Prediction of conserved long-range RNA-RNA interactions in full viral genomes

Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

(2015) Markus Fricke et al.   RNA

IRBIS: a systematic search for conserved complementarity

(2014) Dmitri D. Pervouchine   RNA

End-to-end crosstalk within the hepatitis C virus genome mediates the conformational switch of the 3′X-tail region

(2013) Cristina Romero-López et al.   NUCLEIC ACIDS RESEARCH

Computational detection of abundant long-range nucleotide covariation in Drosophila genomes

(2013) E. Bindewald et al.   RNA

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

A twist in the tail: SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication

(2012) Andrew Tuplin et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

The functional RNA domain 5BSL3.2 within the NS5B coding sequence influences hepatitis C virus IRES-mediated translation

(2011) Cristina Romero-López et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

MicroRNA-122 antagonism against hepatitis C virus genotypes 1-6 and reduced efficacy by host RNA insertion or mutations in the HCV 5' UTR

(2011) Y.-P. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove

(2011) M. E. Filbin et al.   RNA

Multifaceted Regulation of Translational Readthrough by RNA Replication Elements in a Tombusvirus

(2011) Peter A. Cimino et al.   PLoS Pathogens

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

(2010) Stefan E. Seemann et al.   BIOINFORMATICS

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

(2010) Yuki Kato et al.   BIOINFORMATICS

Interplay of RNA Elements in the Dengue Virus 5' and 3' Ends Required for Viral RNA Replication

(2010) P. Friebe et al.   JOURNAL OF VIROLOGY

Circularization of the HIV-1 genome facilitates strand transfer during reverse transcription

(2010) N. Beerens et al.   RNA

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

(2009) Parvez Anandam et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

A long-range RNA-RNA interaction between the 5' and 3' ends of the HCV genome

(2009) C. Romero-Lopez et al.   RNA

A Discontinuous RNA Platform Mediates RNA Virus Replication: Building an Integrated Model for RNA–based Regulation of Viral Processes

(2009) Baodong Wu et al.   PLoS Pathogens

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Co-selection of West Nile virus nucleotides that confer resistance to an antisense oligomer while maintaining long-distance RNA/RNA base pairings

(2008) Bo Zhang et al.   VIROLOGY

Context-influenced cap-independent translation of Tombusvirus mRNAs in vitro

(2008) Beth L. Nicholson et al.   VIROLOGY