Joshua Z Levin

Summary

Publications

  1. pmc 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. pmc Comparative analysis of RNA sequencing methods for degraded or low-input samples
    Xian Adiconis
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 10:623-9. 2013
  3. pmc 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
  4. pmc 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. pmc 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. pmc RNA-SeQC: RNA-seq metrics for quality control and process optimization
    David S DeLuca
    Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Bioinformatics 28:1530-2. 2012
  7. pmc 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
  8. pmc 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
  9. pmc Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
    Alex K Shalek
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nature 498:236-40. 2013
  10. pmc 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

Publications18

  1. pmc 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. pmc Comparative analysis of RNA sequencing methods for degraded or low-input samples
    Xian Adiconis
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 10:623-9. 2013
    ..SMART and NuGEN had distinct strengths for measuring low-quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development. ..
  3. pmc 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...
  4. pmc 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. pmc 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. pmc RNA-SeQC: RNA-seq metrics for quality control and process optimization
    David S DeLuca
    Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Bioinformatics 28:1530-2. 2012
    ..Availability and implementation: See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool...
  7. pmc 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...
  8. pmc 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...
  9. pmc Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
    Alex K Shalek
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nature 498:236-40. 2013
    ..Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits...
  10. pmc 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...
  11. pmc 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...
  12. doi Genomics of Loa loa, a Wolbachia-free filarial parasite of humans
    Christopher A Desjardins
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 45:495-500. 2013
    ..These results suggest that the role of Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and nonparasitic nematodes...
  13. pmc Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
    Christine M Malboeuf
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Nucleic Acids Res 41:e13. 2013
    ....
  14. pmc De novo assembly of highly diverse viral populations
    Xiao Yang
    The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Genomics 13:475. 2012
    ....
  15. pmc Peptidomic discovery of short open reading frame-encoded peptides in human cells
    Sarah A Slavoff
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Chem Biol 9:59-64. 2013
    ..In addition, coding sORFs are present in a small fraction (8 out of 1,866) of long intergenic noncoding RNAs. Together, these results provide strong evidence that the human proteome is more complex than previously appreciated...
  16. pmc Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
    Georgia Giannoukos
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Genome Biol 13:R23. 2012
    ..The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA...
  17. pmc Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica
    Rays H Y Jiang
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Genet 9:e1003272. 2013
    ..parasitica...
  18. pmc Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
    Christina A Cuomo
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 22:2478-88. 2012
    ..Together these events may explain the emergence and success of these diverse intracellular parasites...