Joshua Z Levin

Summary

Publications

  1. ncbi Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
    Joshua Z Levin
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Genome Biol 10:R115. 2009
  2. ncbi Comprehensive comparative analysis of strand-specific RNA sequencing methods
    Joshua Z Levin
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 7:709-15. 2010
  3. ncbi Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
    Moran Yassour
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 11:R87. 2010
  4. ncbi Integrative analysis of the melanoma transcriptome
    Michael F Berger
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 20:413-27. 2010
  5. ncbi Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
    Michal Rabani
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:436-42. 2011
  6. ncbi Full-length transcriptome assembly from RNA-Seq data without a reference genome
    Manfred G Grabherr
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:644-52. 2011
  7. ncbi Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    Mitchell Guttman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:503-10. 2010
  8. ncbi Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    Andrea Pauli
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Genome Res 22:577-91. 2012

Collaborators

Detail Information

Publications8

  1. ncbi Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
    Joshua Z Levin
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Genome Biol 10:R115. 2009
    ..Thus, targeted RNA-Seq produces an enhanced view of the molecular state of a set of "high interest" genes...
  2. ncbi Comprehensive comparative analysis of strand-specific RNA sequencing methods
    Joshua Z Levin
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 7:709-15. 2010
    ..Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in other organisms...
  3. ncbi Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
    Moran Yassour
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 11:R87. 2010
    ..However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been suggested that most antisense transcripts may result from promiscuous bi-directional transcription in a dense genome...
  4. ncbi Integrative analysis of the melanoma transcriptome
    Michael F Berger
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 20:413-27. 2010
    ..Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types...
  5. ncbi Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
    Michal Rabani
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:436-42. 2011
    ..Certain transcripts, including those encoding cytokines and transcription factors, mature faster. Our study provides a quantitative approach to study the integrative process of RNA regulation...
  6. ncbi Full-length transcriptome assembly from RNA-Seq data without a reference genome
    Manfred G Grabherr
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:644-52. 2011
    ..Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome...
  7. ncbi Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    Mitchell Guttman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:503-10. 2010
    ..Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes...
  8. ncbi Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    Andrea Pauli
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Genome Res 22:577-91. 2012
    ..Our study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies...