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Jonathan Livny, PH.D.

TitleInstructor in Medicine
InstitutionBrigham and Women's Hospital
DepartmentMedicine
AddressChanning Laboratory
181 Longwood Ave
Boston MA 02115

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Tsai CH, Baranowski C, Livny J, McDonough KA, Wade JT, Contreras LM. Identification of Novel sRNAs in Mycobacterial Species. PLoS One. 2013; 8(11):e79411.
    View in: PubMed
  2. Taveirne ME, Theriot CM, Livny J, Dirita VJ. The Complete Campylobacter jejuni Transcriptome during Colonization of a Natural Host Determined by RNAseq. PLoS One. 2013; 8(8):e73586.
    View in: PubMed
  3. Chao MC, Pritchard JR, Zhang YJ, Rubin EJ, Livny J, Davis BM, Waldor MK. High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res. 2013 Oct 1; 41(19):9033-48.
    View in: PubMed
  4. Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J. How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? BMC Genomics. 2012; 13:734.
    View in: PubMed
  5. Vvedenskaya IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, Nickels BE. Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. Genes Dev. 2012 Jul 1; 26(13):1498-507.
    View in: PubMed
  6. Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol. 2012; 13(3):R23.
    View in: PubMed
  7. Livny J. Bioinformatic discovery of bacterial regulatory RNAs using SIPHT. Methods Mol Biol. 2012; 905:3-14.
    View in: PubMed
  8. Mandlik A, Livny J, Robins WP, Ritchie JM, Mekalanos JJ, Waldor MK. RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression. Cell Host Microbe. 2011 Aug 18; 10(2):165-74.
    View in: PubMed
  9. Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE. NanoRNAs prime transcription initiation in vivo. Mol Cell. 2011 Jun 24; 42(6):817-25.
    View in: PubMed
  10. Postic G, Frapy E, Dupuis M, Dubail I, Livny J, Charbit A, Meibom KL. Identification of small RNAs in Francisella tularensis. BMC Genomics. 2010; 11:625.
    View in: PubMed
  11. Faucher SP, Friedlander G, Livny J, Margalit H, Shuman HA. Legionella pneumophila 6S RNA optimizes intracellular multiplication. Proc Natl Acad Sci U S A. 2010 Apr 20; 107(16):7533-8.
    View in: PubMed
  12. DiChiara JM, Contreras-Martinez LM, Livny J, Smith D, McDonough KA, Belfort M. Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. Nucleic Acids Res. 2010 Jul; 38(12):4067-78.
    View in: PubMed
  13. Livny J, Waldor MK. Mining regulatory 5'UTRs from cDNA deep sequencing datasets. Nucleic Acids Res. 2010 Mar; 38(5):1504-14.
    View in: PubMed
  14. Grall N, Livny J, Waldor M, Barel M, Charbit A, Meibom KL. Pivotal role of the Francisella tularensis heat-shock sigma factor RpoH. Microbiology. 2009 Aug; 155(Pt 8):2560-72.
    View in: PubMed
  15. Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A. Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res. 2009 Apr; 37(6):e46.
    View in: PubMed
  16. Livny J, Larock CN, Friedman DI. Identification and isolation of lysogens with induced prophage. Methods Mol Biol. 2009; 501:253-65.
    View in: PubMed
  17. Valverde C, Livny J, Schl├╝ter JP, Reinkensmeier J, Becker A, Parisi G. Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics. 2008; 9:416.
    View in: PubMed
  18. Livny J, Teonadi H, Livny M, Waldor MK. High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One. 2008; 3(9):e3197.
    View in: PubMed
  19. Livny J, Yamaichi Y, Waldor MK. Distribution of centromere-like parS sites in bacteria: insights from comparative genomics. J Bacteriol. 2007 Dec; 189(23):8693-703.
    View in: PubMed
  20. Livny J, Waldor MK. Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol. 2007 Apr; 10(2):96-101.
    View in: PubMed
  21. Livny J. Efficient annotation of bacterial genomes for small, noncoding RNAs using the integrative computational tool sRNAPredict2. Methods Mol Biol. 2007; 395:475-88.
    View in: PubMed
  22. Slamti L, Livny J, Waldor MK. Global gene expression and phenotypic analysis of a Vibrio cholerae rpoH deletion mutant. J Bacteriol. 2007 Jan; 189(2):351-62.
    View in: PubMed
  23. Livny J, Brencic A, Lory S, Waldor MK. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res. 2006; 34(12):3484-93.
    View in: PubMed
  24. Livny J, Fogel MA, Davis BM, Waldor MK. sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res. 2005; 33(13):4096-105.
    View in: PubMed
  25. Livny J, Friedman DI. Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system. Mol Microbiol. 2004 Mar; 51(6):1691-704.
    View in: PubMed
  26. Wagner PL, Livny J, Neely MN, Acheson DW, Friedman DI, Waldor MK. Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli. Mol Microbiol. 2002 May; 44(4):957-70.
    View in: PubMed
  27. Gillian AL, Schmechel SC, Livny J, Schiff LA, Nibert ML. Reovirus protein sigmaNS binds in multiple copies to single-stranded RNA and shares properties with single-stranded DNA binding proteins. J Virol. 2000 Jul; 74(13):5939-48.
    View in: PubMed
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