Prediction of conserved long-range RNA-RNA interactions in full viral genomes (Q39691579)

14 September 2017

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

1 reference

14 September 2017

2

Manja Marz

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14 September 2017

Markus Fricke

1

1 reference

PubMed ID

27288498

14 September 2017

language of work or name

English

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publication date

10 June 2016

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14 September 2017

8

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inferred from page(s)

published in

Bioinformatics

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14 September 2017

32

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14 September 2017

19

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14 September 2017

2928-2935

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A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon

14 September 2017

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

RNA-RNA interaction prediction and antisense RNA target search.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Long-Range RNA-RNA Interactions Circularize the Dengue Virus Genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Role of the trans-activation response element in dimerization of HIV-1 RNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Secondary structure prediction of interacting RNA molecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Partition function and base pairing probabilities of RNA heterodimers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

RNAalifold: improved consensus structure prediction for RNA alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Multifaceted regulation of translational readthrough by RNA replication elements in a tombusvirus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Fine Mapping of a cis-Acting Sequence Element in Yellow Fever Virus RNA That Is Required for RNA Replication and Cyclization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

5'-3' RNA-RNA interaction facilitates cap- and poly(A) tail-independent translation of tomato bushy stunt virus mrna: a potential common mechanism for tombusviridae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Analysis of a 3'-translation enhancer in a tombusvirus: a dynamic model for RNA-RNA interactions of mRNA termini

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Interplay of RNA elements in the dengue virus 5' and 3' ends required for viral RNA replication

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Kissing-loop interaction in the 3' end of the hepatitis C virus genome essential for RNA replication

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Mutations in the TAR hairpin affect the equilibrium between alternative conformations of the HIV-1 leader RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Essential role of cyclization sequences in flavivirus RNA replication

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Circos: an information aesthetic for comparative genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

The Los Alamos hepatitis C sequence database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

A complex network of RNA-RNA interactions controls subgenomic mRNA transcription in a tombusvirus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

21 January 2018

ViennaRNA Package 2.0

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Thermodynamics of RNA-RNA binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Circularization of the HIV-1 RNA genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

IRBIS: a systematic search for conserved complementarity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

Fast and effective prediction of microRNA/target duplexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

RNAplex: a fast tool for RNA-RNA interaction search

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions between 5'- and 3'-terminal regions that influence RNA structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW323

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27288498

12 December 2020

inferred from PubMed ID database lookup

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27288498

12 December 2020

inferred from PubMed ID database lookup

A phylogenetically conserved stem-loop structure at the 5' border of the internal ribosome entry site of hepatitis C virus is required for cap-independent viral translation.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27288498

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1093/BIOINFORMATICS/BTW323

1 reference

journals/bioinformatics/FrickeM16

14 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

0 references

1 reference

PubMed ID

27288498