hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions

(2014) Stefanie Grosswendt et al.   MOLECULAR CELL

Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins

(2014) Hani Goodarzi et al.   NATURE

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Functional signature for the recognition of specific target mRNAs by human Staufen1 protein

(2014) Susana de Lucas et al.   NUCLEIC ACIDS RESEARCH

Cell cycle-dependent regulation of the RNA-binding protein Staufen1

(2014) Karine Boulay et al.   NUCLEIC ACIDS RESEARCH

The multifunctional Staufen proteins: conserved roles from neurogenesis to synaptic plasticity

(2014) Jacki E. Heraud-Farlow et al.   TRENDS IN NEUROSCIENCES

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

STAU1 binding 3' UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown

(2013) R. A. Elbarbary et al.   GENES & DEVELOPMENT

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

Structures of the human and Drosophila 80S ribosome

(2013) Andreas M. Anger 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

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

(2013) Michael T Lovci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Staufen1 senses overall transcript secondary structure to regulate translation

(2013) Emiliano P Ricci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity

(2013) John D. Laver et al.   NUCLEIC ACIDS RESEARCH

The intimate relationships of mRNA decay and translation

(2013) Bijoyita Roy et al.   TRENDS IN GENETICS

Staufen2 Regulates Neuronal Target RNAs

(2013) Jacki E. Heraud-Farlow et al.   Cell Reports

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells

(2012) Jun Cho et al.   CELL

RNA Targets and Specificity of Staufen, a Double-stranded RNA-binding Protein inCaenorhabditis elegans

(2012) Jacqueline Baca LeGendre et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

ViennaRNA Package 2.0

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

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

The ribosome uses two active mechanisms to unwind messenger RNA during translation

(2011) Xiaohui Qu et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation

(2011) P. Walter et al.   SCIENCE

SylArray: a web server for automated detection of miRNA effects from expression data

(2010) N. Bartonicek et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mammalian endoplasmic reticulum stress sensor IRE1 signals by dynamic clustering

(2010) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY