Ivan Ovcharenko Research Group at NCBI

	Computational Biology Branch

	Ivan Ovcharenko Research Group


Research Projects	Publications	Collaborations	Resources	Group Members	Principal Investigator	Visiting us

Group Members
			Leila Taher, Ph.D. Postdoctoral Fellow January 2008 - present Sequence composition of gene regulatory elements The main goal of my project is to design an alphabet for transcriptional regulation. Transcription factor binding sites can be modeled as combinations of letters representing binding specificities. Then, enhancers common to several sequences can be identified by looking for good alignments between these letters. Such a simple representation of the regulatory code will provide an original means to indirectly compare sequences of multiple species or co-expressed genes for which traditional methods are unable to detect any sequence homology. Taher L, Ovcharenko I. Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics (2009) 25(5):578-84
			Valer Gotea, Ph.D. Research Fellow September 2007 - present Primeval Gene Regulation in Vertebrates The clustering of transcription factor binding sites (TFBS), which provides a simple mechanism for transcriptional cis-regulation, is known to exist in organisms such as yeast and Drosophila. It is well known that vertebrate cis-regulatory modules (CRMs) also consist of TFBS clusters. I am interested in finding the extent and nuances of how vertebrates use the modularity of CRMs to establish the mechanisms of gene regulation. The redundancy offered by TFBS clusters can provide a robust regulatory mechanism for basic functional genes or transcription factors, but can also be used for regulating gene dosage or tissue specificity. Detailed knowledge of the use of this mechanism could ultimately reveal a basic regulatory network, conserved among vertebrates, on top of which specific complexity evolved. Gotea V, Ovcharenko I. DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Res. (2008) 36:W133-9
			Chao Tian, Ph.D. Research Fellow July 2009 - present TBA TBA

Alumni
Leelavati Narlikar, Ph.D., Postdoctoral Fellow from April 2008 to July 2009. Currently a Postdoctoral Fellow at the University of Pune, Pune, India. Narlikal L, Ovcharenko I. Identifying regulatory elements in eukaryotic genomes Brief Funct Genomic Proteomic, 2009 Andrew Heekin, Summer Student (2009). Currently a Graduate Student at George Mason University. Yevgeniy Gindin, Summer Student (2009). Currently a Graduate Student at Boston University. David Tao, High School Summer Student (2009). Brian Abraham, Summer Student (2008). Currently a Graduate Student at Boston University. Ryan Vo, High School Summer Student (2008).

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Last modified: April 22, 2009