Rationally designed, heterologousS. cerevisiaetranscripts expose novel expression determinants

Properties and determinants of codon decoding time distributions

(2014) Alexandra Dana et al.   BMC GENOMICS

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

(2014) Renana Sabi et al.   DNA RESEARCH

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

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Multiple roles of the coding sequence 5′ end in gene expression regulation

(2014) Tamir Tuller et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Justin Gardin et al.   eLife

Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae

(2013) Hadas Zur et al.   BMC BIOINFORMATICS

Translation elongation can control translation initiation on eukaryotic mRNAs

(2013) Dominique Chu et al.   EMBO JOURNAL

Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

(2013) D. B. Goodman et al.   SCIENCE

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

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

New Universal Rules of Eukaryotic Translation Initiation Fidelity

(2013) Hadas Zur et al.   PLoS Computational Biology

Strong association between mRNA folding strength and protein abundance in S. cerevisiae

(2012) Hadas Zur et al.   EMBO REPORTS

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Speeding with control: codon usage, tRNAs, and ribosomes

(2012) Eva Maria Novoa et al.   TRENDS IN GENETICS

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

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

(2011) Nicholas T. Ingolia et al.   CELL

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

(2011) M. V. Lee et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Understanding the contribution of synonymous mutations to human disease

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

Analysis and Prediction of Translation Rate Based on Sequence and Functional Features of the mRNA

(2011) Tao Huang et al.   PLoS One

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

(2011) Tamir Tuller et al.   GENOME BIOLOGY

The mRNA landscape at yeast translation initiation sites

(2010) A. Robbins-Pianka et al.   BIOINFORMATICS

On Relevance of Codon Usage to Expression of Synthetic and Natural Genes in Escherichia coli

(2010) F. Supek et al.   GENETICS

Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames

(2010) Malin Allert et al.   JOURNAL OF MOLECULAR BIOLOGY

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

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

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

Translation efficiency is determined by both codon bias and folding energy

(2010) Tamir Tuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

(2010) Wanjun Gu et al.   PLoS Computational Biology

The evolutionary consequences of erroneous protein synthesis

(2009) D. Allan Drummond et al.   NATURE REVIEWS GENETICS

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

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

Recursive construction of perfect DNA molecules from imperfect oligonucleotides

(2008) Gregory Linshiz et al.   Molecular Systems Biology