Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

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

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

Emerging roles of tRNA in adaptive translation, signalling dynamics and disease

(2014) Sebastian Kirchner et al.   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

Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae

(2014) Yuanhui Mao et al.   NUCLEIC ACIDS RESEARCH

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

(2014) Joao C. Guimaraes et al.   NUCLEIC ACIDS RESEARCH

The effect of tRNA levels on decoding times of mRNA codons

(2014) Alexandra Dana et al.   NUCLEIC ACIDS RESEARCH

Quantifying the Effect of Ribosomal Density on mRNA Stability

(2014) Shlomit Edri et al.   PLoS One

Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding

(2014) Jian-Rong Yang et al.   PLOS BIOLOGY

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

Efficient translation initiation dictates codon usage at gene start

(2013) K. Bentele et al.   Molecular Systems Biology

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

Dynamics of translation by single ribosomes through mRNA secondary structures

(2013) Chunlai Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability

(2013) Sibylle E. Wohlgemuth et al.   NUCLEIC ACIDS RESEARCH

Effect of ribosome shielding on mRNA stability

(2013) Carlus Deneke et al.   PHYSICAL BIOLOGY

Probing the Limits of Genetic Recoding in Essential Genes

(2013) M. J. Lajoie et al.   SCIENCE

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

A computational framework for the design of optimal protein synthesis

(2012) Julien Racle et al.   BIOTECHNOLOGY AND BIOENGINEERING

tRNA concentration fine tunes protein solubility

(2012) Ivan Fedyunin et al.   FEBS LETTERS

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

(2012) Gene-Wei Li et al.   NATURE

Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome

(2012) Hila Gingold et al.   NUCLEIC ACIDS RESEARCH

Transfer RNA modifications: nature's combinatorial chemistry playground

(2012) Jane E. Jackman et al.   Wiley Interdisciplinary Reviews-RNA

The Functional Half-Life of an mRNA Depends on the Ribosome Spacing in an Early Coding Region

(2011) Margit Pedersen et al.   JOURNAL OF MOLECULAR BIOLOGY

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

Evolutionary optimization of speed and accuracy of decoding on the ribosome

(2011) I. Wohlgemuth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations

(2011) Gabriela R. Moura et al.   PLoS One

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

(2011) Shlomi Reuveni et al.   PLoS Computational Biology

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

A Role for Codon Order in Translation Dynamics

(2010) Gina Cannarozzi et al.   CELL

Folding at the birth of the nascent chain: coordinating translation with co-translational folding

(2010) Gong Zhang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Global and local depletion of ternary complex limits translational elongation

(2010) Gong Zhang et al.   NUCLEIC ACIDS RESEARCH

pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA

(2010) M. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain

(2009) Germán L Rosano et al.   Microbial Cell Factories

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

(2009) Gong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

tRNA over-expression in breast cancer and functional consequences

(2009) Mariana Pavon-Eternod et al.   NUCLEIC ACIDS RESEARCH

Universal function-specificity of codon usage

(2009) Hamed Shateri Najafabadi et al.   NUCLEIC ACIDS RESEARCH

Generic Algorithm to Predict the Speed of Translational Elongation: Implications for Protein Biogenesis

(2009) Gong Zhang et al.   PLoS One

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

(2009) Mark Welch et al.   PLoS One

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

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Following translation by single ribosomes one codon at a time

(2008) Jin-Der Wen et al.   NATURE

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

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

Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study

(2008) Nicola A. Burgess-Brown et al.   PROTEIN EXPRESSION AND PURIFICATION