The extent of ribosome queuing in budding yeast

Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination

(2017) Nikolay E Shirokikh et al.   Nature Protocols

Computational analysis of nascent peptides that induce ribosome stalling and their proteomic distribution in Saccharomyces cerevisiae

(2017) Renana Sabi et al.   RNA

Estimation of ribosome profiling performance and reproducibility at various levels of resolution

(2016) Alon Diament et al.   Biology Direct

Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast

(2016) Caitlin E. Gamble et al.   CELL

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

(2016) Fuad Mohammad et al.   Cell Reports

A comparative genomics study on the effect of individual amino acids on ribosome stalling

(2015) Renana Sabi et al.   BMC GENOMICS

Codon Bias as a Means to Fine-Tune Gene Expression

(2015) Tessa E.F. Quax et al.   MOLECULAR CELL

Ribosome A and P sites revealed by length analysis of ribosome profiling data

(2015) Andrew T. Martens et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Rationally designed, heterologousS. cerevisiaetranscripts expose novel expression determinants

(2015) Tuval Ben-Yehezkel et al.   RNA Biology

High-Precision Analysis of Translational Pausing by Ribosome Profiling in Bacteria Lacking EFP

(2015) Christopher J. Woolstenhulme et al.   Cell Reports

Charting the dynamics of translation

(2014) Dominique Chu et al.   BIOSYSTEMS

Dom34 Rescues Ribosomes in 3′ Untranslated Regions

(2014) Nicholas R. Guydosh et al.   CELL

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

(2014) Carlo G. Artieri et al.   GENOME RESEARCH

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

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

The effect of tRNA levels on decoding times of mRNA codons

(2014) Alexandra Dana et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Tamir Tuller et al.   NUCLEIC ACIDS RESEARCH

Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration

(2014) R. Ishimura et al.   SCIENCE

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Co-translational mechanisms of protein maturation

(2013) Felix Gloge et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Translation elongation can control translation initiation on eukaryotic mRNAs

(2013) Dominique Chu et al.   EMBO JOURNAL

An in vivo control map for the eukaryotic mRNA translation machinery

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

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Control of ribosome traffic by position-dependent choice of synonymous codons

(2013) Namiko Mitarai et al.   PHYSICAL 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

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

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

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

(2012) Gene-Wei Li et al.   NATURE

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells

(2012) Alexandra Dana et al.   PLoS Computational Biology

MATHEMATICAL AND COMPUTATIONAL MODELLING OF RIBOSOMAL MOVEMENT AND PROTEIN SYNTHESIS: AN OVERVIEW

(2012) Tobias von der Haar   Computational and Structural Biotechnology Journal

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

(2011) Nicholas T. Ingolia et al.   CELL

Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

(2011) R. K. P. Zia et al.   JOURNAL OF STATISTICAL PHYSICS

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

The role of codon selection in regulation of translation efficiency deduced from synthetic libraries

(2011) Sivan Navon et al.   GENOME 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

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

(2010) F. Supek et al.   GENETICS

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

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

A Complete Set of Nascent Transcription Rates for Yeast Genes

(2010) Vicent Pelechano 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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A quantitative estimation of the global translational activity in logarithmically growing yeast cells

(2008) Tobias von der Haar   BMC Systems Biology

Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization

(2008) Namiko Mitarai et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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