(Q24607140)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

title

GraphClust: alignment-free structural clustering of local RNA secondary structures (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

computational mathematics

4 February 2020

main subject

0 references

author

Steffen Heyne

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

Fabrizio Costa

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

Rolf Backofen

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

author name string

Dominic Rose

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

language of work or name

English

0 references

publication date

1 June 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

volume

28

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

page(s)

i224-32

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

issue

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

4 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Rfam: Wikipedia, clans and the "decimal" release

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Long non-coding RNAs in nervous system function and disease

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Infernal 1.0: inference of RNA alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

RNAalifold: improved consensus structure prediction for RNA alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Identification and classification of conserved RNA secondary structures in the human genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

A benchmark of multiple sequence alignment programs upon structural RNAs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Fast and reliable prediction of noncoding RNAs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

7 April 2017

Abstract shapes of RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

The Eukaryotic Genome as an RNA Machine

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

RNAs everywhere: genome-wide annotation of structured RNAs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

NCBI Reference Sequences: current status, policy and new initiatives

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

The reality of pervasive transcription

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

De novo prediction of structured RNAs from genomic sequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

The long and the short of noncoding RNAs

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Finding non-coding RNAs through genome-scale clustering.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Directed acyclic graph kernels for structural RNA analysis

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Computational RNomics of drosophilids

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

RADAR: a web server for RNA data analysis and research.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Multiple structural alignment and clustering of RNA sequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

RNA stem-loops: to be or not to be cleaved by RNAse III.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

A method for rapid similarity analysis of RNA secondary structures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Pure multiple RNA secondary structure alignments: a progressive profile approach

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

CMfinder--a covariance model based RNA motif finding algorithm

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3371856

Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.

27 September 2017

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTS224

Structural profiles of human miRNA families from pairwise clustering.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTS224

Duplicated RNA genes in teleost fish genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTS224

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTS224

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22689765

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTS224

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

journals/bioinformatics/HeyneCRB12

4 February 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22689765%20AND%20SRC:MED&resulttype=core&format=json