The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

Ribosome pausing, arrest and rescue in bacteria and eukaryotes

(2017) Allen R. Buskirk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Computational analysis of nascent peptides that induce ribosome stalling and their proteomic distribution in Saccharomyces cerevisiae

(2017) Renana Sabi et al.   RNA

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

(2016) Dmitry E. Andreev et al.   NUCLEIC ACIDS RESEARCH

Ribonuclease selection for ribosome profiling

(2016) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

Quantitative assessment of ribosome drop-off inE. coli

(2016) Celine Sin et al.   NUCLEIC ACIDS RESEARCH

Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

(2016) Daniel A. Nissley et al.   Nature Communications

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

(2016) Patrick B. F. O’Connor 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

A comparative genomics study on the effect of individual amino acids on ribosome stalling

(2015) Renana Sabi et al.   BMC GENOMICS

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

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

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

Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome

(2015) Christian Schmidt 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

Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast

(2015) Jeffrey A. Hussmann et al.   PLoS Genetics

An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation

(2014) Arvind R. Subramaniam et al.   CELL

Dom34 Rescues Ribosomes in 3′ Untranslated Regions

(2014) Nicholas R. Guydosh et al.   CELL

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

(2014) Carlo G. Artieri et al.   GENOME RESEARCH

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

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

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo

(2014) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translation inhibitors cause abnormalities in ribosome profiling experiments

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

The effect of tRNA levels on decoding times of mRNA codons

(2014) Alexandra Dana et al.   NUCLEIC ACIDS RESEARCH

Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling

(2014) C. C. Williams et al.   SCIENCE

The Effects of Codon Context on In Vivo Translation Speed

(2014) Fabienne F. V. Chevance et al.   PLoS Genetics

Measurement of average decoding rates of the 61 sense codons in vivo

(2014) Justin Gardin et al.   eLife

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

(2014) Liana F Lareau et al.   eLife

Co-translational targeting and translocation of proteins to the endoplasmic reticulum

(2013) Yvonne Nyathi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Translation elongation can control translation initiation on eukaryotic mRNAs

(2013) Dominique Chu et al.   EMBO JOURNAL

Widespread Regulation of Translation by Elongation Pausing in Heat Shock

(2013) Reut Shalgi et al.   MOLECULAR CELL

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

(2013) David Sehnal et al.   Journal of Cheminformatics

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

(2013) Catherine A. Charneski et al.   PLOS BIOLOGY

Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation

(2013) Luca Ciandrini et al.   PLoS Computational Biology

Multisite Ribosomal Stalling: A Unique Mode of Regulatory Nascent Chain Action Revealed for MifM

(2012) Shinobu Chiba et al.   MOLECULAR CELL

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

Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells

(2012) Alexandra Dana et al.   PLoS Computational Biology

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

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

(2011) Xiaohui Qu et al.   NATURE

Non-equilibrium statistical mechanics: from a paradigmatic model to biological transport

(2011) T Chou et al.   REPORTS ON PROGRESS IN PHYSICS

Composite effects of gene determinants on the translation speed and density of ribosomes

(2011) Tamir Tuller et al.   GENOME BIOLOGY

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Global and local depletion of ternary complex limits translational elongation

(2010) Gong Zhang et al.   NUCLEIC ACIDS RESEARCH

Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel

(2010) Del Lucent et al.   PLoS Computational Biology

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

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

(2009) N. T. Ingolia et al.   SCIENCE

Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates

(2008) Jianli Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

The Most Conserved Genome Segments for Life Detection on Earth and Other Planets

(2008) Thomas A. Isenbarger et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Slow peptide bond formation by proline and other N-alkylamino acids in translation

(2008) M. Y. Pavlov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA