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

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

(2018) Khanh Dao Duc et al.   PLoS Genetics

Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution

(2018) Han Fang et al.   Cell Systems

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

eIF5A Functions Globally in Translation Elongation and Termination

(2017) Anthony P. Schuller et al.   MOLECULAR CELL

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells

(2017) Fangzhou Zhao et al.   NUCLEIC ACIDS RESEARCH

Alteration of protein function by a silent polymorphism linked to tRNA abundance

(2017) Sebastian Kirchner et al.   PLOS BIOLOGY

Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning

(2017) Sai Zhang et al.   Cell Systems

Prediction of ribosome footprint profile shapes from transcript sequences

(2016) Tzu-Yu Liu et al.   BIOINFORMATICS

Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast

(2016) Caitlin E. Gamble 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

Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor

(2016) Shintaro Iwasaki 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

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

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

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

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

(2014) Carlo G. Artieri 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

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

(2014) R. Ishimura et al.   SCIENCE

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

(2014) Justin Gardin et al.   eLife

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Translation elongation can control translation initiation on eukaryotic mRNAs

(2013) Dominique Chu et al.   EMBO JOURNAL

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

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

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

(2012) Alexandra Dana et al.   PLoS Computational Biology

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Wobble base-pairing slows in vivo translation elongation in metazoans

(2011) M. Stadler et al.   RNA

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

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

Control of translation efficiency in yeast by codon-anticodon interactions

(2010) D. P. Letzring et al.   RNA

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

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

(2009) N. T. Ingolia et al.   SCIENCE

Using flowViz to visualize flow cytometry data

(2008) D. Sarkar et al.   BIOINFORMATICS

qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis

(2008) C. Ritz et al.   BIOINFORMATICS