(Q41371820)

30 September 2017

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs (English)

1 reference

30 September 2017

0 references

3

1 reference

30 September 2017

2

Jody Clements

0 references

author name string

Elena Rivas

series ordinal

1

1 reference

PMCID

5554622

30 September 2017

Jody Clements

series ordinal

2

1 reference

30 September 2017

7 November 2016

1 reference

30 September 2017

1 reference

30 September 2017

14

1 reference

30 September 2017

1

1 reference

30 September 2017

45-48

1 reference

https://scigraph.springernature.com/pub.10.1038/nmeth.4066

30 September 2017

0 references

cites work

3D RNA and Functional Interactions from Evolutionary Couplings

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Parameterizing sequence alignment with an explicit evolutionary model

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

HOTAIR forms an intricate and modular secondary structure.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Rfam 12.0: updates to the RNA families database

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Dfam: a database of repetitive DNA based on profile hidden Markov models

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Genome regulation by long noncoding RNAs.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

A survey of sRNA families in α-proteobacteria

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Detecting coevolving positions in a molecule: why and how to account for phylogeny

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

R2R--software to speed the depiction of aesthetic consensus RNA secondary structures

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

FastTree 2--approximately maximum-likelihood trees for large alignments

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

2-D structure of the A region of Xist RNA and its implication for PRC2 association

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Identification of direct residue contacts in protein-protein interaction by message passing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Measuring covariation in RNA alignments: physical realism improves information measures

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

STRUCTURE OF A RIBONUCLEIC ACID

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Secondary structure prediction for aligned RNA sequences

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

5S Ribosomal RNA Database

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Modeling RNA tertiary structure from patterns of sequence variation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Phylogenetic analysis of tmRNA secondary structure.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Secondary structure model for 23S ribosomal RNA.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Using information theory to search for co-evolving residues in proteins.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Influence of conservation on calculations of amino acid covariance in multiple sequence alignments

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Phylogenetically enhanced statistical tools for RNA structure prediction.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

MatrixPlot: visualizing sequence constraints.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

Volume changes in protein evolution.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5554622

A Mathematical Theory of Communication

19 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.4066

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.4066

Detecting the coevolution of biosequences--an example of RNA interaction prediction

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27819659

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The log likelihood ratio test (the G-test); methods and tables for tests of heterogeneity in contingency tables

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27819659

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NMETH.4066

1 reference

30 September 2017

1 reference

30 September 2017

1 reference

PMCID

5554622