相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life
Sinan Ugur Umu et al.
BIOINFORMATICS (2017)
Ablation of Programmed-1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity
Joseph A. Kendra et al.
JOURNAL OF VIROLOGY (2017)
A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs
Elena Rivas et al.
NATURE METHODS (2017)
Virus Variation Resource - improved response to emergent viral outbreaks
Eneida L. Hatcher et al.
NUCLEIC ACIDS RESEARCH (2017)
RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation
Rolf Backofen et al.
JOURNAL OF BIOTECHNOLOGY (2017)
Recent advances in RNA folding
Joerg Fallmann et al.
JOURNAL OF BIOTECHNOLOGY (2017)
In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression
Irmtraud M. Meyer
METHODS (2017)
Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis
Jian Wang et al.
NUCLEIC ACIDS RESEARCH (2017)
Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot
Yu-Ting Chen et al.
NUCLEIC ACIDS RESEARCH (2017)
Rewriting nature's assembly manual for a ssRNA virus
Nikesh Patel et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme
Zhichao Miao et al.
RNA (2017)
Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops
Andy Phan et al.
RNA (2017)
Regulation Mechanisms of Viral IRES-Driven Translation
Kuo-Ming Lee et al.
TRENDS IN MICROBIOLOGY (2017)
Differential regulation of hepatitis B virus core protein expression and genome replication by a small upstream open reading frame and naturally occurring mutations in the precore region
Li Zong et al.
VIROLOGY (2017)
Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes
Alba Fernandez-Sanles et al.
FRONTIERS IN MICROBIOLOGY (2017)
Non-canonical Translation in Plant RNA Viruses
Manuel Miras et al.
FRONTIERS IN PLANT SCIENCE (2017)
Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C
Maria A. Prostova et al.
PEERJ (2017)
Exploring RNA conformational space under sparse distance restraints
William R. Taylor et al.
SCIENTIFIC REPORTS (2017)
HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells
Thomas A. Hilimire et al.
ACS CHEMICAL BIOLOGY (2017)
LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex
Jenniffer Angulo et al.
NUCLEIC ACIDS RESEARCH (2016)
A comprehensive comparison of general RNA-RNA interaction prediction methods
Daniel Lai et al.
NUCLEIC ACIDS RESEARCH (2016)
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
Nuala A. O'Leary et al.
NUCLEIC ACIDS RESEARCH (2016)
Structure and function of RNA elements present in enteroviral genomes
Mariola Dutkiewicz et al.
ACTA BIOCHIMICA POLONICA (2016)
New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure
Maciej Antczak et al.
ACTA BIOCHIMICA POLONICA (2016)
Prediction of conserved long-range RNA-RNA interactions in full viral genomes
Markus Fricke et al.
BIOINFORMATICS (2016)
Computational modeling of RNA 3D structures and interactions
Wayne K. Dawson et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)
Structural and Functional Characterization of Programmed Ribosomal Frameshift Signals in West Nile Virus Strains Reveals High Structural Plasticity Among cis-Acting RNA Elements
Christine Moomau et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2016)
Modeling Three-Dimensional Structural Motifs of Viral IRES
Gloria Lozano et al.
JOURNAL OF MOLECULAR BIOLOGY (2016)
Predicting RNA secondary structures from sequence and probing data
Ronny Lorenz et al.
METHODS (2016)
Initiation on the divergent Type I cadicivirus IRES: factor requirements and interactions with the translation apparatus
Mukta Asnani et al.
NUCLEIC ACIDS RESEARCH (2016)
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
John F. Atkins et al.
NUCLEIC ACIDS RESEARCH (2016)
RNAlien - Unsupervised RNA family model construction
Florian Eggenhofer et al.
NUCLEIC ACIDS RESEARCH (2016)
JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs
James Roll et al.
NUCLEIC ACIDS RESEARCH (2016)
Structural features of influenza A virus panhandle RNA enabling the activation of RIG-I independently of 5'-triphosphate
Mi-Kyung Lee et al.
NUCLEIC ACIDS RESEARCH (2016)
A novel role for poly(C) binding proteins in programmed ribosomal frameshifting
Sawsan Napthine et al.
NUCLEIC ACIDS RESEARCH (2016)
SimRNAweb: a web server for RNA 3D structure modeling with optional restraints
Marcin Magnus et al.
NUCLEIC ACIDS RESEARCH (2016)
tRNA-Related Sequences Trigger Systemic mRNA Transport in Plants
Wenna Zhang et al.
PLANT CELL (2016)
HIV-1 leader RNA dimeric interface revealed by NMR
Laura R. Gansera et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Bridging the gap between in vitro and in vivo RNA folding
Kathleen A. Leamy et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2016)
Hepatitis B virus nuclear export elements: RNA stem-loop and , key parts of the HBV post-transcriptional regulatory element
Chun Shen Lim et al.
RNA BIOLOGY (2016)
Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production
Yuki Kobayashi et al.
RNA BIOLOGY (2016)
Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures
Michael F. Sloma et al.
RNA (2016)
Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease
Benjamin M. Akiyama et al.
SCIENCE (2016)
Translation from the 5′ untranslated region shapes the integrated stress response
Shelley R. Starck et al.
SCIENCE (2016)
RNA Structure Duplications and Flavivirus Host Adaptation
Sergio M. Villordo et al.
TRENDS IN MICROBIOLOGY (2016)
The Emerging World of Small ORFs
Roger P. Hellens et al.
TRENDS IN PLANT SCIENCE (2016)
The Life-Cycle of the HIV-1 Gag-RNA Complex
Elodie Mailler et al.
VIRUSES-BASEL (2016)
Prohead RNA: a noncoding viral RNA of novel structure and function
Alyssa C. Hill et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2016)
Small molecules targeting viral RNA
Thomas Hermann
WILEY INTERDISCIPLINARY REVIEWS-RNA (2016)
Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture
Tian Jiang et al.
PLOS ONE (2016)
IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES)
Pandurang Kolekar et al.
SCIENTIFIC REPORTS (2016)
Subtype-specific structural constraints in the evolution of influenza A virus hemagglutinin genes
Alexander P. Gultyaev et al.
SCIENTIFIC REPORTS (2016)
The Influenza A PB1-F2 and N40 Start Codons Are Contained within an RNA Pseudoknot
Salvatore F. Priore et al.
BIOCHEMISTRY (2015)
mRNAs that specifically interact with eukaryotic ribosomal subunits
Jules Deforges et al.
BIOCHIMIE (2015)
RNA motif discovery: a computational overview
Avinash Achar et al.
BIOLOGY DIRECT (2015)
Review toward all RNA structures, concisely
Kevin M. Weeks
BIOPOLYMERS (2015)
Multiple Mechanisms of Reinitiation on Bicistronic Calicivirus mRNAs
Alexandra Zinoviev et al.
MOLECULAR CELL (2015)
A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation
Marta Soszynska-Jozwiak et al.
PLoS One (2015)
Four RNA families with functional transient structures
Jing Yun A. Zhu et al.
RNA BIOLOGY (2015)
Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae
Mukta Asnani et al.
VIROLOGY (2015)
An RNA cassette from Helminthosporium victoriae virus 190S necessary and sufficient for stop/restart translation
Hua Li et al.
VIROLOGY (2015)
Cis-acting RNA elements in positive-strand RNA plant virus genomes
Laura R. Newburn et al.
VIROLOGY (2015)
Cis- and trans-regulation of luteovirus gene expression by the 3′ end of the viral genome
W. Allen Miller et al.
VIRUS RESEARCH (2015)
Functions of the 3′ and 5′ genome RNA regions of members of the genus Flavivirus
Margo A. Brinton et al.
VIRUS RESEARCH (2015)
cis-Acting RNA elements in the hepatitis C virus RNA genome
Selena M. Sagan et al.
VIRUS RESEARCH (2015)
Exploring the architecture of viral RNA genomes
Beth L. Nicholson et al.
CURRENT OPINION IN VIROLOGY (2015)
Dengue Virus RNA Structure Specialization Facilitates Host Adaptation
Sergio M. Villordo et al.
PLOS PATHOGENS (2015)
FRESCo: finding regions of excess synonymous constraint in diverse viruses
Rachel S. Sealfon et al.
GENOME BIOLOGY (2015)
The RNA shapes studio
Stefan Janssen et al.
BIOINFORMATICS (2015)
NCBI Viral Genomes Resource
J. Rodney Brister et al.
NUCLEIC ACIDS RESEARCH (2015)
Rfam 12.0: updates to the RNA families database
Eric P. Nawrocki et al.
NUCLEIC ACIDS RESEARCH (2015)
The Highly Conserved Codon following the Slippery Sequence Supports-1 Frameshift Efficiency at the HIV-1 Frameshift Site
Suneeth F. Mathew et al.
PLOS ONE (2015)
HIV-1 and Human PEG10 Frameshift Elements Are Functionally Distinct and Distinguished by Novel Small Molecule Modulators
Tony S. Cardno et al.
PLOS ONE (2015)
RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure
Corinna Theis et al.
PLOS ONE (2015)
Challenges in RNA virus bioinformatics
Manja Marz et al.
BIOINFORMATICS (2014)
The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA
Timothy M. Colussi et al.
NATURE (2014)
Enabling the 'host jump': structural determinants of receptor-binding specificity in influenza A viruses
Yi Shi et al.
NATURE REVIEWS MICROBIOLOGY (2014)
Functional long-range RNA-RNA interactions in positive-strand RNA viruses
Beth L. Nicholson et al.
NATURE REVIEWS MICROBIOLOGY (2014)
The Nucleic Acid Database: new features and capabilities
Buvaneswari Coimbatore Narayanan et al.
NUCLEIC ACIDS RESEARCH (2014)
Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses
Andrew E. Firth
NUCLEIC ACIDS RESEARCH (2014)
RNA structural constraints in the evolution of the influenza A virus genome NP segment
Alexander P. Gultyaev et al.
RNA BIOLOGY (2014)
The Structural Basis of Pathogenic Subgenomic Flavivirus RNA (sfRNA) Production
Erich G. Chapman et al.
SCIENCE (2014)
An infectious RNA with a hepta-adenosine stretch responsible for programmed-1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus
Shengniao Niu et al.
VIROLOGY (2014)
Progress and outlook in structural biology of large viral RNAS
William A. Cantara et al.
VIRUS RESEARCH (2014)
Prospects for inhibiting the post-transcriptional regulation of gene expression in hepatitis B virus
Augustine Chen et al.
WORLD JOURNAL OF GASTROENTEROLOGY (2014)
RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA
Erich G. Chapman et al.
ELIFE (2014)
Transcription regulation mechanisms of bacteriophages Recent advances and future prospects
Haiquan Yang et al.
BIOENGINEERED (2014)
3 ' Cap-Independent Translation Enhancers of Plant Viruses
Anne E. Simon et al.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 67 (2013)
Infernal 1.1: 100-fold faster RNA homology searches
Eric P. Nawrocki et al.
BIOINFORMATICS (2013)
CMCompare webserver: comparing RNA families via covariance models
Florian Eggenhofer et al.
NUCLEIC ACIDS RESEARCH (2013)
RNAstructure: web servers for RNA secondary structure prediction and analysis
Stanislav Bellaousov et al.
NUCLEIC ACIDS RESEARCH (2013)
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction
Tomasz Puton et al.
NUCLEIC ACIDS RESEARCH (2013)
Analysis Tool Web Services from the EMBL-EBI
Hamish McWilliam et al.
NUCLEIC ACIDS RESEARCH (2013)
Viral IRES Prediction System - a Web Server for Prediction of the IRES Secondary Structure In Silico
Jun-Jie Hong et al.
PLOS ONE (2013)
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
Christine E. Hajdin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Unmasking the information encoded as structural motifs of viral RNA genomes: a potential antiviral target
Cristina Romero-Lopez et al.
REVIEWS IN MEDICAL VIROLOGY (2013)
Computational detection of abundant long-range nucleotide covariation in Drosophila genomes
Eckart Bindewald et al.
RNA (2013)
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
Anton I. Petrov et al.
RNA (2013)
Viral subversion of host functions for picornavirus translation and RNA replication
Amanda J. Chase et al.
FUTURE VIROLOGY (2012)
Non-canonical translation in RNA viruses
Andrew E. Firth et al.
JOURNAL OF GENERAL VIROLOGY (2012)
Japanese encephalitis virus NS1′ protein depends on pseudoknot secondary structure and is cleaved by caspase during virus infection and cell apoptosis
Jin Sun et al.
MICROBES AND INFECTION (2012)
The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses
Carla Kuiken et al.
NUCLEIC ACIDS RESEARCH (2012)
Global or local? Predicting secondary structure and accessibility in mRNAs
Sita J. Lange et al.
NUCLEIC ACIDS RESEARCH (2012)
Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes
Xiaowei Sylvia Chen et al.
NUCLEIC ACIDS RESEARCH (2012)
R-chie: a web server and R package for visualizing RNA secondary structures
Daniel Lai et al.
NUCLEIC ACIDS RESEARCH (2012)
Automated 3D structure composition for large RNAs
Mariusz Popenda et al.
NUCLEIC ACIDS RESEARCH (2012)
The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin
Walter N. Moss et al.
PLOS ONE (2012)
Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches
Sergey M. Dibrov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Efficient-2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein
Ying Fang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Distinct families ofcis-acting RNA replication elements epsilon from hepatitis B viruses
Augustine Chen et al.
RNA Biology (2012)
The influenza A segment 7 mRNA 3′ splice site pseudoknot/hairpin family
Walter N. Moss et al.
RNA BIOLOGY (2012)
Automated and fast building of three-dimensional RNA structures
Yunjie Zhao et al.
SCIENTIFIC REPORTS (2012)
Short ORF-Dependent Ribosome Shunting Operates in an RNA Picorna-Like Virus and a DNA Pararetrovirus that Cause Rice Tungro Disease
Mikhail M. Pooggin et al.
PLOS PATHOGENS (2012)
ViennaRNA Package 2.0
Ronny Lorenz et al.
ALGORITHMS FOR MOLECULAR BIOLOGY (2011)
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
Torbjorn Rognes
BMC BIOINFORMATICS (2011)
Identification of Cis-Acting Elements in the 3′-Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication
Mark Manzano et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2011)
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures
Jean-Francois Taly et al.
NATURE PROTOCOLS (2011)
Viral subversion of the host protein synthesis machinery
Derek Walsh et al.
NATURE REVIEWS MICROBIOLOGY (2011)
ViralZone: a knowledge resource to understand virus diversity
Chantal Hulo et al.
NUCLEIC ACIDS RESEARCH (2011)
Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3′ UTR structures
Alex Michael Ward et al.
RNA BIOLOGY (2011)
Identification of potential conserved RNA secondary structure throughout influenza A coding regions
Walter N. Moss et al.
RNA (2011)
The Cap-Binding Translation Initiation Factor, elF4E, Binds a Pseudoknot in a Viral Cap-Independent Translation Element
Zhaohui Wang et al.
STRUCTURE (2011)
A long-distance RNA-RNA interaction plays an important role in programmed-1 ribosomal frameshifting in the translation of p88 replicase protein of Red clover necrotic mosaic virus
Yuri Tajima et al.
VIROLOGY (2011)
Translational termination-reinitiation in RNA viruses
Michael L. Powell
BIOCHEMICAL SOCIETY TRANSACTIONS (2010)
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
Ari Loeytynoja et al.
BMC BIOINFORMATICS (2010)
Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cryo-Electron Tomography
Yasuyuki Miyazaki et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
The RNA Virus Quasispecies: Fact or Fiction?
Edward C. Holmes
JOURNAL OF MOLECULAR BIOLOGY (2010)
Frameshifting in Alphaviruses: A Diversity of 3′ Stimulatory Structures
Betty Y. -W. Chung et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
NS1′ of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness
Ezequiel Balmori Melian et al.
JOURNAL OF VIROLOGY (2010)
Recode-2: new design, new search tools, and many more genes
Michael Bekaert et al.
NUCLEIC ACIDS RESEARCH (2010)
IRESite-a tool for the examination of viral and cellular internal ribosome entry sites
Martin Mokrejs et al.
NUCLEIC ACIDS RESEARCH (2010)
Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LocARNA
Cameron Smith et al.
NUCLEIC ACIDS RESEARCH (2010)
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model
Jana Sperschneider et al.
NUCLEIC ACIDS RESEARCH (2010)
A family of non-classical pseudoknots in influenza A and B viruses
Alexander P. Gultyaev et al.
RNA BIOLOGY (2010)
Retroviral RNA Dimerization and Packaging: The What, How, When, Where, and Why
Silas F. Johnson et al.
PLOS PATHOGENS (2010)
Quasispecies Theory and the Behavior of RNA Viruses
Adam S. Lauring et al.
PLOS PATHOGENS (2010)
Viral tRNAs and tRNA-like structures
Theo W. Dreher
WILEY INTERDISCIPLINARY REVIEWS-RNA (2010)
Cis-acting RNA elements in human and animal plus-strand RNA viruses
Ying Liu et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2009)
VARNA: Interactive drawing and editing of the RNA secondary structure
Kevin Darty et al.
BIOINFORMATICS (2009)
Jalview Version 2-a multiple sequence alignment editor and analysis workbench
Andrew M. Waterhouse et al.
BIOINFORMATICS (2009)
Rev: beyond nuclear export
H. C. T. Groom et al.
JOURNAL OF GENERAL VIROLOGY (2009)
Architecture and secondary structure of an entire HIV-1 RNA genome
Joseph M. Watts et al.
NATURE (2009)
Molecular dissection of the prototype foamy virus (PFV) RNA 5 '-UTR identifies essential elements of a ribosomal shunt
Mikhail Schepetilnikov et al.
NUCLEIC ACIDS RESEARCH (2009)
Frequency and isostericity of RNA base pairs
Jesse Stombaugh et al.
NUCLEIC ACIDS RESEARCH (2009)
Expression of the VP2 Protein of Murine Norovirus by a Translation Termination-Reinitiation Strategy
Sawsan Napthine et al.
PLOS ONE (2009)
The structure-function relationship of the enterovirus 3′-UTR
Jan Zoll et al.
VIRUS RESEARCH (2009)
Frameshifting RNA pseudoknots: Structure and mechanism
David P. Giedroc et al.
VIRUS RESEARCH (2009)
RNAalifold: improved consensus structure prediction for RNA alignments
Stephan H. Bernhart et al.
BMC BIOINFORMATICS (2008)
A Highly Structured, Nuclease-Resistant, Noncoding RNA Produced by Flaviviruses Is Required for Pathogenicity
Gorben P. Pijlman et al.
CELL HOST & MICROBE (2008)
Structural domains within the 3′ untranslated region of Turnip crinkle virus
John C. McCormack et al.
JOURNAL OF VIROLOGY (2008)
KnotInFrame: prediction of-1 ribosomal frameshift events
Corinna Theis et al.
NUCLEIC ACIDS RESEARCH (2008)
WAR: Webserver for aligning structural RNAs
Elfar Torarinsson et al.
NUCLEIC ACIDS RESEARCH (2008)
The Vienna RNA Websuite
Andreas R. Gruber et al.
NUCLEIC ACIDS RESEARCH (2008)
Co-selection of West Nile virus nucleotides that confer resistance to an antisense oligomer while maintaining long-distance RNA/RNA base pairings
Bo Zhang et al.
VIROLOGY (2008)
3 ' RNA elements in hepatitis C virus replication: Kissing partners and long poly(U)
Shihyun You et al.
JOURNAL OF VIROLOGY (2008)
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
Eckart Bindewald et al.
NUCLEIC ACIDS RESEARCH (2008)
Viral RNA pseudoknots: versatile motifs in gene expression and replication
Ian Brierley et al.
NATURE REVIEWS MICROBIOLOGY (2007)
Prospects for a dengue virus vaccine
Stephen S. Whitehead et al.
NATURE REVIEWS MICROBIOLOGY (2007)
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures
Andreas R. Gruber et al.
NUCLEIC ACIDS RESEARCH (2007)
Detecting overlapping coding sequences in virus genomes
AE Firth et al.
BMC BIOINFORMATICS (2006)
CMfinder - a covariance model based RNA motif finding algorithm
ZZ Yao et al.
BIOINFORMATICS (2006)
A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting
PV Cornish et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
The Los Alamos hepatitis C sequence database
C Kuiken et al.
BIOINFORMATICS (2005)
RALEE-RNA ALignment Editor in Emacs
S Griffiths-Jones
BIOINFORMATICS (2005)
A heuristic approach for detecting RNA H-type pseudoknots
CH Huang et al.
BIOINFORMATICS (2005)
A benchmark of multiple sequence alignment programs upon structural RNAs
PP Gardner et al.
NUCLEIC ACIDS RESEARCH (2005)
NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus
V D'Souza et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
A comprehensive comparison of comparative RNA structure prediction approaches
PP Gardner et al.
BMC BIOINFORMATICS (2004)
Visualization of RNA-protein interactions in living cells: FMRP and IMP1 interact on mRNAs
O Rackham et al.
EMBO JOURNAL (2004)
Conserved RNA secondary structures in viral genomes: a survey
IL Hofacker et al.
BIOINFORMATICS (2004)
Dimerization of retroviral RNA genomes: An inseparable pair
JC Paillart et al.
NATURE REVIEWS MICROBIOLOGY (2004)
Fast and effective prediction of microRNA/target duplexes
M Rehmsmeier et al.
RNA (2004)
Mfold web server for nucleic acid folding and hybridization prediction
M Zuker
NUCLEIC ACIDS RESEARCH (2003)
A-1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA
JK Barry et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus
A Tuplin et al.
RNA (2002)
Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution
M Egli et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
DH Mathews et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
A sequence required for-1 ribosomal frameshifting located four kilobases downstream of the frameshift site
CP Paul et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Expression of the ORF-2 protein of the human respiratory syncytial virus M2 gene is initiated by a ribosomal termination-dependent reinitiation mechanism
G Ahmadian et al.
EMBO JOURNAL (2000)