4.5 Review

Evolutionary conservation of RNA sequence and structure

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Estimating the power of sequence covariation for detecting conserved RNA structure

Elena Rivas et al.

BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

Assessing the accuracy of direct-coupling analysis for RNA contact prediction

Francesca Cuturello et al.

Article Biochemistry & Molecular Biology

An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano

Alisha N. Jones et al.

Article Cell & Tissue Engineering

The Long Non-coding RNA Cyrano Is Dispensable for Pluripotency of Murine and Human Pluripotent Stem Cells

Hannah J. Hunkler et al.

STEM CELL REPORTS (2020)

Article Biochemistry & Molecular Biology

Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements

Ilaria Manfredonia et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemical Research Methods

RNA structure prediction using positive and negative evolutionary information

Elena Rivas

PLOS COMPUTATIONAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures

Rafael C. A. Tavares et al.

JOURNAL OF MOLECULAR BIOLOGY (2019)

Article Multidisciplinary Sciences

RNA base-pairing complexity in living cells visualized by correlated chemical probing

Anthony M. Mustoe et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

Ioanna Kalvari et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

Benjamin Kleaveland et al.

Article Biochemistry & Molecular Biology

MicroRNA degradation by a conserved target RNA regulates animal behavior

Angelo Bitetti et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Article Biochemistry & Molecular Biology

MicroRNA degradation by a conserved target RNA regulates animal behavior

Angelo Bitetti et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Article Biochemical Research Methods

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

Elena Rivas et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase

James Chen et al.

MOLECULAR CELL (2017)

Article Biochemistry & Molecular Biology

Visualizing the secondary and tertiary architectural domains of lnc RNA RepA

Fei Liu et al.

NATURE CHEMICAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding

Danny Incarnato et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

3D RNA and Functional Interactions from Evolutionary Couplings

Caleb Weinreb et al.

Article Biochemistry & Molecular Biology

HOTAIR Forms an Intricate and Modular Secondary Structure

Srinivas Somarowthu et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

Four RNA families with functional transient structures

Jing Yun A. Zhu et al.

RNA BIOLOGY (2015)

Article Genetics & Heredity

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

Rui Fang et al.

PLOS GENETICS (2015)

Review Biophysics

Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes

Sean R. Eddy

ANNUAL REVIEW OF BIOPHYSICS, VOL 43 (2014)

Article Biochemistry & Molecular Biology

Ten lessons with Carl Woese about RNA and comparative analysis

Robin R Gutell

RNA Biology (2014)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

Zsuzsanna Sukosd et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Physics, Fluids & Plasmas

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

Magnus Ekeberg et al.

PHYSICAL REVIEW E (2013)

Article Multidisciplinary Sciences

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

Hetunandan Kamisetty et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

Justin Ritz et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Biochemical Research Methods

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

Julien Y. Dutheil

BRIEFINGS IN BIOINFORMATICS (2012)

Article Multidisciplinary Sciences

The complex of tmRNA-SmpB and EF-G on translocating ribosomes

David J. F. Ramrath et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

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

Irina V. Novikova et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

Stefan Washietl et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction

Kourosh Zarringhalam et al.

PLOS ONE (2012)

Article Biochemical Research Methods

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

Zasha Weinberg et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

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

Brian J. Parker et al.

GENOME RESEARCH (2011)

Article Multidisciplinary Sciences

Protein 3D Structure Computed from Evolutionary Sequence Variation

Debora S. Marks et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

Faruck Morcos et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

RNAstructure: software for RNA secondary structure prediction and analysis

Jessica S. Reuter et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Invariant U2 snRNA Nucleotides Form a Stem Loop to Recognize the Intron Early in Splicing

Rhonda Perriman et al.

MOLECULAR CELL (2010)

Article Multidisciplinary Sciences

Structurally conserved five nucleotide bulge determines the overall topology of the core domain of human telomerase RNA

Qi Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemistry & Molecular Biology

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

Sylvain Maenner et al.

PLOS BIOLOGY (2010)

Article Biochemical Research Methods

Prediction of RNA secondary structure using generalized centroid estimators

Michiaki Hamada et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

Architecture and secondary structure of an entire HIV-1 RNA genome

Joseph M. Watts et al.

NATURE (2009)

Article Multidisciplinary Sciences

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

Martin Weigt et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Accurate SHAPE-directed RNA structure determination

Katherine E. Deigan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

Improved RNA secondary structure prediction by maximizing expected pair accuracy

Zhi John Lu et al.

Article Biochemical Research Methods

RNAalifold: improved consensus structure prediction for RNA alignments

Stephan H. Bernhart et al.

BMC BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

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

Elfar Torarinsson et al.

GENOME RESEARCH (2008)

Article Biochemical Research Methods

Detecting coevolution in and among protein domains

Chen-Hsiang Yeang et al.

PLOS COMPUTATIONAL BIOLOGY (2007)

Article Biochemical Research Methods

Efficient parameter estimation for RNA secondary structure prediction

Mirela Andronescu et al.

BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

Structured RNAs in the ENCODE selected regions of the human genome

Stefan Washietl et al.

GENOME RESEARCH (2007)

Article Biochemical Research Methods

Measuring covariation in RNA alignments: physical realism improves information measures

S. Lindgreen et al.

BIOINFORMATICS (2006)

Article Biochemical Research Methods

CONTRAfold: RNA secondary structure prediction without physics-based models

Chuong B. Do et al.

BIOINFORMATICS (2006)

Article Multidisciplinary Sciences

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

Rebecca K. Montange et al.

NATURE (2006)

Article Biochemical Research Methods

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

Jakob Skou Pedersen et al.

PLOS COMPUTATIONAL BIOLOGY (2006)

Article Biochemical Research Methods

CMfinder - a covariance model based RNA motif finding algorithm

ZZ Yao et al.

BIOINFORMATICS (2006)

Article Biotechnology & Applied Microbiology

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

S Washietl et al.

NATURE BIOTECHNOLOGY (2005)

Article Biochemistry & Molecular Biology

A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation

DM Layton et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Physics, Multidisciplinary

Efficient computation of RNA folding dynamics

MT Wolfinger et al.

JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL (2004)

Article Biochemical Research Methods

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

RC Edgar

BMC BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Sfold web server for statistical folding and rational design of nucleic acids

Y Ding et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Chemistry, Multidisciplinary

A partition function algorithm for nucleic acid secondary structure including pseudoknots

RM Dirks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)

Article Biochemistry & Molecular Biology

Tools for the automatic identification and classification of RNA base pairs

HW Yang et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

RNAsoft:: a suite of RNA secondary structure prediction and design software tools

M Andronescu et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Secondary structure prediction for aligned RNA sequences

IL Hofacker et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Biochemistry & Molecular Biology

Computational identification of noncoding RNAs in E-coli by comparative genomics

E Rivas et al.

CURRENT BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Geometric nomenclature and classification of RNA base pairs

NB Leontis et al.

Review Multidisciplinary Sciences

Initial sequencing and analysis of the human genome

ES Lander et al.

NATURE (2001)

Article Biochemical Research Methods

Phylogenetically enhanced statistical tools for RNA structure prediction

VR Akmaev et al.

BIOINFORMATICS (2000)

Article Biochemistry & Molecular Biology

RNA folding at elementary step resolution

C Flamm et al.