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. ncbi 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. ncbi request reprint Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying Vibrio parahaemolyticus gene expression during infection
    Jonathan Livny
    The Broad Institute, Cambridge, MA, USA Division of Infectious Diseases, Department of Microbiology and Immunobiology, Brigham and Women s Hospital, Harvard Medical School and HHMI, 181 Longwood Ave, Boston, MA, USA
    Nucleic Acids Res 42:12212-23. 2014
  4. pmc Identification of small RNAs in Francisella tularensis
    Guillaume Postic
    INSERM U1002, Paris, France
    BMC Genomics 11:625. 2010
  5. pmc High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs
    Jonathan Livny
    Channing Laboratories, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 3:e3197. 2008
  6. pmc Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2
    Jonathan Livny
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, MA 02111, USA
    Nucleic Acids Res 34:3484-93. 2006
  7. pmc sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes
    Jonathan Livny
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, MA 02111, USA
    Nucleic Acids Res 33:4096-105. 2005
  8. 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
  9. 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
  10. pmc RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression
    Anjali Mandlik
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
    Cell Host Microbe 10:165-74. 2011

Collaborators

Detail Information

Publications15

  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. ncbi 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. ncbi request reprint Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying Vibrio parahaemolyticus gene expression during infection
    Jonathan Livny
    The Broad Institute, Cambridge, MA, USA Division of Infectious Diseases, Department of Microbiology and Immunobiology, Brigham and Women s Hospital, Harvard Medical School and HHMI, 181 Longwood Ave, Boston, MA, USA
    Nucleic Acids Res 42:12212-23. 2014
    ..cholerae, likely due to the distinct ways in which these diarrheal pathogens interact with and modulate the environment in the small intestine...
  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-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs
    Jonathan Livny
    Channing Laboratories, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 3:e3197. 2008
    ..The relative paucity of genome-wide sRNA prediction represents a critical gap in current annotations of bacterial genomes and has limited examination of larger issues in sRNA biology, such as sRNA evolution...
  6. pmc Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2
    Jonathan Livny
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, MA 02111, USA
    Nucleic Acids Res 34:3484-93. 2006
    ..Our findings suggest that numerous genes have been missed in the current annotations of bacterial genomes and that, by using improved bioinformatic approaches and tools, much remains to be discovered in 'intergenic' sequences...
  7. pmc sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes
    Jonathan Livny
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, MA 02111, USA
    Nucleic Acids Res 33:4096-105. 2005
    ..Our findings suggest that sRNAPredict can be used to efficiently identify novel sRNAs even in bacteria for which promoter consensus sequences are not available...
  8. 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. ..
  9. 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...
  10. pmc RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression
    Anjali Mandlik
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
    Cell Host Microbe 10:165-74. 2011
    ..RNA-seq-based transcriptome analysis of pathogens during infection produces a robust, sensitive, and accessible data set for evaluation of regulatory responses driving pathogenesis...
  11. pmc Distribution of centromere-like parS sites in bacteria: insights from comparative genomics
    Jonathan Livny
    Channing Laboratory, Brigham and Women s Hospital, 181 Longwood Avenue, Boston MA 02115, USA
    J Bacteriol 189:8693-703. 2007
    ..Furthermore, parS sites on secondary chromosomes are not well conserved among different species, suggesting that the evolutionary histories of secondary chromosomes are more diverse than those of primary chromosomes...
  12. pmc Global gene expression and phenotypic analysis of a Vibrio cholerae rpoH deletion mutant
    Leyla Slamti
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
    J Bacteriol 189:351-62. 2007
    ..Bioinformatic analyses of the microarray data were used to define a putative sigma(32) consensus binding sequence and subsequently to identify genes that are likely to be directly regulated by RpoH in the whole V. cholerae genome...
  13. ncbi request reprint Identification of small RNAs in diverse bacterial species
    Jonathan Livny
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, MA 02111, USA
    Curr Opin Microbiol 10:96-101. 2007
    ..Although the number of known sRNAs has dramatically increased in recent years, many challenges in the identification and characterization of sRNAs lie ahead...
  14. pmc Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing
    Jane M Liu
    HHMI, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
    Nucleic Acids Res 37:e46. 2009
    ....
  15. 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...