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Results: 1 to 20 of 33

1.

Simultaneous generation of many RNA-seq libraries in a single reaction.

Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J.

Nat Methods. 2015 Apr;12(4):323-5. doi: 10.1038/nmeth.3313. Epub 2015 Mar 2.

PMID:
25730492
2.

Pilicide ec240 disrupts virulence circuits in uropathogenic Escherichia coli.

Greene SE, Pinkner JS, Chorell E, Dodson KW, Shaffer CL, Conover MS, Livny J, Hadjifrangiskou M, Almqvist F, Hultgren SJ.

MBio. 2014 Oct 28;5(6):e02038. doi: 10.1128/mBio.02038-14.

3.

Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying Vibrio parahaemolyticus gene expression during infection.

Livny J, Zhou X, Mandlik A, Hubbard T, Davis BM, Waldor MK.

Nucleic Acids Res. 2014 Oct 29;42(19):12212-23. doi: 10.1093/nar/gku891. Epub 2014 Sep 27.

4.

Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY.

Brinsmade SR, Alexander EL, Livny J, Stettner AI, Segrè D, Rhee KY, Sonenshein AL.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8227-32. doi: 10.1073/pnas.1321308111. Epub 2014 May 19.

5.

TargetRNA2: identifying targets of small regulatory RNAs in bacteria.

Kery MB, Feldman M, Livny J, Tjaden B.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W124-9. doi: 10.1093/nar/gku317. Epub 2014 Apr 21.

6.

High-throughput sequencing of Campylobacter jejuni insertion mutant libraries reveals mapA as a fitness factor for chicken colonization.

Johnson JG, Livny J, Dirita VJ.

J Bacteriol. 2014 Jun;196(11):1958-67. doi: 10.1128/JB.01395-13. Epub 2014 Mar 14.

7.

Identification of novel sRNAs in mycobacterial species.

Tsai CH, Baranowski C, Livny J, McDonough KA, Wade JT, Contreras LM.

PLoS One. 2013 Nov 14;8(11):e79411. doi: 10.1371/journal.pone.0079411. eCollection 2013.

8.

The complete Campylobacter jejuni transcriptome during colonization of a natural host determined by RNAseq.

Taveirne ME, Theriot CM, Livny J, DiRita VJ.

PLoS One. 2013 Aug 21;8(8):e73586. doi: 10.1371/journal.pone.0073586. eCollection 2013.

9.

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data.

Chao MC, Pritchard JR, Zhang YJ, Rubin EJ, Livny J, Davis BM, Waldor MK.

Nucleic Acids Res. 2013 Oct;41(19):9033-48. doi: 10.1093/nar/gkt654. Epub 2013 Jul 30.

10.

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J.

BMC Genomics. 2012 Dec 27;13:734. doi: 10.1186/1471-2164-13-734.

11.

Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs.

Vvedenskaya IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, Nickels BE.

Genes Dev. 2012 Jul 1;26(13):1498-507. doi: 10.1101/gad.192732.112.

12.

Bioinformatic discovery of bacterial regulatory RNAs using SIPHT.

Livny J.

Methods Mol Biol. 2012;905:3-14. doi: 10.1007/978-1-61779-949-5_1.

PMID:
22735994
13.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.

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.

Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23.

14.

RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.

Mandlik A, Livny J, Robins WP, Ritchie JM, Mekalanos JJ, Waldor MK.

Cell Host Microbe. 2011 Aug 18;10(2):165-74. doi: 10.1016/j.chom.2011.07.007.

15.

NanoRNAs prime transcription initiation in vivo.

Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE.

Mol Cell. 2011 Jun 24;42(6):817-25. doi: 10.1016/j.molcel.2011.06.005.

16.

Identification of small RNAs in Francisella tularensis.

Postic G, Frapy E, Dupuis M, Dubail I, Livny J, Charbit A, Meibom KL.

BMC Genomics. 2010 Nov 10;11:625. doi: 10.1186/1471-2164-11-625.

17.

Legionella pneumophila 6S RNA optimizes intracellular multiplication.

Faucher SP, Friedlander G, Livny J, Margalit H, Shuman HA.

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7533-8. doi: 10.1073/pnas.0911764107. Epub 2010 Apr 5.

18.

Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis.

DiChiara JM, Contreras-Martinez LM, Livny J, Smith D, McDonough KA, Belfort M.

Nucleic Acids Res. 2010 Jul;38(12):4067-78. doi: 10.1093/nar/gkq101. Epub 2010 Feb 24.

19.

Mining regulatory 5'UTRs from cDNA deep sequencing datasets.

Livny J, Waldor MK.

Nucleic Acids Res. 2010 Mar;38(5):1504-14. doi: 10.1093/nar/gkp1121. Epub 2009 Dec 7.

20.

Pivotal role of the Francisella tularensis heat-shock sigma factor RpoH.

Grall N, Livny J, Waldor M, Barel M, Charbit A, Meibom KL.

Microbiology. 2009 Aug;155(Pt 8):2560-72. doi: 10.1099/mic.0.029058-0. Epub 2009 May 14.

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