Research Interests

My general research interests are in computational biology and statistical learning, with a focus on applying statistical methods and machine learning techniques to discover significant DNA motifs in eukaryotic genomes. I am particularly interested in finding DNA binding sites of different proteins and protein complexes involved in regulation of transcription initiation and replication initiation.

Publications

  1. Gordân,R., Hartemink,A.J., & Bulyk,M.L. (2009) “Distinguishing direct versus indirect transcription factor-DNA interactions.” Genome Research, Epub Aug 3, 2009.

  2. Gordân,R.*, Narlikar,L.*, & Hartemink,A. (2008) “A fast, alignment-free, conservation-based method for transcription factor binding site discovery.” Research in Computational Molecular Biology 2008 (RECOMB08). Lecture Notes in Bioinformatics, eds. 4955, April 2008. pp. 98–111. (* equal contribution) [Supp. Info.]

  3. Gordân,R. & Hartemink,A. (2007) “Using DNA Duplex Stability Information to Discover Transcription Factor Binding Sites.” Pacific Symposium on Biocomputing 2008 (PSB08), 13:453–464, January 2008. [Supp. Info.]

  4. Narlikar,L.*, Gordân,R.*, & Hartemink,A. (2007) “A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast.” PLoS Computational Biology, 3(11):e215, November 2007. (* equal contribution).

  5. Narlikar,L.*, Gordân,R.*, & Hartemink,A. (2007) “Nucleosome occupancy information improves de novo motif discovery.” Research in Computational Molecular Biology 2007 (RECOMB07). Lecture Notes in Bioinformatics, eds. 4453, April 2007. pp. 107–121. (* equal contribution) [Supp. Info.]

  6. Narlikar,L., Gordân,R., Ohler,U., & Hartemink,A. (2006) “Informative Priors Based on Transcription Factor Structural Class Improve de novo Motif Discovery.” Intelligent Systems in Molecular Biology 2006 (ISMB06), Bioinformatics, 22, July 2006. pp. e384–e392. [Supp. Info.] [Code] [Input Data]