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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.PMID: 18793445 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021.

Ulvé VM, Sevin EW, Chéron A, Barloy-Hubler F.

BMC Genomics. 2007 Dec 19;8:467.PMID: 18093320 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.

del Val C, Rivas E, Torres-Quesada O, Toro N, Jiménez-Zurdo JI.

Mol Microbiol. 2007 Dec;66(5):1080-91. Epub 2007 Oct 25.PMID: 17971083 [PubMed - indexed for MEDLINE]Related articlesFree article

High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs.

Livny J, Teonadi H, Livny M, Waldor MK.

PLoS One. 2008 Sep 12;3(9):e3197. Erratum in: PLoS ONE. 2008;3(11). doi: 10.1371/annotation/a03e1870-1dd7-4c16-8c46-2268eeb2a50a. PMID: 18787707 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2.

Livny J, Brencic A, Lory S, Waldor MK.

Nucleic Acids Res. 2006;34(12):3484-93.PMID: 16870723 [PubMed - indexed for MEDLINE]Related articlesFree article

Biocomputational prediction of small non-coding RNAs in Streptomyces.

Pánek J, Bobek J, Mikulík K, Basler M, Vohradský J.

BMC Genomics. 2008 May 13;9:217.PMID: 18477385 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of bacterial small non-coding RNAs: experimental approaches.

Altuvia S.

Curr Opin Microbiol. 2007 Jun;10(3):257-61. Epub 2007 Jun 5. Review.PMID: 17553733 [PubMed - indexed for MEDLINE]Related articles

sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes.

Livny J, Fogel MA, Davis BM, Waldor MK.

Nucleic Acids Res. 2005 Jul 26;33(13):4096-105. Print 2005.PMID: 16049021 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species.

González N, Heeb S, Valverde C, Kay E, Reimmann C, Junier T, Haas D.

BMC Genomics. 2008 Apr 13;9:167.PMID: 18405392 [PubMed - indexed for MEDLINE]Related articlesFree article

Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence.

Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I, Margalit H, Altuvia S.

Nucleic Acids Res. 2008 Apr;36(6):1913-27. Epub 2008 Feb 11.PMID: 18267966 [PubMed - indexed for MEDLINE]Related articlesFree article

RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria.

Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, Wagner EG.

Nucleic Acids Res. 2003 Nov 15;31(22):6435-43.PMID: 14602901 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of small, noncoding RNAs in bacteria using heterogeneous data.

Tjaden B.

J Math Biol. 2008 Jan;56(1-2):183-200. Epub 2007 Mar 13.PMID: 17354017 [PubMed - indexed for MEDLINE]Related articles

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli.

Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S.

Curr Biol. 2001 Jun 26;11(12):941-50.PMID: 11448770 [PubMed - indexed for MEDLINE]Related articles

Sequence analysis of the 144-kilobase accessory plasmid pSmeSM11a, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment.

Stiens M, Schneiker S, Keller M, Kuhn S, Pühler A, Schlüter A.

Appl Environ Microbiol. 2006 May;72(5):3662-72.PMID: 16672515 [PubMed - indexed for MEDLINE]Related articlesFree article

Small non-coding RNAs in Streptomyces coelicolor.

Swiercz JP, Hindra, Bobek J, Bobek J, Haiser HJ, Di Berardo C, Tjaden B, Elliot MA.

Nucleic Acids Res. 2008 Dec;36(22):7240-51. Epub 2008 Nov 12.PMID: 19008244 [PubMed - indexed for MEDLINE]Related articlesFree article

Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.

Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiss S, Hackermüller J, Hüttenhofer A, Stadler PF, Bläsi U, Moll I.

Microbiology. 2008 Oct;154(Pt 10):3175-87.PMID: 18832323 [PubMed - indexed for MEDLINE]Related articlesFree article

How to find small non-coding RNAs in bacteria.

Vogel J, Sharma CM.

Biol Chem. 2005 Dec;386(12):1219-38. Review.PMID: 16336117 [PubMed - indexed for MEDLINE]Related articles

Small non-coding RNAs in Caulobacter crescentus.

Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L.

Mol Microbiol. 2008 May;68(3):600-14. Epub 2008 Mar 25.PMID: 18373523 [PubMed - indexed for MEDLINE]Related articles

Efficient annotation of bacterial genomes for small, noncoding RNAs using the integrative computational tool sRNAPredict2.

Livny J.

Methods Mol Biol. 2007;395:475-88.PMID: 17993693 [PubMed - indexed for MEDLINE]Related articles

A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome.

Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB.

Biosystems. 2002 Mar-May;65(2-3):157-77.PMID: 12069726 [PubMed - indexed for MEDLINE]Related articles