Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States

Quantification of GC-biased gene conversion in the human genome

(2015) Sylvain Glémin et al.   GENOME RESEARCH

Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses

(2015) Lauren Endres et al.   RNA Biology

Translational selection in human: more pronounced in housekeeping genes

(2014) Lina Ma et al.   Biology Direct

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

(2014) Hila Gingold et al.   CELL

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders

(2014) S. Blanco et al.   EMBO JOURNAL

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface

(2014) Bianca M. Schmitt 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

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

(2014) Sebastian Kirchner et al.   NATURE REVIEWS GENETICS

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

(2014) Nuno A. Fonseca et al.   PLoS One

A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

(2014) Zohar Bloom-Ackermann et al.   PLoS Genetics

Gene duplication and neofunctionalization: POLR3G and POLR3GL

(2013) M. Renaud et al.   GENOME RESEARCH

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Environmental shaping of codon usage and functional adaptation across microbial communities

(2013) Maša Roller et al.   NUCLEIC ACIDS RESEARCH

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

A Genome-Wide Systematic Analysis Reveals Different and Predictive Proliferation Expression Signatures of Cancerous vs. Non-Cancerous Cells

(2013) Yedael Y. Waldman et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A Role for tRNA Modifications in Genome Structure and Codon Usage

(2012) Eva Maria Novoa et al.   CELL

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

(2012) D. Canella et al.   GENOME RESEARCH

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

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

RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

(2012) Francesca Tuorto et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

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

(2011) Nicholas T. Ingolia et al.   CELL

Mutation Bias is the Driving Force of Codon Usage in the Gallus gallus genome

(2011) Y. Rao et al.   DNA RESEARCH

Determinants of translation efficiency and accuracy

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

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes

(2011) Claudia Kutter et al.   NATURE GENETICS

Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells

(2011) Lucie Carrière et al.   NUCLEIC ACIDS RESEARCH

Wobble base-pairing slows in vivo translation elongation in metazoans

(2011) M. Stadler et al.   RNA

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

tRNA biology charges to the front

(2010) E. M. Phizicky et al.   GENES & DEVELOPMENT

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

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

Pol II and its associated epigenetic marks are present at Pol III–transcribed noncoding RNA genes

(2010) Artem Barski et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

(2010) Andrew J Oler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

(2010) Zarmik Moqtaderi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

RNA Processing and Export

(2010) S. Hocine et al.   Cold Spring Harbor Perspectives in Biology

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Selection on Codon Bias

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

How many human genes can be defined as housekeeping with current expression data?

(2008) Jiang Zhu et al.   BMC GENOMICS

Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids

(2008) David Horn   BMC GENOMICS

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Estimating Translational Selection in Eukaryotic Genomes

(2008) M. dos Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics