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

author

Sean Eddy

2000 -

Jody Clements

published in: Nature Methods

date of publication: 2016-11-07

main subject: statistics

Cites articles 42

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2016-04-13

3D RNA and Functional Interactions from Evolutionary Couplings

Chris Sander, Debora Marks, Caleb Weinreb
2015-12-19

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

Aviv Regev, Zhe Ji
2015-12-10

Parameterizing sequence alignment with an explicit evolutionary model
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Probing Xist RNA Structure in Cells Using Targeted Structure-Seq
2015-12-01

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

Thomas Cech, Chen Davidovich
2015-09-29

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

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2015-04-09

HOTAIR forms an intricate and modular secondary structure

Isabel Chillón
2015-01

Rfam 12.0: updates to the RNA families database

Robert D. Finn, Alex Bateman, Evan Floden, Jennifer Daub, Paul P. Gardner, Sean Eddy, Ruth Y. Eberhardt
2013-02-08

Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria
2013-01

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

Robert D. Finn, Jody Clements, Sean Eddy, Travis J. Wheeler, Robert Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit
2012-01-01

Genome regulation by long noncoding RNAs

John L. Rinn
2012-02-01

A survey of sRNA families in α-proteobacteria

Coral del Val, Omar Torres-Quesada, Nicolás Toro
2012-02-22

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

Karissa Sanbonmatsu, Scott P Hennelly, Irina V Novikova
2012-02

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

Sean Eddy, Elena Rivas, R. Lang
2011-09-24

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

Julien Y Dutheil
2011-06-28

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

Sean Eddy, Seolkyoung Jung, Estienne C. Swart, Patrick Minx, Vincent Magrini, Elaine Mardis, Laura Landweber
2011-01-04

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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
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Philippe Clerc, Alain Van Dorsselaer, Sarah Sanglier-Cianférani, Christiane Branlant
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Identification of direct residue contacts in protein-protein interaction by message passing

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

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2004-08-01

Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
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Article - wd:Q41371820

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