(Q41933545)

14 October 2017

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

1 reference

14 October 2017

1 reference

5

1 reference

14 October 2017

Andreas S Richter

2

0 references

Tanja Gesell

object named as

Tanja Gesell

series ordinal

3

0 references

Rolf Backofen

series ordinal

4

object named as

Rolf Backofen

1 reference

14 October 2017

Stefan E Seemann

1

1 reference

PMC publication ID

3018821

14 October 2017

language of work or name

English

0 references

publication date

18 November 2010

1 reference

14 October 2017

1 reference

14 October 2017

27

1 reference

14 October 2017

2

1 reference

14 October 2017

211-219

1 reference

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

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

The primary transcriptome of the major human pathogen Helicobacter pylori

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Computational prediction of sRNAs and their targets in bacteria.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Fast prediction of RNA-RNA interaction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

De novo prediction of structured RNAs from genomic sequences

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Target prediction and a statistical sampling algorithm for RNA-RNA interaction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

The tedious task of finding homologous noncoding RNA genes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Long noncoding RNAs: functional surprises from the RNA world

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

A partition function algorithm for interacting nucleic acid strands

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Local RNA structure alignment with incomplete sequence

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Regulatory RNAs in bacteria

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Non-coding RNA annotation of the genome of Trichoplax adhaerens

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Rfam: updates to the RNA families database

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Recent developments in the MAFFT multiple sequence alignment program

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Specific expression of long noncoding RNAs in the mouse brain

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Variations on RNA folding and alignment: lessons from Benasque.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Partition function and base pairing probabilities of RNA heterodimers

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Thermodynamics of RNA-RNA binding

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

A benchmark of multiple sequence alignment programs upon structural RNAs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Fast and effective prediction of microRNA/target duplexes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Identification of 13 novel human modification guide RNAs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Pfold: RNA secondary structure prediction using stochastic context-free grammars

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

RNA loop-loop interactions as dynamic functional motifs.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

The expanding snoRNA world

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Discovering common stem-loop motifs in unaligned RNA sequences

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Modification of U6 spliceosomal RNA is guided by other small RNAs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Evolutionary trees from DNA sequences: A maximum likelihood approach

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Partition function and base pairing probabilities for RNA-RNA interaction prediction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

RNAplex: a fast tool for RNA-RNA interaction search

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

The relationship between non-protein-coding DNA and eukaryotic complexity.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

RNA-RNA interaction prediction and antisense RNA target search.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

In silico sequence evolution with site-specific interactions along phylogenetic trees.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

IRIS: intermolecular RNA interaction search.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Secondary structure prediction of interacting RNA molecules.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

IQPNNI: moving fast through tree space and stopping in time.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3018821

Thermodynamic Analysis of Interacting Nucleic Acid Strands

30 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTQ634

Fast folding and comparison of RNA secondary structures

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTQ634

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTQ634

fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21088024

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTQ634

1 reference

journals/bioinformatics/SeemannRGBG11

14 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

3018821

14 October 2017

PubMed publication ID

21088024

1 reference

PMC publication ID

3018821