Welcome Ertuğrul Özbudak, PhD

Ertuğrul Özbudak, PhD, grew up in Istanbul and obtained his undergraduate degree in physics at Bogazici (i.e., Bosphorus) University in Istanbul. He then obtained his doctorate in physics at Massachusetts Institute of Technology and completed his thesis project in the lab of Alexander van Oudenaarden. During his PhD program, he investigated the underlying causes of stochastic gene expression, the functional roles of feedback loops in generating bistability (hysteresis), triggering symmetry breaking and establishing cell polarity. Later, he completed his postdoctoral studies in the labs of the late Julian Lewis and Olivier Pourquie. To support his studies, Ertuğrul received the Merck/MIT computational biology predoctoral fellowship, as well as the Cancer Research UK and Marie Curie and European Molecular Biology Organization postdoctoral fellowships. Most recently, he was selected as an Alfred P. Sloan Research Faculty Fellow.

During embryonic development, each tissue and organ establish characteristic patterns composed of several spatially organized cells. Ertuğrul considers tissue/organ patterns as a form of biological “art.” Since his postdoctoral studies, he has been investigating the mechanism controlling somite segmentation in vertebrates (an example of developmental pattern formation).

In his free time, Ertuğrul enjoys spending time with his family, playing soccer and chess, and watching epic or science-fiction movies.

The Özbudak Lab’s overriding interest is to achieve a systems-level understanding of embryonic development and pattern formation by integrating quantitative experiments with computational 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 Hes/Her gene family, known as the vertebrate segmentation clock;
2. the synchronization of oscillations among neighboring cells by Delta/Notch signaling;
3. the instruction of segment boundaries by the Fgf/pErk signaling gradient; and
4. a network of transcription factors and cytoskeletal regulators completing mesenchymal-to-epithelial transition, downstream of the segmentation clock and signaling pathways.

In the Özbudak Lab, single-cell confocal microscopy measurements are combined with 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.

See Ertuğrul's publications on PubMed.