Ramana V Davuluri

Summary

Affiliation: The Ohio State University
Country: USA

Publications

  1. doi request reprint The functional consequences of alternative promoter use in mammalian genomes
    Ramana V Davuluri
    Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Trends Genet 24:167-77. 2008
  2. pmc An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules
    Huaxia Qin
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    BMC Syst Biol 3:73. 2009
  3. pmc Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
    Gregory A C Singer
    Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH, USA
    BMC Genomics 9:349. 2008
  4. pmc MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
    Hao Sun
    Department of Molecular Virology, Immunology and Medical Genetics, Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio Stage University, 420 W 12th Avenue, TMRF 524, Columbus, OH 43210, USA
    Nucleic Acids Res 34:D98-103. 2006
  5. ncbi request reprint Bioinformatics tools for modeling transcription factor target genes and epigenetic changes
    Ramana V Davuluri
    OSU Comprehensive Cancer Center, Ohio State University, Columbus, USA
    Methods Mol Biol 408:129-51. 2007
  6. pmc Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray
    Victor X Jin
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Nucleic Acids Res 32:6627-35. 2004
  7. pmc Aberrant transforming growth factor beta1 signaling and SMAD4 nuclear translocation confer epigenetic repression of ADAM19 in ovarian cancer
    Michael Wy Chan
    Human Cancer Genetics Program, Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210 1234, USA
    Neoplasia 10:908-19. 2008
  8. pmc The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type
    Jaroslaw Jendrzejewski
    Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
    Proc Natl Acad Sci U S A 109:8646-51. 2012
  9. doi request reprint Application of FirstEF to find promoters and first exons in the human genome
    Ramana V Davuluri
    Ohio State University, Columbus, Ohio, USA
    Curr Protoc Bioinformatics . 2003
  10. ncbi request reprint Changes in gene expression associated with loss of function of the NSDHL sterol dehydrogenase in mouse embryonic fibroblasts
    David Cunningham
    Center for Molecular and Human Genetics, Columbus Children s Research Institute, Ohio State University, Columbus, OH, USA
    J Lipid Res 46:1150-62. 2005

Research Grants

Collaborators

Detail Information

Publications25

  1. doi request reprint The functional consequences of alternative promoter use in mammalian genomes
    Ramana V Davuluri
    Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Trends Genet 24:167-77. 2008
    ..Here we discuss the functional consequences of use and misuse of alternative promoters in normal and disease genomes and review the molecular mechanisms regulating alternative promoter use in mammalian genomes...
  2. pmc An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules
    Huaxia Qin
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    BMC Syst Biol 3:73. 2009
    ..The regulatory effect of SMAD complex likely depends on transcriptional modules, in which the SMAD binding elements and partner transcription factor binding sites (SMAD modules) are present in specific context...
  3. pmc Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
    Gregory A C Singer
    Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH, USA
    BMC Genomics 9:349. 2008
    ..Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell...
  4. pmc MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
    Hao Sun
    Department of Molecular Virology, Immunology and Medical Genetics, Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio Stage University, 420 W 12th Avenue, TMRF 524, Columbus, OH 43210, USA
    Nucleic Acids Res 34:D98-103. 2006
    ..MPromDb serves as a portal for genome-wide promoter analysis of data generated by ChIP-chip experimental studies. MPromDb can be accessed from http://bioinformatics.med.ohio-state.edu/MPromDb...
  5. ncbi request reprint Bioinformatics tools for modeling transcription factor target genes and epigenetic changes
    Ramana V Davuluri
    OSU Comprehensive Cancer Center, Ohio State University, Columbus, USA
    Methods Mol Biol 408:129-51. 2007
    ..A list of these programs is provided along with their web Uniform Resource Locator (URLs) and guidelines for successful application are suggested...
  6. pmc Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray
    Victor X Jin
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Nucleic Acids Res 32:6627-35. 2004
    ..This integrated approach, therefore, sets a paradigm in which the iterative process of model refinement and experimental verification will continue until an accurate prediction of promoter target sequences is derived...
  7. pmc Aberrant transforming growth factor beta1 signaling and SMAD4 nuclear translocation confer epigenetic repression of ADAM19 in ovarian cancer
    Michael Wy Chan
    Human Cancer Genetics Program, Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210 1234, USA
    Neoplasia 10:908-19. 2008
    ..Given the emerging role of ADAMs family proteins in growth factor regulation in normal cells, we suggest that epigenetic dysregulation of ADAM19 may contribute to the neoplastic process in ovarian cancer...
  8. pmc The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type
    Jaroslaw Jendrzejewski
    Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
    Proc Natl Acad Sci U S A 109:8646-51. 2012
    ..Our data suggest that SNP rs944289 predisposes to PTC through a previously uncharacterized, long intergenic noncoding RNA gene (PTCSC3) that has the characteristics of a tumor suppressor...
  9. doi request reprint Application of FirstEF to find promoters and first exons in the human genome
    Ramana V Davuluri
    Ohio State University, Columbus, Ohio, USA
    Curr Protoc Bioinformatics . 2003
    ..This unit presents FirstEF as a method for predicting the first exons and promoters. A combines FirstEF predictions with other information such as cDNA/EST matches...
  10. ncbi request reprint Changes in gene expression associated with loss of function of the NSDHL sterol dehydrogenase in mouse embryonic fibroblasts
    David Cunningham
    Center for Molecular and Human Genetics, Columbus Children s Research Institute, Ohio State University, Columbus, OH, USA
    J Lipid Res 46:1150-62. 2005
    ..Of the 21 remaining genes, 16 are known genes, some of which have been implicated previously in cholesterol homeostasis or lipid-mediated signaling, and 5 are uncharacterized cDNA clones...
  11. pmc Aberrant DNA methylation of OLIG1, a novel prognostic factor in non-small cell lung cancer
    Romulo M Brena
    Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
    PLoS Med 4:e108. 2007
    ..However, the overall survival of patients with resectable tumors varies significantly, indicating the need for additional prognostic factors to better predict the outcome of the disease, particularly within a given TNM subset...
  12. ncbi request reprint Prognostic DNA methylation biomarkers in ovarian cancer
    Susan H Wei
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
    Clin Cancer Res 12:2788-94. 2006
    ..Correspondingly, distinct combinations of methylated loci can function as biomarkers for numerous clinical correlates of ovarian and other cancers...
  13. pmc CpG island methylation in a mouse model of lymphoma is driven by the genetic configuration of tumor cells
    Rene Opavsky
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA
    PLoS Genet 3:1757-69. 2007
    ..The ability to predict genome-wide epigenetic silencing based on relatively few genetic alterations will allow for a more complete classification of tumors and understanding of tumor cell biology...
  14. pmc AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks
    Saranyan K Palaniswamy
    Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210, USA
    Plant Physiol 140:818-29. 2006
    ..The current release of AtRegNet contains a total of 187 (September 2005) direct targets for 66 TFs. AGRIS can be accessed at http://Arabidopsis.med.ohio-state.edu...
  15. pmc Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs
    Victor X Jin
    Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    BMC Bioinformatics 7:114. 2006
    ..The motifs for these core promoter elements are highly degenerate, which tends to lead to a high false discovery rate when attempting to detect them in promoter sequences...
  16. ncbi request reprint Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters
    Alfred S L Cheng
    Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA
    Mol Cell 21:393-404. 2006
    ..These results suggest that ERalpha and c-MYC physically interact to stabilize the ERalpha-coactivator complex, thereby permitting other signal transduction pathways to fine-tune estrogen-mediated signaling networks...
  17. ncbi request reprint Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer
    Yu Wei Leu
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
    Cancer Res 64:8184-92. 2004
    ..The results imply, for the first time, the significance of epigenetic regulation on ERalpha target genes, providing new direction for research in this classical signaling pathway...
  18. ncbi request reprint OMGProm: a database of orthologous mammalian gene promoters
    Saranyan K Palaniswamy
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
    Bioinformatics 21:835-6. 2005
    ..The current version of OMGProm contains 8550 promoter pairs of 6373 orthologous human and mouse genes, where supporting experimental evidence for transcription start site annotation exists in at least one species...
  19. pmc MicroRNA genes are frequently located near mouse cancer susceptibility loci
    Cinzia Sevignani
    Department of Microbiology and Immunology, Kimmel Cancer Center, Jefferson Medical College, Philadelphia, PA 19107, USA
    Proc Natl Acad Sci U S A 104:8017-22. 2007
    ..These data provide a catalog of miRNA genes in inbred strains that could represent genes involved in the development and penetrance of solid tumors...
  20. ncbi request reprint A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha
    Lang Li
    Division of Biostatistics, Department of Medicine, Indiana University School of Medicine Indianapolis, IN 47405, USA
    Bioinformatics 22:2210-6. 2006
    ....
  21. ncbi request reprint A NotI-EcoRV promoter library for studies of genetic and epigenetic alterations in mouse models of human malignancies
    Li Yu
    Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Genomics 84:647-60. 2004
    ..Luciferase assays using NotI-EcoRV clones confirmed that the library is enriched for promoter sequences. Thus, this library will support future genetic and epigenetic studies in mouse models...
  22. pmc HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development
    Twyla T Pohar
    Division of Human Cancer Genetics, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University, Columbus, OH 43210, USA
    Nucleic Acids Res 32:D86-90. 2004
    ..med.ohio-state.edu/HemoPDB. Links to the documentation and other technical details are provided on this website...
  23. ncbi request reprint Computer software to find genes in plant genomic DNA
    Ramana V Davuluri
    Department of Molecular Virology, Immunology, and Medical Genetics, Human Cancer Genetics Program, The Ohio State University, Columbus, OH, USA
    Methods Mol Biol 236:87-108. 2003
    ..We provide a list of these programs along with their. Web uniform resource locators (URLs) and suggest guidelines for successful gene finding...
  24. ncbi request reprint Direct coupling of the cell cycle and cell death machinery by E2F
    Zaher Nahle
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nat Cell Biol 4:859-64. 2002
    ..The data also underscore how cell cycle progression can be coupled to the apoptotic machinery...
  25. pmc An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands
    Zunyan Dai
    Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
    Genome Res 12:1591-8. 2002
    ..Feasibility of this system is shown in three tumor types, medulloblastomas, lung cancers, and head and neck cancers. We report the cloning of 178 AscI RLGS fragments via two methods by use of this library...

Research Grants1

  1. Genomewide discovery & analysis of alternative promoters
    Ramana Davuluri; Fiscal Year: 2007
    ....