Raja Jothi

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 362:861-75. 2006
  2. ncbi Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 8:173. 2007
  3. ncbi Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    Suresh Cuddapah
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 19:24-32. 2009
  4. ncbi Chromatin poises miRNA- and protein-coding genes for expression
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 19:1742-51. 2009
  5. ncbi COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 22:779-88. 2006
  6. ncbi Predicting protein domain interactions from coevolution of conserved regions
    Maricel G Kann
    Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 67:811-20. 2007
  7. ncbi ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder
    Leelavati Narlikar
    National Institutes of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
    Methods Mol Biol 802:305-22. 2012
  8. ncbi Predicting protein-protein interaction by searching evolutionary tree automorphism space
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:i241-50. 2005
  9. ncbi Predicting domain-domain interactions using a parsimony approach
    Katia S Guimarães
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 7:R104. 2006
  10. ncbi Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
    Raja Jothi
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
    Mol Syst Biol 5:294. 2009

Collaborators

Detail Information

Publications18

  1. ncbi Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 362:861-75. 2006
    ....
  2. ncbi Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 8:173. 2007
    ..Here, proteins with similar profiles are inferred to be functionally related under the assumption that proteins involved in the same metabolic pathway or cellular system are likely to have been co-inherited during evolution...
  3. ncbi Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    Suresh Cuddapah
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 19:24-32. 2009
    ..Our data indicate that CTCF may play important roles in the barrier activity of insulators, and this study provides a resource for further investigation of the CTCF function in organizing chromatin in the human genome...
  4. ncbi Chromatin poises miRNA- and protein-coding genes for expression
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 19:1742-51. 2009
    ..Our data suggest that miRNA- and protein-coding genes share similar mechanisms of regulation by chromatin modifications, which poise inducible genes for activation in response to environmental stimuli...
  5. ncbi COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 22:779-88. 2006
    ..These methods do not attempt to preserve the non-transitivity and hierarchic nature of the orthology relation...
  6. ncbi Predicting protein domain interactions from coevolution of conserved regions
    Maricel G Kann
    Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 67:811-20. 2007
    ..We provide a theoretical validation of our results leading to new insights into the interplay between coevolution and speciation of interacting proteins...
  7. ncbi ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder
    Leelavati Narlikar
    National Institutes of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
    Methods Mol Biol 802:305-22. 2012
    ....
  8. ncbi Predicting protein-protein interaction by searching evolutionary tree automorphism space
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:i241-50. 2005
    ..When compared with related computational approaches, our method reduces the search space by approximately 3 x 10(5)-fold and at the same time increases the accuracy of predicting correct binding partners...
  9. ncbi Predicting domain-domain interactions using a parsimony approach
    Katia S Guimarães
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 7:R104. 2006
    ..This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts...
  10. ncbi Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
    Raja Jothi
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
    Mol Syst Biol 5:294. 2009
    ..We propose that the interplay between network organization and TF dynamics could permit differential utilization of the same underlying network by distinct members of a clonal cell population...
  11. ncbi Genome-wide characterization of menin-dependent H3K4me3 reveals a specific role for menin in the regulation of genes implicated in MEN1-like tumors
    Sunita K Agarwal
    Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e37952. 2012
    ....
  12. ncbi Differences in evolutionary pressure acting within highly conserved ortholog groups
    Teresa M Przytycka
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 8:208. 2008
    ..g. Proteobacteria or Firmicutes)...
  13. ncbi Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types
    Gang Wei
    Laboratory of Molecular Immunology, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Immunity 35:299-311. 2011
    ....
  14. ncbi RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo
    Yukimasa Takeda
    Cell Biology Section, Systems Biology Group, Biostatistics Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 40:8519-35. 2012
    ....
  15. ncbi Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells
    Liqi Li
    Section on Cellular and Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
    Nat Immunol 12:129-36. 2011
    ..Our results identify a central role for Ldb1 in regulating the transcriptional program responsible for the maintenance of HSCs...
  16. ncbi DOMINE: a comprehensive collection of known and predicted domain-domain interactions
    Sailu Yellaboina
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 39:D730-5. 2011
    ..The contents of the DOMINE are available at http://domine.utdallas.edu...
  17. ncbi Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    Raja Jothi
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:5221-31. 2008
    ..Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding...
  18. ncbi DOMINE: a database of protein domain interactions
    Balaji Raghavachari
    Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083, USA
    Nucleic Acids Res 36:D656-61. 2008
    ..DOMINE is freely available at http://domine.utdallas.edu...