Areas of Research: Systems biology, genetics, developmental precision, incomplete penetrance, scoliosis, pattern formation, segmentation clock, oscillation, morphogen gradient, cell signaling, stochastic gene expression, mathematical modeling.
Systems Developmental Biology
Systems-level analysis of developmental timing and pattern formation
The vertebrate segmentation clock is a gene expression oscillator pacing rhythmic segmentation of the vertebral column during embryonic development. The period of the segmentation clock dictates the number and sizes of vertebrae. Fgf, Wnt, Notch and Retinoic Acid (RA) cell-to-cell signaling pathways interact with each other and act upstream the segmentation clock genes to regulate segmentation and differentiation of cells in the tissue. Defects in somite segmentation process result in birth defects (congenital scoliosis).
In our lab, we focus on the following research topics:
Quantitative developmental biology, pattern formation, the pacemaker mechanism of the segmentation clock, regulation of the gene expression oscillations, morphogen gradients, stochastic gene expression and achieving precision in segmentation, mathematical modeling and computational simulations.
We aim to understand how these processes are controlled by the signaling pathways and their transcription factor targets. We utilize real-time imaging tools, time-controlled perturbation experiments, mathematical modeling, genome-wide techniques and bioinformatics to achieve these objectives. We use zebrafish as the model organism.
Please visit our lab website for further information: https://sites.google.com/site/ozbudaklab/home
ResearchGate Profile: https://www.researchgate.net/profile/Ertugrul_Ozbudak/?ev=hdr_xprf
Google Scholar Profile:http://scholar.google.com/citations?user=awIzgXAAAAAJ&hl=en
- 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 survival. Biology 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. Development, 141(21), 4158-4167, (2014).
More Information About Dr. Ertugrul Ozbudak
Material in this section is provided by individual faculty members who are solely responsible for its accuracy and content.