Raja Jothi

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc 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
  2. pmc 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
  3. pmc Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
    Johannes M Freudenberg
    Systems Biology Section, Biostatistics Branch, National Institute of Environmental Health Sciences NIEHS, National Institutes of Health NIH, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 40:3364-77. 2012
  4. pmc Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells
    Daniel Menendez
    Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences NIEHS, National Institutes of Health NIH, Research Triangle Park, NC 27709, USA, Systems Biology Group, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences NIEHS, National Institutes of Health NIH, Research Triangle Park, NC 27709, USA, William G Enloe High School, Raleigh, NC 27610, USA and Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
    Nucleic Acids Res 41:7286-301. 2013
  5. pmc 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
  6. pmc 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
  7. pmc Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis
    Senthilkumar Cinghu
    Systems Biology Section and Stem Cell Biology Section, Laboratory of Molecular Carcinogenesis, and Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
    Proc Natl Acad Sci U S A 111:E1581-90. 2014
  8. pmc 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
  9. pmc 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
  10. pmc 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

Collaborators

Detail Information

Publications26

  1. pmc 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...
  2. pmc 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...
  3. pmc Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
    Johannes M Freudenberg
    Systems Biology Section, Biostatistics Branch, National Institute of Environmental Health Sciences NIEHS, National Institutes of Health NIH, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 40:3364-77. 2012
    ....
  4. pmc Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells
    Daniel Menendez
    Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences NIEHS, National Institutes of Health NIH, Research Triangle Park, NC 27709, USA, Systems Biology Group, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences NIEHS, National Institutes of Health NIH, Research Triangle Park, NC 27709, USA, William G Enloe High School, Raleigh, NC 27610, USA and Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
    Nucleic Acids Res 41:7286-301. 2013
    ..We discovered 149 putative new p53 target genes including several that are relevant to tumor suppression, revealing potential new targets for cancer therapy and expanding our understanding of the p53 regulatory network. ..
  5. pmc 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...
  6. pmc 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...
  7. pmc Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis
    Senthilkumar Cinghu
    Systems Biology Section and Stem Cell Biology Section, Laboratory of Molecular Carcinogenesis, and Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
    Proc Natl Acad Sci U S A 111:E1581-90. 2014
    ..The proposed computational framework, by helping to prioritize and preselect candidate genes for tests using complex and expensive genetic screens, provides a powerful yet inexpensive means for identification of key cell identity genes. ..
  8. pmc 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...
  9. pmc 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...
  10. pmc 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
    ..Many of these methods are limited by the fact that they can handle only a small number of protein sequences. Also, details on evolutionary tree topology are missing as they use similarity matrices in lieu of the trees...
  11. pmc Cnot1, Cnot2, and Cnot3 maintain mouse and human ESC identity and inhibit extraembryonic differentiation
    Xiaofeng Zheng
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, RTP, North Carolina, USA
    Stem Cells 30:910-22. 2012
    ..Together, our results indicate that Cnot1, Cnot2, and Cnot3 represent a novel component of the core self-renewal and pluripotency circuitry conserved in mouse and human ESCs...
  12. ncbi request reprint 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...
  13. pmc 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. pmc Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation
    Liqi Li
    Section on Cellular and Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Blood 121:4575-85. 2013
    ..Together, these results provide a foundation for defining the mechanism and scope of Ldb1 complex activity during erythropoiesis...
  15. doi request reprint 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
    ....
  16. pmc 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
    ....
  17. pmc 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...
  18. pmc 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
    ....
  19. pmc 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...
  20. pmc 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...
  21. pmc Retinoic acid-related orphan receptor γ (RORγ): a novel participant in the diurnal regulation of hepatic gluconeogenesis and insulin sensitivity
    Yukimasa Takeda
    Cell Biology Section, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
    PLoS Genet 10:e1004331. 2014
    ..The inhibition of the activation of several metabolic gene promoters by an RORγ antagonist suggests that antagonists may provide a novel strategy in the management of metabolic diseases, including type 2 diabetes...
  22. pmc 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)...
  23. pmc 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
    ....
  24. pmc 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...
  25. pmc Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal
    Brad Lackford
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
    EMBO J 33:878-89. 2014
    ..Together, our data highlight the role for post-transcriptional control in stem cell self-renewal, provide mechanistic insight on APA regulation in development, and establish an important function for APA in cell fate specification. ..
  26. pmc INO80 Facilitates Pluripotency Gene Activation in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development
    Li Wang
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    Cell Stem Cell 14:575-91. 2014
    ....