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Faculty Profile

Ertugrul M. Ozbudak, Ph.D.

Dr. Ertugrul M. Ozbudak

Assistant Professor, Department of Genetics


Professional Interests

Systems Developmental Biology



We focus on two major research areas:


1- Stem cell proliferation, muscle differentiation and regeneration:

Muscle diseases occur due to genetic-, injury- or aging-related causes. It is crucial to discover the gene regulatory network that controls the differentiation of muscle cells to be able to induce adult muscle stem cells to proliferate and differentiate. Moreover, the regulation of metabolism in muscle cells needs deeper understanding to prevent and cure metabolic defects, such as insulin resistance in muscle cells. We are investigating how the proliferation, differentiation and metabolism of the muscle stem cells are controlled by the signaling pathways and their transcription factor targets. We are investigating the roles of these transcription factors by loss- and gain-of-function experiments followed by detailed investigation of the impacts of these perturbations on: muscle stem cell proliferation, muscle differentiation and regeneration, and metabolism in muscle cells. Genome-wide studies, molecular perturbation experiments and imaging will be integrated to achieve these objectives.


2- Gene expression oscillations and vertebral segmentation:

The axis of vertebrates is characterized by the iteration of vertebrae. The precursors of the vertebrae are derived from embryonic somite segments. Embryos elongate from their posterior end and a new somite appears at a species-specific pre-determined time. The periodicity of this spatial pattern formation is controlled by a gene-expression oscillator, called the segmentation clock that ticks in the cells residing in the unsegmented tissue. Breakdown of the oscillations disrupts somite boundaries and results in vertebral defects. It is important to identify the genes involved at different stages of segmentation in order to develop future therapies for patients. We aim to identify novel regulators of vertebral segmentation and integrate the experimental data with mathematical modeling to unravel the regulatory network that paces the rhythm of the periodic gene expression and spatial pattern formation.



Please visit our lab website for further information:

ResearchGate Profile:

Google Scholar Profile: 


Selected Publications




  • Özbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nature Genetics, 31(1):69-73, (2002). Faculty of 1000 Biology Evaluation: (Exceptional) (Jun 2002).PDF
  • Özbudak EM, Thattai M, Lim HN, Shraiman BI, Van Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature, 427(6976):737-740, (2004).Faculty of 1000 Biology Evaluation: (Exceptional) (Jun 2004).PDF
  • Özbudak EM, Becskei A, van Oudenaarden A. A system of counteracting feedback loops regulates Cdc42p activity during spontaneous cell polarization. Dev. Cell. 9(4):565-571, (2005). Faculty of 1000 Biology Evaluation: (Recommended) (Nov 2005).PDF
  • Mettetal JT, Muzzey D, Pedraza JM, Özbudak EM, van Oudenaarden A. Predicting stochastic gene expression dynamics in single cells. Proc Natl Acad Sci USA, 103(19):7304-9, (2006).PDF
  • Giudicelli F, Özbudak EM, Lewis J. Setting the Tempo in Development: an Investigation of the Zebrafish Somite Clock Mechanism. PLoS Biology, 5(6):e150, (2007).PDF
  • Lewis J, Özbudak EM. Deciphering the somite segmentation clock: Beyond mutants and morphants. Dev Dyn., 236(6):1410-1415, (2007).PDF
  • Özbudak EM,Pourquié O. The Vertebrate Segmentation Clock: the Tip of the Iceberg. Current Opinion in Development and Genetics, 18(4):317-23, (2008).Abstract
  • Özbudak EM, Lewis J.Notch signalling synchronises the zebrafish somite segmentation clock but is not needed to create somite boundaries. PLoS Genetics, 4(2):e15, (2008).PDF
  • Gomez C, Özbudak EM, Wunderlich J, Baumann D, Lewis J, Pourquié O. Control of segment Number in vertebrate embryos. Nature, 454(7202):335-339, (2008). Faculty of 1000 Biology Evaluation: (Must Read) (Jul 2008). Abstract
  • Özbudak EM,Tassy O, Pourquié O. Spatiotemporal compartmentalization of key physiological processes during muscle precursor differentiation. Proc Natl Acad Sci USA.107(9):4224-9, (2010).PDF
  • Hanisch A, Holder M, Choorapoikayil S, Gajewski M, Özbudak EM*, Lewis J*. The elongation rate of RNA Polymerase II in the zebrafish and its significance in the somite segmentation clock. (* co-corresponding authors). Development, 140, 444-453 (2013). Abstract
  • Devakanmalai GS, Zumrut H, Özbudak EM. Cited3 activates Mef2c to control muscle cell differentiation and survivalBiology Open, 2:505-514 (2013). PDF
  • Ay A, Knierer S, Sperlea A, Holland J & Özbudak EM. Short-lived Her Proteins Drive Robust Synchronized Oscillations in the Zebrafish Segmentation Clock. Development,140(15), 3244-3253, (2013).
  • Ay A, Sperlea A, Devakanmalai GS, Holland J, Knierer S, Sangervasi S & Özbudak EM. Gradients of gene expression time-delays set the pace of the traveling segmentation clock waves. Accepted to Development, (2014).

More Information About Dr. Ertugrul Ozbudak

Lab Website

ResearchGate Profile

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Albert Einstein College of Medicine
Jack and Pearl Resnick Campus
1300 Morris Park Avenue
Ullmann Building, Room 711
Bronx, NY 10461

Tel: 718.430.3241
Fax: 718.430.8778

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