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Items: 1 to 20 of 218

1.

Plant noncoding RNA gene discovery by "single-genome comparative genomics".

Chen CJ, Zhou H, Chen YQ, Qu LH, Gautheret D.

RNA. 2011 Mar;17(3):390-400. doi: 10.1261/rna.2426511. Epub 2011 Jan 10.

2.

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. doi: 10.1186/1471-2164-10-123.

3.

De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring.

Larsson P, Hinas A, Ardell DH, Kirsebom LA, Virtanen A, Söderbom F.

Genome Res. 2008 Jun;18(6):888-99. doi: 10.1101/gr.069104.107. Epub 2008 Mar 17.

4.

A comparative genome-wide study of ncRNAs in trypanosomatids.

Doniger T, Katz R, Wachtel C, Michaeli S, Unger R.

BMC Genomics. 2010 Nov 4;11:615. doi: 10.1186/1471-2164-11-615.

5.

Computational methods in noncoding RNA research.

Machado-Lima A, del Portillo HA, Durham AM.

J Math Biol. 2008 Jan;56(1-2):15-49. Epub 2007 Sep 4. Review.

PMID:
17786447
6.

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.

7.

The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa.

Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH.

Nucleic Acids Res. 2003 May 15;31(10):2601-13.

8.

In Silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula.

Wen J, Parker BJ, Weiller GF.

In Silico Biol. 2007;7(4-5):485-505.

PMID:
18391239
9.

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes.

Soldà G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A.

Brief Bioinform. 2009 Sep;10(5):475-89. doi: 10.1093/bib/bbp022. Epub 2009 Apr 21. Review.

PMID:
19383843
10.

Conservation and divergence of microRNAs in Populus.

Barakat A, Wall PK, Diloreto S, Depamphilis CW, Carlson JE.

BMC Genomics. 2007 Dec 31;8:481. doi: 10.1186/1471-2164-8-481.

11.

The map-based sequence of the rice genome.

International Rice Genome Sequencing Project.

Nature. 2005 Aug 11;436(7052):793-800.

PMID:
16100779
12.

Duplicated RNA genes in teleost fish genomes.

Rose D, Jöris J, Hackermüller J, Reiche K, Li Q, Stadler PF.

J Bioinform Comput Biol. 2008 Dec;6(6):1157-75.

PMID:
19090022
13.

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana.

Song D, Yang Y, Yu B, Zheng B, Deng Z, Lu BL, Chen X, Jiang T.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S36. doi: 10.1186/1471-2105-10-S1-S36.

14.

Conservation and functional element discovery in 20 angiosperm plant genomes.

Hupalo D, Kern AD.

Mol Biol Evol. 2013 Jul;30(7):1729-44. doi: 10.1093/molbev/mst082. Epub 2013 May 2.

PMID:
23640124
15.

smyRNA: a novel Ab initio ncRNA gene finder.

Salari R, Aksay C, Karakoc E, Unrau PJ, Hajirasouliha I, Sahinalp SC.

PLoS One. 2009;4(5):e5433. doi: 10.1371/journal.pone.0005433. Epub 2009 May 5.

17.

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions.

Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K.

BMC Biol. 2007 Jun 18;5:25.

18.

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, Gaspin C.

RNA. 2011 Nov;17(11):1947-56. doi: 10.1261/rna.2844911. Epub 2011 Sep 23.

20.

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J.

Genome Res. 2008 Feb;18(2):242-51. Epub 2007 Dec 20.

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