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

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

The genetic code as expressed through relationships between mRNA structure and protein function

(2013) David M. Mauger et al.   FEBS LETTERS

Number Variation of High Stability Regions Is Correlated with Gene Functions

(2013) Yuanhui Mao et al.   Genome Biology and Evolution

An in vivo control map for the eukaryotic mRNA translation machinery

(2013) H. Firczuk et al.   Molecular Systems Biology

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

(2013) Jinwei Zhang et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu 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

Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific

(2013) Tong Wang et al.   NUCLEIC ACIDS RESEARCH

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

(2013) S. A. Shabalina et al.   NUCLEIC ACIDS RESEARCH

Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly

(2013) C. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast

(2013) S. Dvir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of in vivo RNA structure in low-abundance transcripts

(2013) Chun Kit Kwok et al.   Nature Communications

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

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

Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme

(2012) Deepa Agashe et al.   MOLECULAR BIOLOGY AND EVOLUTION

A mechanistic overview of translation initiation in eukaryotes

(2012) Colin Echeverría Aitken et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translation drives mRNA quality control

(2012) Christopher J Shoemaker et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translational control by changes in poly(A) tail length: recycling mRNAs

(2012) Laure Weill et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2012) Hila Gingold et al.   NUCLEIC ACIDS RESEARCH

The Elongation, Termination, and Recycling Phases of Translation in Eukaryotes

(2012) T. E. Dever et al.   Cold Spring Harbor Perspectives in Biology

The Mechanism of Eukaryotic Translation Initiation: New Insights and Challenges

(2012) A. G. Hinnebusch et al.   Cold Spring Harbor Perspectives in Biology

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

Codon usage variability determines the correlation between proteome and transcriptome fold changes

(2011) Roberto Olivares-Hernández et al.   BMC Systems Biology

Determinants of translation efficiency and accuracy

(2011) H. Gingold et al.   Molecular Systems Biology

mRNA pseudoknot structures can act as ribosomal roadblocks

(2011) Jesper Tholstrup et al.   NUCLEIC ACIDS RESEARCH

The Structure of the Eukaryotic Ribosome at 3.0 A Resolution

(2011) A. Ben-Shem et al.   SCIENCE

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

(2011) Shlomi Reuveni et al.   PLoS Computational Biology

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

A Role for Codon Order in Translation Dynamics

(2010) Gina Cannarozzi et al.   CELL

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

A conserved structure within the HIV gag open reading frame that controls translation initiation directly recruits the 40S subunit and eIF3

(2010) Nicolas Locker et al.   NUCLEIC ACIDS RESEARCH

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

Riboswitch-mediated control of gene expression in eukaryotes

(2010) Andreas Wachter   RNA Biology

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

(2010) Qi Zheng et al.   PLoS Genetics

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

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

Eukaryotic initiation factor 6 is rate-limiting in translation, growth and transformation

(2008) Valentina Gandin et al.   NATURE

Following translation by single ribosomes one codon at a time

(2008) Jin-Der Wen et al.   NATURE

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Vienna RNA Websuite

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

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH