Literature DB >> 15231541

Conserved RNA secondary structures in viral genomes: a survey.

I L Hofacker1, P F Stadler, R R Stocsits.   

Abstract

SUMMARY: The genomes of RNA viruses often carry conserved RNA structures that perform vital functions during the life cycle of the virus. Such structures can be detected using a combination of structure prediction and co-variation analysis. Here we present results from pilot studies on a variety of viral families performed during bioinformatics computer lab courses in past years.

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Year:  2004        PMID： 15231541     DOI： 10.1093/bioinformatics/bth108

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  23 in total

1.  Crucial role of the 5' conserved structure of bamboo mosaic virus satellite RNA in downregulation of helper viral RNA replication.

Authors:  Yau-Heiu Hsu; Hsin-Chuan Chen; Jeannie Cheng; Padmanaban Annamalai; Padmanaban Annamali; Bin-Yen Lin; Chiang-Tai Wu; Wen-Bin Yeh; Na-Sheng Lin
Journal:  J Virol       Date:  2006-03       Impact factor: 5.103

2.  Evolutionary patterns of non-coding RNAs.

Authors:  Athanasius F Bompfünewerer; Christoph Flamm; Claudia Fried; Guido Fritzsch; Ivo L Hofacker; Jörg Lehmann; Kristin Missal; Axel Mosig; Bettina Müller; Sonja J Prohaska; Bärbel M R Stadler; Peter F Stadler; Andrea Tanzer; Stefan Washietl; Christina Witwer
Journal:  Theory Biosci       Date:  2005-04       Impact factor: 1.919

3.  Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions.

Authors:  Wilson Li; Emily Manktelow; Johann C von Kirchbach; Julia R Gog; Ulrich Desselberger; Andrew M Lever
Journal:  Nucleic Acids Res       Date:  2010-07-29       Impact factor: 16.971

4.  Influenza A Virus Panhandle Structure Is Directly Involved in RIG-I Activation and Interferon Induction.

Authors:  GuanQun Liu; Hong-Su Park; Hyun-Mi Pyo; Qiang Liu; Yan Zhou
Journal:  J Virol       Date:  2015-03-25       Impact factor: 5.103

Review 5.  Cytoplasm and Beyond: Dynamic Innate Immune Sensing of Influenza A Virus by RIG-I.

Authors:  GuanQun Liu; Yan Zhou
Journal:  J Virol       Date:  2019-04-03       Impact factor: 5.103

Review 6.  Computational analysis of RNA structures with chemical probing data.

Authors:  Ping Ge; Shaojie Zhang
Journal:  Methods       Date:  2015-02-14       Impact factor: 3.608

7.  A U-turn motif-containing stem-loop in the coronavirus 5' untranslated region plays a functional role in replication.

Authors:  Pinghua Liu; Lichun Li; Jason J Millership; Hyojeung Kang; Julian L Leibowitz; David P Giedroc
Journal:  RNA       Date:  2007-03-12       Impact factor: 4.942

8.  Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus.

Authors:  Martin Schlee; Andreas Roth; Veit Hornung; Cristina Amparo Hagmann; Vera Wimmenauer; Winfried Barchet; Christoph Coch; Markus Janke; Aleksandra Mihailovic; Greg Wardle; Stefan Juranek; Hiroki Kato; Taro Kawai; Hendrik Poeck; Katherine A Fitzgerald; Osamu Takeuchi; Shizuo Akira; Thomas Tuschl; Eicke Latz; Janos Ludwig; Gunther Hartmann
Journal:  Immunity       Date:  2009-07-02       Impact factor: 31.745

9.  Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene.

Authors:  Qi Wang; Ian Barr; Feng Guo; Christopher Lee
Journal:  RNA       Date:  2008-10-30       Impact factor: 4.942

10.  Base composition and translational selection are insufficient to explain codon usage bias in plant viruses.

Authors:  Daniel J Cardinale; Kate DeRosa; Siobain Duffy
Journal:  Viruses       Date:  2013-01-15       Impact factor: 5.048
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