Computational approaches to discovering noncoding RNA

Wiley Interdisciplinary Reviews. RNA
Paul M KrzyzanowskiMiguel A Andrade-Navarro

Abstract

New developments are being brought to the field of molecular biology with the mounting evidence that RNA transcripts not translated into protein (noncoding RNAs, ncRNAs) hold a variety of biological functions. Computational discovery of ncRNAs is one of these developments, fueled not only by the urge to characterize these sequences but also by necessity to prioritize ones with the most relevant functions for experimental verification. The heterogeneity in size and mode of activity of ncRNAs is reflected in the corresponding diversity of computational methods for their study. Sequence and structural analysis, conservation across species, and relative position to other genomic elements are being used for ncRNA detection. In addition, the recent development of techniques that allow deep sequencing of cell transcripts either globally or from isolated ncRNA-related material is leading the field toward increased use of such high-throughput data. We expect that imminent breakthroughs will include the classification of newer types of ncRNA and new insights into miRNA and piRNA biology, eventually leading toward the completion of a catalog of all human ncRNAs.

References

Nov 1, 1972·Proceedings of the National Academy of Sciences of the United States of America·W G SpiegelmanH Eisen
Apr 25, 1997·Journal of Molecular Biology·C Burge, S Karlin
Feb 28, 1998·Nucleic Acids Research·S L SalzbergO White
Jul 13, 2001·Current Biology : CB·L ArgamanS Altuvia
Jan 22, 2002·BMC Bioinformatics·E Rivas, S R Eddy
Jan 31, 2002·Trends in Genetics : TIG·Ben LehnerChristopher M Sanderson
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Jan 10, 2003·Nucleic Acids Research·D KarolchikUNKNOWN University of California Santa Cruz
Jan 17, 2003·Genome Research·Scott SchwartzWebb Miller
Mar 18, 2003·Nature Biotechnology·Rodrigo YelinGalit Rotman
Apr 4, 2003·Genes & Development·Lee P LimDavid P Bartel
Jan 6, 2004·Nucleic Acids Research·Dean Laslett, Bjorn Canback
Jan 22, 2004·Bioinformatics·I L HofackerP F Stadler
Apr 23, 2004·Trends in Biochemical Sciences·Giovanni LavorgnaGiorgio Casari
May 18, 2004·Bioinformatics·Lori E DoddEric Y Chuang
Jun 25, 2004·Nucleic Acids Research·André LambertDaniel Gautheret
Jan 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Stefan WashietlPeter F Stadler
Apr 5, 2005·Nature Genetics·Azra KrekNikolaus Rajewsky
Jun 21, 2005·Nature Genetics·Isaac BentwichZvi Bentwich
Jun 28, 2005·Nucleic Acids Research·Yuanji Zhang
Nov 9, 2005·BMC Bioinformatics·Alain SewerMihaela Zavolan
Dec 31, 2005·Nucleic Acids Research·Laurent Lestrade, Michel J Weber
Jan 27, 2006·Nucleic Acids Research·Alexander Hüttenhofer, Jörg Vogel
Apr 22, 2006·PLoS Computational Biology·Jakob Skou PedersenDavid Haussler
Dec 6, 2006·Nucleic Acids Research·Ken C PangJohn S Mattick
Mar 27, 2007·Current Opinion in Microbiology·Paul Babitzke, Tony Romeo
Apr 25, 2007·Nucleic Acids Research·Karin LagesenDavid W Ussery
Jun 8, 2007·Current Opinion in Microbiology·Shoshy Altuvia
Jun 15, 2007·Nucleic Acids Research·Dmitriy SkvortsovSimon Tavaré
Sep 21, 2007·Nucleic Acids Research·S Sai Lakshmi, Shipra Agrawal
Sep 26, 2007·Nature Genetics·Michael KerteszEran Segal
Nov 10, 2007·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Nov 15, 2007·Nucleic Acids Research·Shunmin HeRunsheng Chen
Dec 26, 2007·Nucleic Acids Research·Doron BetelChris Sander
Mar 29, 2008·Methods in Molecular Biology·Edyta Z Bajak, Curt H Hagedorn
Apr 9, 2008·Nature Biotechnology·Marc R FriedländerNikolaus Rajewsky
Jun 11, 2008·Nature Biotechnology·Marcelo A GermanPamela J Green
Jun 20, 2008·Genome Research·Marcel E DingerJohn S Mattick
Oct 25, 2008·Nucleic Acids Research·Toutai MituyamaKiyoshi Asai
Oct 30, 2008·Nucleic Acids Research·Giorgos L PapadopoulosArtemis G Hatzigeorgiou

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Citations

Aug 15, 2014·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Bing YanLong Liu
Nov 13, 2012·Journal of Cancer Research and Clinical Oncology·Feng YangGuoen Fang
Jun 9, 2016·Journal of Experimental & Clinical Cancer Research : CR·Chun-Chun MaBing Zhao
Oct 7, 2016·Frontiers in Endocrinology·Matheus Trovão QueirozVânia D'Almeida
Apr 20, 2013·Experimental and Therapeutic Medicine·Min FanZhiming Wang
May 30, 2017·BioMed Research International·Yi ZhangJialiang Yang

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