Genome-wide quantification of 5′-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics

Dying mRNA Tells a Story of Its Life

(2015) Edward W.J. Wallace et al.   CELL

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

(2015) Vicent Pelechano et al.   CELL

Dom34 Rescues Ribosomes in 3′ Untranslated Regions

(2014) Nicholas R. Guydosh et al.   CELL

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

(2014) Søren Lykke-Andersen et al.   GENES & DEVELOPMENT

Genome-wide identification of transcript start and end sites by transcript isoform sequencing

(2014) Vicent Pelechano et al.   Nature Protocols

Translation inhibitors cause abnormalities in ribosome profiling experiments

(2014) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes—GMUCT 2.0

(2013) Matthew R. Willmann et al.   METHODS

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

(2013) Stefan Wilkening et al.   NUCLEIC ACIDS RESEARCH

The intimate relationships of mRNA decay and translation

(2013) Bijoyita Roy et al.   TRENDS IN GENETICS

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

(2013) Joshua G Dunn et al.   eLife

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

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

RNA Degradation in Saccharomyces cerevisae

(2012) Roy Parker   GENETICS

Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets

(2012) M. Stadler et al.   GENOME RESEARCH

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

(2012) Gene-Wei Li 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 mRNA decay intermediates in Saccharomyces cerevisiae

(2012) Y. Harigaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

(2012) M. V. Gerashchenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Nicholas T. Ingolia et al.   CELL

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

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

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

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

(2009) M. Morgan et al.   BIOINFORMATICS

Co-translational mRNA decay in Saccharomyces cerevisiae

(2009) Wenqian Hu et al.   NATURE

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

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

(2009) N. T. Ingolia et al.   SCIENCE

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY