Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells

(2018) Alicia M. Darnell et al.   MOLECULAR CELL

Accurate design of translational output by a neural network model of ribosome distribution

(2018) Robert Tunney et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Accurate design of translational output by a neural network model of ribosome distribution

(2018) Robert Tunney et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

(2018) Khanh Dao Duc et al.   PLoS Genetics

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Renana Sabi et al.   RNA

The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan

(2017) Nitish Mittal et al.   Nature Communications

Protein charge distribution in proteomes and its impact on translation

(2017) Rodrigo D. Requião et al.   PLoS Computational Biology

Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics

(2017) Tzu-Yu Liu et al.   Cell Systems

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

(2016) Erik Ahrné et al.   JOURNAL OF PROTEOME RESEARCH

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

The relationship between the nucleolus and cancer: Current evidence and emerging paradigms

(2016) Ines Orsolic et al.   SEMINARS IN CANCER BIOLOGY

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

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

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

(2016) Konrad L. M. Rudolph et al.   PLoS Genetics

On the Ribosomal Density that Maximizes Protein Translation Rate

(2016) Yoram Zarai et al.   PLoS One

A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging

(2015) Mark A. McCormick et al.   Cell Metabolism

Regulation of mammalian nucleotide metabolism and biosynthesis

(2015) Andrew N. Lane et al.   NUCLEIC ACIDS RESEARCH

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

(2014) Hila Gingold et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

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

(2014) Yuanhui Mao et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling

(2014) C. H. Jan et al.   SCIENCE

Global Proteome Turnover Analyses of the Yeasts S. cerevisiae and S. pombe

(2014) Romain Christiano et al.   Cell Reports

The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now

(2014) Stacia R. Engel et al.   G3-Genes Genomes Genetics

The regulatory potential of upstream open reading frames in eukaryotic gene expression

(2014) Klaus Wethmar   Wiley Interdisciplinary Reviews-RNA

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Coordinated conformational and compositional dynamics drive ribosome translocation

(2013) Jin Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly

(2013) Brittany Lott et al.   BMC Biophysics

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

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

To the pore and through the pore: A story of mRNA export kinetics

(2012) Marlene Oeffinger et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2012) Samuel Marguerat et al.   CELL

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

(2012) Hadas Zur et al.   EMBO REPORTS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

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

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Alexandra Dana et al.   PLoS Computational Biology

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

Nascent Peptide Side Chains Induce Rearrangements in Distinct Locations of the Ribosomal Tunnel

(2011) Jianli Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

The Human Proteome Project: Current State and Future Direction

(2011) Pierre Legrain et al.   MOLECULAR & CELLULAR PROTEOMICS

The ribosome uses two active mechanisms to unwind messenger RNA during translation

(2011) Xiaohui Qu et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Yeast Life Span Extension by Depletion of 60S Ribosomal Subunits Is Mediated by Gcn4

(2008) Kristan K. Steffen et al.   CELL

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

(2008) D. Allan Drummond et al.   CELL

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

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

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