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

3D RNA and Functional Interactions from Evolutionary Couplings

(2016) Caleb Weinreb et al.   CELL

Parameterizing sequence alignment with an explicit evolutionary model

(2015) Elena Rivas et al.   BMC BIOINFORMATICS

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

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

(2015) Chen Davidovich et al.   RNA

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Yang Fu et al.   NUCLEIC ACIDS RESEARCH

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

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

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

A survey of sRNA families in α-proteobacteria

(2012) Coral del Val et al.   RNA Biology

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

(2011) Zasha Weinberg et al.   BMC BIOINFORMATICS

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

(2011) J. Y. Dutheil   BRIEFINGS IN BIOINFORMATICS

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

(2011) S. Jung et al.   NUCLEIC ACIDS RESEARCH

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

(2011) E. Rivas et al.   RNA

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

(2010) Sylvain Maenner et al.   PLOS BIOLOGY

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

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA