Ravi Gupta

Summary

Affiliation: The Wistar Institute
Country: USA

Publications

  1. ncbi Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
    Ravi Gupta
    Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
    BMC Bioinformatics 11:S65. 2010
  2. ncbi Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq
    Hao Sun
    Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
    Nucleic Acids Res 39:190-201. 2011
  3. ncbi Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
    Sharmistha Pal
    Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania 19019, USA
    Genome Res 21:1260-72. 2011
  4. ncbi IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data
    Hyunsoo Kim
    Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 4268, USA
    BMC Bioinformatics 12:305. 2011
  5. ncbi Alternative transcription and alternative splicing in cancer
    Sharmistha Pal
    Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, USA Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
    Pharmacol Ther 136:283-94. 2012
  6. ncbi Tree-based position weight matrix approach to model transcription factor binding site profiles
    Yingtao Bi
    Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 6:e24210. 2011
  7. ncbi MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data
    Ravi Gupta
    Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
    Nucleic Acids Res 39:D92-7. 2011

Collaborators

  • Ramana V Davuluri
  • Hyunsoo Kim
  • Jiejun Wu
  • Sharmistha Pal
  • Louise C Showe
  • Priyankara Wickramasinghe
  • Hao Sun
  • Yingtao Bi
  • Francisco J Agosto-Perez
  • Tim H M Huang
  • Nadia Dahmane
  • Valerie Baubet
  • Anirban Bhattacharyya

Detail Information

Publications7

  1. ncbi Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
    Ravi Gupta
    Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
    BMC Bioinformatics 11:S65. 2010
    ..Further, the use of these methods is limited by their high cost and strong dependence on cellular type and context...
  2. ncbi Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq
    Hao Sun
    Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
    Nucleic Acids Res 39:190-201. 2011
    ..The promoter annotations and ChIP-seq data presented here will aid ongoing efforts of characterizing gene regulatory regions in mammalian genomes...
  3. ncbi Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
    Sharmistha Pal
    Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania 19019, USA
    Genome Res 21:1260-72. 2011
    ..The transcriptomes of developing and adult cerebella presented in this study emphasize the importance of analyzing gene regulation and function at the isoform level...
  4. ncbi IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data
    Hyunsoo Kim
    Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 4268, USA
    BMC Bioinformatics 12:305. 2011
    ..Estimating the expression levels of transcript isoforms from mRNA-Seq data is a challenging problem due to the presence of constitutive exons...
  5. ncbi Alternative transcription and alternative splicing in cancer
    Sharmistha Pal
    Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, USA Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
    Pharmacol Ther 136:283-94. 2012
    ..This review highlights the role and regulation of alternative transcription and splicing mechanisms in generating the transcriptome, and the misuse and diagnostic/prognostic potential of alternative transcription and splicing in cancer...
  6. ncbi Tree-based position weight matrix approach to model transcription factor binding site profiles
    Yingtao Bi
    Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 6:e24210. 2011
    ..The improved accuracy is the result of modelling the complete dependent structure of the motifs and better prediction of true positive rate. The findings could lead to better understanding of the mechanisms of TF-DNA interactions...
  7. ncbi MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data
    Ravi Gupta
    Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
    Nucleic Acids Res 39:D92-7. 2011
    ..We have also integrated GBrowse genome browser with MPromDb for visualization of ChIP-seq profiles and to display the annotations. The current release of MPromDb can be accessed at http://bioinformatics.wistar.upenn.edu/MPromDb/...