Quantitative developmental biology

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Division of labor between specialized cell types is a principle of multicellular life. We study mechanisms of cell fate decisions in health and disease. To do so, we develop and use methods in single-cell genomics, including strategies for massively parallel lineage analysis, single cell RNA labeling, and spatially-resolved transcriptomics. Our projects typically combine experimental and theoretical approaches We use these methods to investigate processes in embryonic development and to understand adult tissue regeneration in the zebrafish, an organism that has the ability to efficiently regenerate many organs that in humans have only limited regenerative capacity. In collaborations we strive to apply our methods also to other systems, including organoids and human patient samples.

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 3 months, the fish reach reproductive age.

Key Publications

Mitic, N., Neuschulz, A., Spanjaard, B., Schneider, J., Fresmann, N., Novoselc, K.T., Strunk, T., Münster, L., Olivares-Chauvet, P., Ninkovic, J., Junker, J.P. (2024) Dissecting the spatiotemporal diversity of adult neural stem cells. Mol Syst Biol 20, 4.

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. (2022) Origin and function of activated fibroblast states during zebrafish heart regeneration. Nat Genet 54, 1227-1237.

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

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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