The identification and functional annotation of RNA structures conserved in vertebrates

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

(2016) Andreas J. Gruber et al.   GENOME RESEARCH

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

(2015) Daniel Sundfeld et al.   BIOINFORMATICS

Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization

(2015) Binyamin D. Berkovits et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Optimizing RNA structures by sequence extensions using RNAcop

(2015) Nikolai Hecker et al.   NUCLEIC ACIDS RESEARCH

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

A Variety of Dicer Substrates in Human and C. elegans

(2014) Agnieszka Rybak-Wolf et al.   CELL

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

(2014) S. Washietl et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

(2014) Tim R Mercer et al.   Nature Protocols

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

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

Comparison of the transcriptional landscapes between human and mouse tissues

(2014) Shin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

(2014) Robin Andersson et al.   Nature Communications

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Life without A tail: New formats of long noncoding RNAs

(2013) Yang Zhang et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread purifying selection on RNA structure in mammals

(2013) Martin A. Smith et al.   NUCLEIC ACIDS RESEARCH

Genome Regulation by Long Noncoding RNAs

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

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor

(2012) Sara Macias et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs

(2011) David Managadze et al.   Genome Biology and Evolution

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

(2011) B. J. Parker et al.   GENOME RESEARCH

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

(2011) Pascal Preker et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis

(2009) Zasha Weinberg et al.   NATURE

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Modulation of alternative splicing by long-range RNA structures in Drosophila

(2009) Veronica A. Raker et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of structured RNAs from genomic sequences

(2009) Jan Gorodkin et al.   TRENDS IN BIOTECHNOLOGY

Dinucleotide controlled null models for comparative RNA gene prediction

(2008) Tanja Gesell et al.   BMC BIOINFORMATICS

The functional repertoires of metazoan genomes

(2008) Chris P. Ponting   NATURE REVIEWS GENETICS

MicroRNA-directed transcriptional gene silencing in mammalian cells

(2008) D. H. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

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

(2007) E. Torarinsson et al.   GENOME RESEARCH