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Results: 1 to 20 of 30

1.

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.

PMID:
24843172
[PubMed - in process]
2.

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.

PMID:
24753424
[PubMed - in process]
Free Article
3.

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.

PMID:
24633877
[PubMed - indexed for MEDLINE]
4.

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.

PMID:
24244498
[PubMed - in process]
Free PMC Article
5.

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.

PMID:
23991199
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23901011
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23270466
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22751503
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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
[PubMed - indexed for MEDLINE]
10.

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.

PMID:
22455878
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
21843873
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
21700226
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
21067590
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
20368425
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
20181675
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
19969537
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
19443547
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.

Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A.

Nucleic Acids Res. 2009 Apr;37(6):e46. doi: 10.1093/nar/gkp080. Epub 2009 Feb 17.

PMID:
19223322
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Identification and isolation of lysogens with induced prophage.

Livny J, Larock CN, Friedman DI.

Methods Mol Biol. 2009;501:253-65. doi: 10.1007/978-1-60327-164-6_22.

PMID:
19066826
[PubMed - indexed for MEDLINE]
20.

Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011.

Valverde C, Livny J, Schlüter JP, Reinkensmeier J, Becker A, Parisi G.

BMC Genomics. 2008 Sep 16;9:416. doi: 10.1186/1471-2164-9-416.

PMID:
18793445
[PubMed - indexed for MEDLINE]
Free PMC Article

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