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Items: 1 to 20 of 119

1.

An improved method for identification of small non-coding RNAs in bacteria using support vector machine.

Barman RK, Mukhopadhyay A, Das S.

Sci Rep. 2017 Apr 6;7:46070. doi: 10.1038/srep46070.

2.

sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes.

Sridhar J, Sambaturu N, Sabarinathan R, Ou HY, Deng Z, Sekar K, Rafi ZA, Rajakumar K.

PLoS One. 2010 Aug 5;5(8):e11970. doi: 10.1371/journal.pone.0011970. Erratum in: PLoS One. 2010;5(9). doi: 10.1371/annotation/71408e55-e1d3-4950-9c3b-d3a3ad66a1ff. Narmada, Suryanarayanan Ramkumar [corrected to Sambaturu, Narmada].

3.

Common and phylogenetically widespread coding for peptides by bacterial small RNAs.

Friedman RC, Kalkhof S, Doppelt-Azeroual O, Mueller SA, Chovancová M, von Bergen M, Schwikowski B.

BMC Genomics. 2017 Jul 21;18(1):553. doi: 10.1186/s12864-017-3932-y.

4.

Prediction of bacterial small RNAs in the RsmA (CsrA) and ToxT pathways: a machine learning approach.

Fakhry CT, Kulkarni P, Chen P, Kulkarni R, Zarringhalam K.

BMC Genomics. 2017 Aug 22;18(1):645. doi: 10.1186/s12864-017-4057-z.

5.

Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA.

Grüll MP, Peña-Castillo L, Mulligan ME, Lang AS.

RNA Biol. 2017 Jul 3;14(7):914-925. doi: 10.1080/15476286.2017.1306175. Epub 2017 Mar 15.

6.

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data.

Rath EC, Pitman S, Cho KH, Bai Y.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):540. doi: 10.1186/s12859-017-1897-0.

7.

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli.

Shinhara A, Matsui M, Hiraoka K, Nomura W, Hirano R, Nakahigashi K, Tomita M, Mori H, Kanai A.

BMC Genomics. 2011 Aug 24;12:428. doi: 10.1186/1471-2164-12-428.

8.

Comparative genomics of small RNAs in bacterial genomes.

Luban S, Kihara D.

OMICS. 2007 Spring;11(1):58-73.

PMID:
17411396
9.

A multiobjective method for robust identification of bacterial small non-coding RNAs.

Arnedo J, Romero-Zaliz R, Zwir I, Del Val C.

Bioinformatics. 2014 Oct 15;30(20):2875-82. doi: 10.1093/bioinformatics/btu398. Epub 2014 Jun 23.

PMID:
24958812
10.

Bacterial small RNAs in the Genus Rickettsia.

Schroeder CL, Narra HP, Rojas M, Sahni A, Patel J, Khanipov K, Wood TG, Fofanov Y, Sahni SK.

BMC Genomics. 2015 Dec 18;16:1075. doi: 10.1186/s12864-015-2293-7.

11.

In silico 'fishing' using known small regulatory RNA (sRNA) candidates as the decoy from Escherichia coli, Salmonella typhi and Salmonella typhimurium manifested 14 novel sRNA candidates in the orthologous region of Proteus mirabilis.

KishanRaj S, Sumitha S, Siventhiran B, Thiviyaa O, Sathasivam KV, Xavier R, Tang TH, Citartan M, Chinni SV.

Mol Biol Rep. 2018 Dec;45(6):2333-2343. doi: 10.1007/s11033-018-4397-z. Epub 2018 Oct 3.

PMID:
30284142
12.

A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts.

Schneider HW, Raiol T, Brigido MM, Walter MEMT, Stadler PF.

BMC Genomics. 2017 Oct 18;18(1):804. doi: 10.1186/s12864-017-4178-4.

13.

Small RNA-mediated regulation in bacteria: A growing palette of diverse mechanisms.

Dutta T, Srivastava S.

Gene. 2018 May 20;656:60-72. doi: 10.1016/j.gene.2018.02.068. Epub 2018 Mar 1. Review.

PMID:
29501814
14.

Prediction and characterization of small non-coding RNAs related to secondary metabolites in Saccharopolyspora erythraea.

Liu WB, Shi Y, Yao LL, Zhou Y, Ye BC.

PLoS One. 2013 Nov 13;8(11):e80676. doi: 10.1371/journal.pone.0080676. eCollection 2013.

15.

Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element.

Hot D, Slupek S, Wulbrecht B, D'Hondt A, Hubans C, Antoine R, Locht C, Lemoine Y.

BMC Genomics. 2011 Apr 27;12:207. doi: 10.1186/1471-2164-12-207.

17.

Experimental identification of small non-coding regulatory RNAs in the opportunistic human pathogen Burkholderia cenocepacia J2315.

Ramos CG, Grilo AM, da Costa PJ, Leitão JH.

Genomics. 2013 Feb;101(2):139-48. doi: 10.1016/j.ygeno.2012.10.006. Epub 2012 Nov 8.

18.

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.

19.

Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae.

Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT.

BMC Genomics. 2011 Jan 30;12:87. doi: 10.1186/1471-2164-12-87.

20.

Identification of small RNAs in diverse bacterial species.

Livny J, Waldor MK.

Curr Opin Microbiol. 2007 Apr;10(2):96-101. Epub 2007 Mar 23. Review.

PMID:
17383222

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