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

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

(2012) Gene-Wei Li et al.   NATURE

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang et al.   NUCLEIC ACIDS RESEARCH

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo

(2011) Eugene Oh et al.   CELL

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

(2011) Nicholas T. Ingolia et al.   CELL

Primary Role for Endoplasmic Reticulum-bound Ribosomes in Cellular Translation Identified by Ribosome Profiling

(2011) David W. Reid et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Translation's coming of age

(2011) C. Vogel   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

(2011) M. Hafner et al.   RNA

Wobble base-pairing slows in vivo translation elongation in metazoans

(2011) M. Stadler et al.   RNA

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

(2011) G. A. Brar et al.   SCIENCE

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Limitations and possibilities of small RNA digital gene expression profiling

(2009) Sam E V Linsen et al.   NATURE METHODS

Altering Chemosensitivity by Modulating Translation Elongation

(2009) Francis Robert et al.   PLoS One

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL

A Hierarchical Network Controls Protein Translation during Murine Embryonic Stem Cell Self-Renewal and Differentiation

(2008) Prabha Sampath et al.   Cell Stem Cell

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology