Computational identification of noncoding RNAs in E. coli by comparative genomics.

By Elena Rivas, R. Klein, Thomas A. Jones, Sean R. Eddy. Current Biology, 2001

434 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0a114fd34faa4d6446d32b3661e219177c0bbba2

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Citations in the corpus

Fast and reliable prediction of noncoding RNAs (2005, positive): “The most widely used program QRNA [22], which has been successfully used to identify ncRNAs in bacteria [23] and yeast [24], is not suitable for screens of large genomes: QRNA is limited to pairwise alignments and its reliability is low especially if the evolutionary distance of the two sequences li”
Global Mapping of Small RNA-Target Interactions in Bacteria (2016, background): “…the sRNAs detected in the ﬁrst genome-wide surveys were predominantly independent transcripts encoded in intergenic regions (Argaman et al., 2001; Rivas et al., 2001; Wassar-man et al., 2001), recent studies revealed expression of candidate sRNAs originating from various genomic regions,…”
The microRNAs of Caenorhabditis elegans. (2003, methodology): “Recent advances have been made in the computational identification of ncRNA genes through comparative genomics, and complex algorithms have been developed to identify ncRNAs in general (Argaman et al. 2001; Rivas et al. 2001; Wassarman et al. 2001), as well as specific ncRNA families such as tRNAs a”
Non–coding RNA genes and the modern RNA world (2001, background): “; and general ncRNA gene-finding exercises using computational comparative genomics in Escherichia coli”
The small RNA regulators of Escherichia coli: roles and mechanisms*. (2004, background): “Another group (77) developed computational approaches to detect conservation of secondary structure (inverted repeats encoding stem-loops) within intergenic regions.”
σE Regulates and Is Regulated by a Small RNA in Escherichia coli (2007, background): “A number of genome-wide searches performed by various groups using computational and biochemical methods have uncovered close to 100 small RNAs (sRNAs) in Escherichia coli (6, 8, 27, 47, 57, 62).”