riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast

(2017) Hao Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide

(2017) Zhen Shi et al.   MOLECULAR CELL

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide identification and differential analysis of translational initiation

(2017) Peng Zhang et al.   Nature Communications

CAN1 Arginine Permease Deficiency Extends Yeast Replicative Lifespan via Translational Activation of Stress Response Genes

(2017) Carine Beaupere et al.   Cell Reports

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

(2016) Yi Zhong et al.   BIOINFORMATICS

A model for competition for ribosomes in the cell

(2016) Alon Raveh et al.   Journal of the Royal Society Interface

Dynamics of ribosome scanning and recycling revealed by translation complex profiling

(2016) Stuart K. Archer et al.   NATURE

Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis

(2016) Polly Yingshan Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide assessment of differential translations with ribosome profiling data

(2016) Zhengtao Xiao et al.   Nature Communications

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

(2016) David E. Weinberg et al.   Cell Reports

RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis

(2015) Rachel Legendre et al.   BIOINFORMATICS

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ribosome A and P sites revealed by length analysis of ribosome profiling data

(2015) Andrew T. Martens et al.   NUCLEIC ACIDS RESEARCH

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

(2015) Alexey A. Gritsenko et al.   PLoS Computational Biology

Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning

(2014) Audrey M Michel et al.   BMC BIOINFORMATICS

Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement

(2014) Tatyana V. Budkevich et al.   CELL

Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation

(2014) Yan Han et al.   CELL RESEARCH

Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias

(2014) Renana Sabi et al.   DNA RESEARCH

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

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

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

(2014) C. Pop et al.   Molecular Systems Biology

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

Mean of the Typical Decoding Rates: A New Translation Efficiency Index Based on the Analysis of Ribosome Profiling Data

(2014) Alexandra Dana et al.   G3-Genes Genomes Genetics

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

(2014) Liana F Lareau et al.   eLife

Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale

(2013) Audrey M. Michel et al.   Wiley Interdisciplinary Reviews-RNA

Unraveling the dynamics of ribosome translocation

(2012) Jin Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

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

(2009) N. T. Ingolia et al.   SCIENCE