Ozbudak Research Lab
Our overriding interest is to achieve a systems-level understanding of embryonic development and pattern formation by integrating quantitative experiments with mathematical modeling. Embryos develop spatiotemporal patterns by encoding and interpreting biological signals in real time. Despite unavoidable fluctuations in gene expression, embryonic development is robust and reproducible, which necessitates several mechanisms buffering stochastic gene expression.
A striking example of robust spatiotemporal patterning is the rhythmic segmentation of somites, which are precursors of the vertebral column. Segmentation of somites is controlled by: 1) the oscillatory expression of the Hes/Her gene family, known as the vertebrate segmentation clock, 2) short-distance Notch signaling, 3) long-distance Fgf, Wnt, and Retinoic Acid (RA) signaling gradients and 4) a network of transcription factors integrating outputs of the segmentation clock and the signaling pathways.
We combine single-cell microscopy measurements, time-resolved perturbation experiments, genome-wide techniques, biophysical modeling and computational simulations to decipher the mechanism underlying robust spatiotemporal pattern formation and cell fate determination.
