 Jonathan Livny, PH.D.
| Title | Instructor in Medicine |
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| Institution | Brigham and Women's Hospital |
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| Department | Medicine |
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| Address | Channing Laboratory
181 Longwood Ave
Boston MA 02115
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 Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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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.
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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.
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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.
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Livny J. Bioinformatic discovery of bacterial regulatory RNAs using SIPHT. Methods Mol Biol. 2012; 905:3-14.
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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.
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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.
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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.
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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.
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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.
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Livny J, Waldor MK. Mining regulatory 5'UTRs from cDNA deep sequencing datasets. Nucleic Acids Res. 2010 Mar; 38(5):1504-14.
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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.
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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.
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Livny J, Larock CN, Friedman DI. Identification and isolation of lysogens with induced prophage. Methods Mol Biol. 2009; 501:253-65.
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Valverde C, Livny J, Schlüter JP, Reinkensmeier J, Becker A, Parisi G. Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics. 2008; 9:416.
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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.
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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.
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Livny J, Waldor MK. Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol. 2007 Apr; 10(2):96-101.
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Livny J. Efficient annotation of bacterial genomes for small, noncoding RNAs using the integrative computational tool sRNAPredict2. Methods Mol Biol. 2007; 395:475-88.
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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.
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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.
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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.
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Livny J, Friedman DI. Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system. Mol Microbiol. 2004 Mar; 51(6):1691-704.
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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.
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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.
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