Kannan Tharakaraman

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    BMC Bioinformatics 7:408. 2006
  2. pmc Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
    Nak Kyeong Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Bioinformatics 9:262. 2008
  3. pmc Identification of cis-regulatory elements in gene co-expression networks using A-GLAM
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 541:1-22. 2009
  4. pmc The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    Nucleic Acids Res 36:2777-86. 2008
  5. pmc Promoter analysis: gene regulatory motif identification with A-GLAM
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
    Methods Mol Biol 537:263-76. 2009
  6. pmc Alignments anchored on genomic landmarks can aid in the identification of regulatory elements
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38A, 8600 Rockville Pike, Bethesda, MD 20894 6075, USA
    Bioinformatics 21:i440-8. 2005

Detail Information

Publications6

  1. pmc Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    BMC Bioinformatics 7:408. 2006
    ..Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set...
  2. pmc Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
    Nak Kyeong Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Bioinformatics 9:262. 2008
    ..Although some programs for identifying sequence motifs exploit positional information, most of them model it only implicitly and with ad hoc methods, making them unsuitable for general motif searches...
  3. pmc Identification of cis-regulatory elements in gene co-expression networks using A-GLAM
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 541:1-22. 2009
    ..Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes...
  4. pmc The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    Nucleic Acids Res 36:2777-86. 2008
    ..By exploiting the phenomenon of positional regulation, it uses position to differentiate the biological functions of subsets of TFBSs sharing a common sequence motif...
  5. pmc Promoter analysis: gene regulatory motif identification with A-GLAM
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
    Methods Mol Biol 537:263-76. 2009
    ..Here we present a survey of recent computational methods for eukaryotic promoter analysis and describe the use of an alignment-based method implemented in the A-GLAM program...
  6. pmc Alignments anchored on genomic landmarks can aid in the identification of regulatory elements
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38A, 8600 Rockville Pike, Bethesda, MD 20894 6075, USA
    Bioinformatics 21:i440-8. 2005
    ..However, since the positional anchors focus A-GLAM on the motif of interest, masking DNA repeats during Gibbs sampling becomes unnecessary...