Approaches to microRNA discovery
MicroRNAs (miRNAs) are noncoding RNAs that can regulate gene expression. Several
hundred genes encoding miRNAs have been experimentally identified in animals, and …
hundred genes encoding miRNAs have been experimentally identified in animals, and …
Annotating noncoding RNA genes
S Griffiths-Jones - Annu. Rev. Genomics Hum. Genet., 2007 - annualreviews.org
Noncoding RNA genes produce a functional RNA product rather than a translated protein.
More than 1500 homologs of known “classical” RNA genes can be annotated in the human …
More than 1500 homologs of known “classical” RNA genes can be annotated in the human …
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs
Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of genomic
regions containing potential structural ncRNAs. The analysis of these data requires highly …
regions containing potential structural ncRNAs. The analysis of these data requires highly …
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering
The RFAM database defines families of ncRNAs by means of sequence similarities that are
sufficient to establish homology. In some cases, such as microRNAs and box H/ACA …
sufficient to establish homology. In some cases, such as microRNAs and box H/ACA …
RNAz 2.0: improved noncoding RNA detection
RNAz is a widely used software package for de novo detection of structured noncoding
RNAs in comparative genomics data. Four years of experience have not only demonstrated …
RNAs in comparative genomics data. Four years of experience have not only demonstrated …
The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint
LF Sempere, CN Cole, MA McPeek… - … Zoology Part B …, 2006 - Wiley Online Library
How complex body plans evolved in animals such as fruit flies and vertebrates, as compared
to the relatively simple jellyfish and sponges, is not known, given the similarity of …
to the relatively simple jellyfish and sponges, is not known, given the similarity of …
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data
J Hertel, PF Stadler - Bioinformatics, 2006 - academic.oup.com
Recently, genome-wide surveys for non-coding RNAs have provided evidence for tens of
thousands of previously undescribed evolutionary conserved RNAs with distinctive …
thousands of previously undescribed evolutionary conserved RNAs with distinctive …
SnoReport: computational identification of snoRNAs with unknown targets
Unlike tRNAs and microRNAs, both classes of snoRNAs, which direct two distinct types of
chemical modifications of uracil residues, have proved to be surprisingly difficult to find in …
chemical modifications of uracil residues, have proved to be surprisingly difficult to find in …
Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression
Recent evidence points to considerable transcription occurring in non-protein-coding
regions of eukaryote genomes. However, their lack of conservation and demonstrated …
regions of eukaryote genomes. However, their lack of conservation and demonstrated …
Evolution of spliceosomal snRNA genes in metazoan animals
While studies of the evolutionary histories of protein families are commonplace, little is
known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in …
known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in …