Our lab investigates how cells self-organize to form multicellular structures, such as embryos, and how these principles can be applied to organoid engineering and regenerative medicine. We integrate advanced experimental techniques with computational modeling to study biological systems across spatial and temporal scales—from single molecules to whole tissues.

Habibi, E., Sinha, A., Yadollahpour, P., Yang, H., Wollensak D. A., Li, Y., Sakkas, D., Boyden, E. S., Guo, M., Regev, A. & Chen, F. Unified Transcriptome and Mechanics Map of the  Intact Mammalian Preimplantation Embryo In Situ (Under peer review).

Di Bella, D. J. *, Habibi, E. *, Stickels, R. R., Scalia, G., Brown, J., Yadollahpour, P., Yang, S. M., Abbate, C., Biancalani, T., Macosko, E. Z., Chen, F., Regev, A. & Arlotta, P. Molecular logic of cellular diversification in the mouse cerebral cortex. Nature595, 554-559, doi:10.1038/s41586-021-03670-5 (2021).

Habibi, E. & Stunnenberg, H. G. Transcriptional and epigenetic control in mouse pluripotency: lessons from in vivo and in vitro studies. Curr Opin Genet Dev 46, 114-122, doi:10.1016/j.gde.2017.07.005 (2017).

von Meyenn, F. *, Iurlaro, M. *, Habibi, E. *, Liu, N. Q., Salehzadeh-Yazdi, A., Santos, F., Petrini, E., Milagre, I., Yu, M., Xie, Z., Kroeze, L. I., Nesterova, T. B., Jansen, J. H., Xie, H., He, C., Reik, W. & Stunnenberg, H. G. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Mol Cell 62, 848-861, doi:10.1016/j.molcel.2016.04.025 (2016).

Novakovic, B. *, Habibi, E. *, Wang, S. Y. *, Arts, R. J. W., Davar, R., Megchelenbrink, W., Kim, B., Kuznetsova, T., Kox, M., Zwaag, J., Matarese, F., van Heeringen, S. J., Janssen-Megens, E. M., Sharifi, N., Wang, C., Keramati, F., Schoonenberg, V., Flicek, P., Clarke, L., Pickkers, P., Heath, S., Gut, I., Netea, M. G., Martens, J. H. A., Logie, C. & Stunnenberg, H. G. beta-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance. Cell 167, 1354-1368 e1314, doi:10.1016/j.cell.2016.09.034 (2016).

Habibi, E., Brinkman, A. B., Arand, J., Kroeze, L. I., Kerstens, H. H., Matarese, F., Lepikhov, K., Gut, M., Brun-Heath, I., Hubner, N. C., Benedetti, R., Altucci, L., Jansen, J. H., Walter, J., Gut, I. G., Marks, H. & Stunnenberg, H. G. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 13, 360-369, doi:10.1016/j.stem.2013.06.002 (2013).