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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

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 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

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

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics.

McCutcheon JP, Eddy SR.

Nucleic Acids Res. 2003 Jul 15;31(14):4119-28.PMID: 12853629 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative genomics of small RNAs in bacterial genomes.

Luban S, Kihara D.

OMICS. 2007 Spring;11(1):58-73.PMID: 17411396 [PubMed - indexed for MEDLINE]Related articles

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

Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach.

Xiao B, Li W, Guo G, Li B, Liu Z, Jia K, Guo Y, Mao X, Zou Q.

Curr Microbiol. 2009 Mar;58(3):258-63. Epub 2009 Jan 3.PMID: 19123032 [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

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

Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome.

Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW.

FEMS Microbiol Lett. 2007 Nov;276(1):83-92.PMID: 17937666 [PubMed - indexed for MEDLINE]Related articles

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

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

Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains.

Pichon C, Felden B.

Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14249-54. Epub 2005 Sep 23. Erratum in: Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16905. PMID: 16183745 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria.

Yuan ZC, Zaheer R, Morton R, Finan TM.

Nucleic Acids Res. 2006 May 22;34(9):2686-97. Print 2006.PMID: 16717279 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.

Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR.

Nucleic Acids Res. 2007;35(14):4809-19. Epub 2007 Jul 9.PMID: 17621584 [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

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

Biocomputational prediction of non-coding RNAs in model cyanobacteria.

Voss B, Georg J, Schön V, Ude S, Hess WR.

BMC Genomics. 2009 Mar 23;10:123.PMID: 19309518 [PubMed - indexed for MEDLINE]Related articlesFree article