Jonathan Livny

Summary

Publications

  1. pmc Mining regulatory 5'UTRs from cDNA deep sequencing datasets
    Jonathan Livny
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Nucleic Acids Res 38:1504-14. 2010
  2. doi request reprint Bioinformatic discovery of bacterial regulatory RNAs using SIPHT
    Jonathan Livny
    The Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Methods Mol Biol 905:3-14. 2012
  3. pmc How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
    Brian J Haas
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Genomics 13:734. 2012
  4. pmc Identification of small RNAs in Francisella tularensis
    Guillaume Postic
    INSERM U1002, Paris, France
    BMC Genomics 11:625. 2010
  5. pmc High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data
    Michael C Chao
    Division of Infectious Disease, Brigham and Women s Hospital, Boston, MA 02115, USA, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA, Howard Hughes Medical Institute, Boston, MA 02115, USA, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA and Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA
    Nucleic Acids Res 41:9033-48. 2013
  6. 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

Collaborators

Detail Information

Publications6

  1. pmc Mining regulatory 5'UTRs from cDNA deep sequencing datasets
    Jonathan Livny
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Nucleic Acids Res 38:1504-14. 2010
    ..Our findings suggest that the number and diversity of pathways regulated by r5'UTRs has been underestimated and that deep sequencing-based transcriptomics will be extremely valuable in the search for novel r5'UTRs...
  2. doi request reprint Bioinformatic discovery of bacterial regulatory RNAs using SIPHT
    Jonathan Livny
    The Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Methods Mol Biol 905:3-14. 2012
    ..Each locus is then annotated for numerous features that provide clues about its potential function and/or enable the most reliable candidates to be identified...
  3. pmc How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
    Brian J Haas
    Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Genomics 13:734. 2012
    ..A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance...
  4. pmc Identification of small RNAs in Francisella tularensis
    Guillaume Postic
    INSERM U1002, Paris, France
    BMC Genomics 11:625. 2010
    ..Relatively little is known about the regulatory networks existing in this organism that allows it to survive in a wide array of environments and no sRNA regulators have been identified so far...
  5. pmc High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data
    Michael C Chao
    Division of Infectious Disease, Brigham and Women s Hospital, Boston, MA 02115, USA, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA, Howard Hughes Medical Institute, Boston, MA 02115, USA, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA and Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA
    Nucleic Acids Res 41:9033-48. 2013
    ..cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data. ..
  6. 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...