Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe

The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality

(2016) Aditya Radhakrishnan et al.   CELL

Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression

(2016) Hani Goodarzi et al.   CELL

Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition

(2016) Ariel A Bazzini et al.   EMBO JOURNAL

Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish

(2016) Yuichiro Mishima et al.   MOLECULAR CELL

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

(2016) P. Eser et al.   Molecular Systems Biology

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

(2016) Grégory Boël et al.   NATURE

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

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

Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae

(2016) B. Neymotin et al.   G3-Genes Genomes Genetics

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

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

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

Synthesis at the Speed of Codons

(2015) Kristin S. Koutmou et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

Principles and Properties of Eukaryotic mRNPs

(2014) Sarah F. Mitchell et al.   MOLECULAR CELL

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

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

Determination of in vivo RNA kinetics using RATE-seq

(2014) Benjamin Neymotin et al.   RNA

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

(2014) Ayesha Hasan et al.   PLoS Genetics

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

(2014) Justin Gardin et al.   eLife

Translation elongation can control translation initiation on eukaryotic mRNAs

(2013) Dominique Chu et al.   EMBO JOURNAL

Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels

(2013) Mai Sun et al.   MOLECULAR CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

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

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide studies of mRNA synthesis and degradation in eukaryotes

(2011) José E. Pérez-Ortín et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Promoter Elements Regulate Cytoplasmic mRNA Decay

(2011) Almog Bregman et al.   CELL

Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

(2011) Tatjana Trcek et al.   CELL

Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

(2011) Sarah E. Munchel et al.   MOLECULAR BIOLOGY OF THE CELL

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Global coordination of transcriptional control and mRNA decay during cellular differentiation

(2010) Maria J Amorim 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

There is a steady-state transcriptome in exponentially growing yeast cells

(2010) Vicent Pelechano et al.   YEAST

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Selection on Codon Bias

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

Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs

(2008) Fumihito Miura et al.   BMC GENOMICS

The Anchor-Away Technique: Rapid, Conditional Establishment of Yeast Mutant Phenotypes

(2008) Hirohito Haruki et al.   MOLECULAR CELL

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

(2008) Ophir Shalem et al.   Molecular Systems Biology

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

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

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

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

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA