Publications Quantitative Developmental Biology

Latest Publications

  • 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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  • 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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  • 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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  • R.N.U. Kok, Homeostasis in intestinal organoids at the single cell level, Delft University of Technology, 2024-04-10

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  • G. Patil and J.S. van Zon, Timers, variability, and body-wide coordination: C. elegans as a model system for whole-animal developmental timing, Curr. Opin. Genet. Dev. 85, 102172: 1-8 (2024)

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  • S. Baglamis, V.M. Sheraton, D. Meijer, H. Qian, R.A. Hoebe, K.J. Lenos, M.A. Betjes, S.J. Tans, J.S. van Zon, L. Vermeulen and P.M. Krawczyk, Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures, Sci. Rep. 13, (1), 18832: 1-13 (2023)

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  • R.N.U. Kok, S.J. Tans and J.S. van Zon, Minimizing cell number fluctuations in self-renewing tissues with a stem-cell niche, Phys. Rev. E 108, (6), 064403: 1-11 (2023)

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  • X. Zheng, M.A. Betjes, P. Ender, Y.J. Goos, G. Huelsz-Prince, H. Clevers, J.S. van Zon and S.J. Tans, Organoid cell fate dynamics in space and time, Sci. Adv. 9, (33), eadd6480: 1-13 (2023)

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  • X. Zheng, Tracking organoid cell fate dynamics in space and time, Delft University of Technology, 2023-06-06

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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)