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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.

BW. Busser*, L. Taher*, Y. Kim, T. Tansey, MJ. Bloom, I. Ovcharenko, AM. Michelson
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis
PLoS Genetics, 8(3):e1002531 (2012) (* - co-first authors) PDF

L. Taher, L. Narlikar, I. Ovcharenko
CLARE: Cracking the LAnguage of Regulatory Elements
Bioinformatics, 28(4):581-3 (2012) PDF

L. Taher, D.M. McGaughey, S. Maragh, I. Aneas, S.L. Bessling, W. Miller, M.A. Nobrega, A.S. McCallion, I. Ovcharenko
Genome-wide identification of conserved regulatory function in diverged sequences
Genome Research, 21(7), 1139-1149 (2011) PDF

L. Taher, N.M. Collette, D. Murugesh, E. Maxwell, I. Ovcharenko, G.G. Loots
Global gene expression analysis of murine limb development
PLoS ONE, 6(12):e28358 (2011)

Martin D, ... Taher L, ... Ovcharenko I, ... Gómez-Skarmeta JL.(22 authors)
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.
Nat Struct Mol Biol. 18(6):708-14 (2011)

Rochman M, Taher L, Kurahashi T, Cherukuri S, Uversky VN, Landsman D, Ovcharenko I, Bustin M.
Effects of HMGN variants on the cellular transcription profile.
Nucleic Acids Res. 39(10):4076-87 (2011)

Hellsten U, ... Ovcharenko I, ... Taher L, ... Rokhsar DS (48 authors)
The Genome of the Western Clawed Frog Xenopus tropicalis.
Science (2010) 328:633-636

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
 



 
Di Huang, Ph.D.
Research Fellow
June 2010 - present

Mapping biological pathways in tissue-specific enhancers
My project is aimed at decoding regulatory pathways underlying the development of specific tissues. An enhancer set driving the development of a specific tissue (e.g., heart) is heterogeneous, regulating different pathways and controlling the development of different sub-tissues. We are developing a method to map enhancers into different pathways, and predict the pathway-specific activity of enhancers. This method will provide novel analytical tools for an in detail characterization of enhancers identified using next-generation sequencing technologies.
 



 
Chih-Hao Hsu, Ph.D.
Postdoctoral Fellow
August 2010 - present

Evolution of gene regulatory elements in vertebrates
I am interested in the study of the evolution of gene regulatory elements in vertebrates. Specifically, I work on an inter-species analysis of epigenetic and transcription factor binding regulatory profiles of vertebrate genomes generated using massively-parallel sequencing technologies. I also study how loss and gain of regulatory elements impacts the expression of nearby genes and the contribution of regulatory changes to the adaptation of species.
 



 
Chris Lasher, Ph.D.
Postdoctoral Fellow
January 2012 - present

TBD
TBD




Alumni


  • Hani Girgis, Postdoctoral Fellow from January 2010 to March 2011. Currently a postdoc with Dr. John L. Spouge
  • Evan Maxwell, Summer Student (2010). Currently a Graduate Student at Boston University.
  • Peter Cote, Summer Student (2010). Currently a Graduate Student at the University of Illinois at Urbana-Champaign.
  • Valer Gotea, Ph.D., Postdoctoral Fellow from September 2007 to May 2010. Currently a Postdoctoral Fellow at NHGRI.

        Gotea V, Ovcharenko I.
        DiRE: identifying distant regulatory elements of co-expressed genes.
        Nucleic Acids Res. (2008) 36:W133-9

        Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I.
        Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.
        Genome Research. (2010) 20(5):565-77

        Jacox E, Gotea V, Ovcharenko I, Elnitski L.
        Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes.
        PLoS One. (2010) 5(8):e12274.

  • Chao Tian, Ph.D., Postdoctoral Fellow from August 2009 to February 2010.
  • 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

        Narlikal L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I.
        Genome-wide discovery of human heart enhancers
        Genome Research, 2010

        L. Taher, L. Narlikar, I. Ovcharenko
        CLARE: Cracking the LAnguage of Regulatory Elements
        Bioinformatics, (2012, in press)

  • 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