Ravi Gupta

Summary

Affiliation: The Wistar Institute
Country: USA

Publications

  1. pmc 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. pmc 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. pmc 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. pmc 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. doi request reprint 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. pmc 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. pmc 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
  8. pmc ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing
    Hiromitsu Ota
    The Wistar Institute, Philadelphia, PA 19104, USA
    Cell 153:575-89. 2013

Collaborators

Detail Information

Publications8

  1. pmc 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. pmc 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. pmc 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. pmc 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. doi request reprint 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. pmc 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. pmc 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/...
  8. pmc ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing
    Hiromitsu Ota
    The Wistar Institute, Philadelphia, PA 19104, USA
    Cell 153:575-89. 2013
    ..As expected, the expression of miRNAs is globally inhibited in ADAR1(-/-) mouse embryos, which, in turn, alters the expression of their target genes and might contribute to their embryonic lethal phenotype...