title: Computational analysis of noncoding RNAs.
abstract: Noncoding RNAs have emerged as important key players in the cell. Understanding their surprisingly diverse range of functions is challenging for experimental and computational biology. Here, we review computational methods to analyze noncoding RNAs. The topics covered include basic and advanced techniques to predict RNA structures, annotation of noncoding RNAs in genomic data, mining RNA-seq data for novel transcripts and prediction of transcript structures, computational aspects of microRNAs, and database resources.
authors.affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA. wash@mit.edu
authors.forename: Stefan
authors.initials: S
authors.lastname: Washietl
authors.forename: Sebastian
authors.initials: S
authors.lastname: Will
authors.forename: David A
authors.initials: DA
authors.lastname: Hendrix
authors.forename: Loyal A
authors.initials: LA
authors.lastname: Goff
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
authors.forename: Bonnie
authors.initials: B
authors.lastname: Berger
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030561:Databases, Nucleic Acid; D023281:Genomics / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D022661:RNA, Untranslated / Q000737:chemistry*
chemical_list: D035683:MicroRNAs; D022661:RNA, Untranslated