Research Topics
Genomes and Genes | Ramana V DavuluriSummaryAffiliation: The Ohio State University Country: USA Publications
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Publications
The functional consequences of alternative promoter use in mammalian genomesRamana 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...
Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promotersAlfred 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...
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling arrayGregory 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...- An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modulesHuaxia 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... - Bioinformatics tools for modeling transcription factor target genes and epigenetic changesRamana 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... - MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental dataHao 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... - Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarrayVictor 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... - Aberrant transforming growth factor beta1 signaling and SMAD4 nuclear translocation confer epigenetic repression of ADAM19 in ovarian cancerMichael 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... - AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networksSaranyan 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... - The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor typeJaroslaw 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... - Application of FirstEF to find promoters and first exons in the human genomeRamana 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... - Prognostic DNA methylation biomarkers in ovarian cancerSusan 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..Such ovarian cancer biomarkers represent a promising approach for the assessment and management of this devastating disease... - Changes in gene expression associated with loss of function of the NSDHL sterol dehydrogenase in mouse embryonic fibroblastsDavid 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... - CpG island methylation in a mouse model of lymphoma is driven by the genetic configuration of tumor cellsRene 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... - Aberrant DNA methylation of OLIG1, a novel prognostic factor in non-small cell lung cancerRomulo 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... - Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairsVictor 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... - Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancerYu-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... - OMGProm: a database of orthologous mammalian gene promotersSaranyan 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... - Direct coupling of the cell cycle and cell death machinery by E2FZaher 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... - Computer software to find genes in plant genomic DNARamana 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... - HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell developmentTwyla 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... - A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alphaLang Li
Division of Biostatistics, Department of Medicine, Indiana University School of Medicine Indianapolis, IN 47405, USA
Bioinformatics 22:2210-6. 2006.... - A NotI-EcoRV promoter library for studies of genetic and epigenetic alterations in mouse models of human malignanciesLi 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... - MicroRNA genes are frequently located near mouse cancer susceptibility lociCinzia 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... - An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islandsZunyan 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 Grants
- Genomewide discovery & analysis of alternative promotersRamana Davuluri; Fiscal Year: 2007....