Quantitative developmental biology

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In development, a single cell, the fertilized egg, turns into a complex organism consisting of millions of cells. The cells of the embryo differentiate into many different cell types, and they are arranged in complex spatial patterns. This process generally proceeds with striking precision. Our group is interested in understanding the mechanisms that ensure the stability of developmental processes despite stochastic perturbations. We use the zebrafish as a model system to study organ development and regeneration. Our projects typically combine experimental and theoretical approaches, and it is our goal to study single cells in their spatio-temporal context. To this end, we use and develop novel genome-wide single-cell approaches.

cartoon fish development
Cartoon representation of zebrafish development. Left: 1-cell stage embryo. The cell (gray) is located on top of the spherical yolk sac (orange). Middle: Embryo at 24 hours post fertilization. The body axes and all major organs have formed. The embryo is still attached to the yolk. Right: adult zebrafish. After 2-3 months, the fish reach reproductive age.

Key Publications

Hu, B., Spanjaard, B., Lelek, S., El-Sammak, H., Simoes, M., Mintcheva, J., Aliee, H., Schäfer, R., Meyer, A.M., Theis, F., Stainier, D.Y.R., Panáková, D., Junker, J.P. Origin and function of activated fibroblast states during zebrafish heart regeneration. Nat Genet doi:10.1038/s41588-022-01129-5, 2022.


Holler, K., Neuschulz, A., Drewe-Boß, P., Mintcheva, J., Spanjaard, B., Arsiè, R., Ohler, U., Landthaler, M., Junker, J.P. Spatio-temporal mRNA tracking in the early zebrafish embryo. Nat Commun 12: 3358, 2021.


Moreno-Ayala, R., Olivares-Chauvet, P., Schäfer, R., Junker, J.P. Variability of an early developmental cell population underlies stochastic laterality defects. Cell Rep 34(2): 108606, 2021.


Spanjaard, B., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., Ninov, N., Junker, J.P. (2018). Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nat Biotechnol 36, 469-473.

Selected by Science as part of the “Breakthrough of the Year 2018


Junker, J.P., Noël, E.S., Guryev, V., Peterson, K.A., Shah, G., Huisken, J., McMahon, A.P., Berezikov, E., Bakkers, J., van Oudenaarden, A. (2014). Genome-wide RNA tomography in the zebrafish embryo. Cell 159, 662-675.


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