Jignesh R Parikh
Affiliation: Boston University
- Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornisNikki 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...
- multiplierz: an extensible API based desktop environment for proteomics data analysisJignesh 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...
- Multi-edge gene set networks reveal novel insights into global relationships between biological themesJignesh 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/...
- Mass spectrometry-based proteomics: qualitative identification to activity-based protein profilingJob 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...
- Discovering causal signaling pathways through gene-expression patternsJignesh 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/...
- Niobium(V) oxide (Nb2O5): application to phosphoproteomicsScott 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...
- Mining immune epitopes in the inner earMichael 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. ..
- Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cellsYu 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. ..