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Results: 1 to 20 of 105

1.

NAPP: the Nucleic Acid Phylogenetic Profile Database.

Ott A, Idali A, Marchais A, Gautheret D.

Nucleic Acids Res. 2012 Jan;40(Database issue):D205-9. doi: 10.1093/nar/gkr807. Epub 2011 Oct 8.

PMID:
21984475
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes.

Zhu Y, Pulukkunat DK, Li Y.

Nucleic Acids Res. 2007;35(7):2283-94. Epub 2007 Mar 27.

PMID:
17389640
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles.

Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D.

Genome Res. 2009 Jun;19(6):1084-92. doi: 10.1101/gr.089714.108. Epub 2009 Feb 23.

PMID:
19237465
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera.

Degnan PH, Ochman H, Moran NA.

PLoS Genet. 2011 Sep;7(9):e1002252. doi: 10.1371/journal.pgen.1002252. Epub 2011 Sep 1.

PMID:
21912528
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

CsfG, a sporulation-specific, small non-coding RNA highly conserved in endospore formers.

Marchais A, Duperrier S, Durand S, Gautheret D, Stragier P.

RNA Biol. 2011 May-Jun;8(3):358-64. Epub 2011 May 1.

PMID:
21532344
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.

Toffano-Nioche C, Ott A, Crozat E, Nguyen AN, Zytnicki M, Leclerc F, Forterre P, Bouloc P, Gautheret D.

RNA Biol. 2013 Jul;10(7):1211-20. doi: 10.4161/rna.25567. Epub 2013 Jul 2.

PMID:
23884177
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes.

Gaspin C, Cavaillé J, Erauso G, Bachellerie JP.

J Mol Biol. 2000 Apr 7;297(4):895-906. Erratum in: J Mol Biol 2000 Jul 21;300(4):1017-8.

PMID:
10736225
[PubMed - indexed for MEDLINE]
8.

Identification of regulatory RNAs in Bacillus subtilis.

Irnov I, Sharma CM, Vogel J, Winkler WC.

Nucleic Acids Res. 2010 Oct;38(19):6637-51. doi: 10.1093/nar/gkq454. Epub 2010 Jun 4.

PMID:
20525796
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

sRNAbase: a Web resource for small RNAs in Enterobacteriaceae.

Sathesh-Kumar S, Sridhar J, Rafi ZA.

In Silico Biol. 2010;10(3):155-61. doi: 10.3233/ISB-2010-0424.

PMID:
22430289
[PubMed - indexed for MEDLINE]
10.

In search of RNase P RNA from microbial genomes.

Li Y, Altman S.

RNA. 2004 Oct;10(10):1533-40. Epub 2004 Aug 30.

PMID:
15337843
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

GtRNAdb: a database of transfer RNA genes detected in genomic sequence.

Chan PP, Lowe TM.

Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7. doi: 10.1093/nar/gkn787. Epub 2008 Nov 4.

PMID:
18984615
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS.

Genome Res. 2011 Nov;21(11):1929-43. doi: 10.1101/gr.112516.110. Epub 2011 Oct 12.

PMID:
21994249
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.

Gruber AR, Neuböck R, Hofacker IL, Washietl S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W335-8. Epub 2007 Apr 22.

PMID:
17452347
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

New insight into RNase P RNA structure from comparative analysis of the archaeal RNA.

Harris JK, Haas ES, Williams D, Frank DN, Brown JW.

RNA. 2001 Feb;7(2):220-32.

PMID:
11233979
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Searching genomes for noncoding RNA using FastR.

Zhang S, Haas B, Eskin E, Bafna V.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Oct-Dec;2(4):366-79.

PMID:
17044173
[PubMed - indexed for MEDLINE]
16.

RNA-seq based transcriptional map of bovine respiratory disease pathogen "Histophilus somni 2336".

Kumar R, Lawrence ML, Watt J, Cooksey AM, Burgess SC, Nanduri B.

PLoS One. 2012;7(1):e29435. doi: 10.1371/journal.pone.0029435. Epub 2012 Jan 20.

PMID:
22276113
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS.

Nucleic Acids Res. 2003 Dec 1;31(23):6748-57.

PMID:
14627808
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes.

Huang HY, Chang HY, Chou CH, Tseng CP, Ho SY, Yang CD, Ju YW, Huang HD.

Nucleic Acids Res. 2009 Jan;37(Database issue):D150-4. doi: 10.1093/nar/gkn852. Epub 2008 Nov 16.

PMID:
19015153
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping.

Matthiesen R, Kirpekar F.

Nucleic Acids Res. 2009 Apr;37(6):e48. doi: 10.1093/nar/gkp139. Epub 2009 Mar 5.

PMID:
19264806
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments.

Cao Y, Wu J, Liu Q, Zhao Y, Ying X, Cha L, Wang L, Li W.

RNA. 2010 Nov;16(11):2051-7. doi: 10.1261/rna.2193110. Epub 2010 Sep 15.

PMID:
20843985
[PubMed - indexed for MEDLINE]
Free PMC Article
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