Jignesh R Parikh

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis
    Nikki Traylor-Knowles
    Department of Biology, Stanford University, Pacific Grove, CA 93950, USA
    BMC Genomics 12:585. 2011
  2. pmc multiplierz: an extensible API based desktop environment for proteomics data analysis
    Jignesh R Parikh
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA, 02115, USA
    BMC Bioinformatics 10:364. 2009
  3. pmc Multi-edge gene set networks reveal novel insights into global relationships between biological themes
    Jignesh R Parikh
    Bioinformatics Program, Boston University, Boston, Massachusetts, USA
    PLoS ONE 7:e45211. 2012
  4. pmc Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling
    Job D Cardoza
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
    Wiley Interdiscip Rev Syst Biol Med 4:141-62. 2012
  5. pmc Discovering causal signaling pathways through gene-expression patterns
    Jignesh R Parikh
    Bioinformatics Program, Boston University, Boston, MA 02115, USA
    Nucleic Acids Res 38:W109-17. 2010
  6. ncbi request reprint Niobium(V) oxide (Nb2O5): application to phosphoproteomics
    Scott B Ficarro
    Department of Cancer Biology and Blais Proteomics Center, Dana Farber Cancer Institute, Boston, Massachusetts 02115 6084, USA
    Anal Chem 80:4606-13. 2008
  7. doi request reprint Mining immune epitopes in the inner ear
    Michael Platt
    Department of Otolaryngology Head and Neck Surgery, Boston University School of Medicine, Boston, Massachusetts, USA
    Otolaryngol Head Neck Surg 150:460-3. 2014
  8. pmc Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells
    Yu Lu
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Cell Stem Cell 15:92-101. 2014

Collaborators

Detail Information

Publications8

  1. pmc Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis
    Nikki Traylor-Knowles
    Department of Biology, Stanford University, Pacific Grove, CA 93950, USA
    BMC Genomics 12:585. 2011
    ..We isolated RNA from colony fragments ("nubbins") exposed to four environmental stressors (heat, desiccation, peroxide, and hypo-saline conditions) or control conditions. The RNA was pooled and sequenced using the 454 platform...
  2. pmc multiplierz: an extensible API based desktop environment for proteomics data analysis
    Jignesh R Parikh
    Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA, 02115, USA
    BMC Bioinformatics 10:364. 2009
    ..Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge...
  3. pmc Multi-edge gene set networks reveal novel insights into global relationships between biological themes
    Jignesh R Parikh
    Bioinformatics Program, Boston University, Boston, Massachusetts, USA
    PLoS ONE 7:e45211. 2012
    ..MetaNet is freely available at http://blaispathways.dfci.harvard.edu/metanet/...
  4. pmc Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling
    Job D Cardoza
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
    Wiley Interdiscip Rev Syst Biol Med 4:141-62. 2012
    ..Collectively, these approaches will facilitate identification of biomarkers and pathways relevant to diagnosis and treatment of human disease...
  5. pmc Discovering causal signaling pathways through gene-expression patterns
    Jignesh R Parikh
    Bioinformatics Program, Boston University, Boston, MA 02115, USA
    Nucleic Acids Res 38:W109-17. 2010
    ..We expose our novel resource and algorithm through a web server called SPEED: Signaling Pathway Enrichment using Experimental Data sets. SPEED can be freely accessed at http://speed.sys-bio.net/...
  6. ncbi request reprint Niobium(V) oxide (Nb2O5): application to phosphoproteomics
    Scott B Ficarro
    Department of Cancer Biology and Blais Proteomics Center, Dana Farber Cancer Institute, Boston, Massachusetts 02115 6084, USA
    Anal Chem 80:4606-13. 2008
    ..Collectively our data indicate that Nb 2O 5 provides efficient enrichment for phosphopeptides and offers a complementary approach for large-scale phosphoproteomics studies...
  7. doi request reprint Mining immune epitopes in the inner ear
    Michael Platt
    Department of Otolaryngology Head and Neck Surgery, Boston University School of Medicine, Boston, Massachusetts, USA
    Otolaryngol Head Neck Surg 150:460-3. 2014
    ..If validated in future clinical trials, these candidate immune epitopes in the inner ear would be potential novel targets for diagnosis and treatment of some inner ear disorders and the resulting hearing loss. ..
  8. pmc Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells
    Yu Lu
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Cell Stem Cell 15:92-101. 2014
    ..These data suggest that OCT4, SFRS2, and MBD2 participate in a positive feedback loop, regulating proteome diversity in support of hPSC self-renewal and reprogramming. ..