls cancer stemness and plasticity through epigenetic regulation, Cell Metab. 37, (4), 903-919 (2025)

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DEVELOPMENTAL BIOLOGY

Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression
J.S. van Zon, S. Kienle, G. Huelsz-Prince, M. Barkoulas, A. van Oudenaarden
Nature Communications 6:8053 (2015)

Microfabricated Polyacrylamide Devices for the Controlled Culture of Growing Cells and Developing Organisms.
P. Nghe, S. Boulineau, S. Gude, P. Recouvreux, J.S. van Zon, S.J. Tans
PLoS ONE 8(9): e75537 (2013)

Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation.
M. Barkoulas, J.S. van Zon, J. Milloz, A. van Oudenaarden, M.A. Félix.
Dev Cell. 24:64-75 (2013)

Direct cell reprogramming is a stochastic process amenable to acceleration.
J. Hanna, K. Saha, B. Pando, J. van Zon, C.J. Lengner, M.P. Creyghton, A. van Oudenaarden, R. Jaenisch.
Nature. 462:595-601 (2009)

 

MODELING OF BIOCHEMICAL NETWORKS

Movement and equipositioning of plasmids by ParA filament disassembly.
S. Ringgaard, J. van Zon, M. Howard, K. Gerdes.
Proc Natl Acad Sci U S A. 106:19369-74 (2009)

A mechanical bottleneck explains the variation in cup growth during FcgammaR phagocytosis.
J.S. van Zon, G. Tzircotis, E. Caron, M. Howard
Mol Syst Biol. 5:298 (2009)

An allosteric model of circadian KaiC phosphorylation.
J.S. van Zon, D.K. Lubensky, P.R. Altena, P.R. ten Wolde.
Proc Natl Acad Sci U S A. 104:7420-5 (2007)

Simulating biochemical networks at the particle level and in time and space: Green’s function reaction dynamics.
J.S. van Zon JS, P.R. ten Wolde
Phys Rev Lett. 94:128103 (2005)