Analysis of computational codon usage models and their association with translationally slow codons

Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness

(2020) Ian M. Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Following Ribosome Footprints to Understand Translation at a Genome Wide Level

(2018) Guillermo Eastman et al.   Computational and Structural Biotechnology Journal

Evidence of evolutionary selection for cotranslational folding

(2017) William M. Jacobs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding

(2017) Anabel Rodriguez et al.   PROTEIN SCIENCE

Synonymous Codons: Choose Wisely for Expression

(2017) Christina E. Brule et al.   TRENDS IN GENETICS

Widespread position-specific conservation of synonymous rare codons within coding sequences

(2017) Julie L. Chaney et al.   PLoS Computational Biology

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

(2016) Alon Diament et al.   Biology Direct

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

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

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

Roles for Synonymous Codon Usage in Protein Biogenesis

(2015) Julie L. Chaney et al.   Annual Review of Biophysics

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

(2015) Renana Sabi et al.   BMC GENOMICS

Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone ‡

(2015) Michael A. Gilchrist et al.   Genome Biology and Evolution

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

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

Expanding Anfinsen’s Principle: Contributions of Synonymous Codon Selection to Rational Protein Design

(2014) Ian M. Sander et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Poly(A)-tail profiling reveals an embryonic switch in translational control

(2014) Alexander O. Subtelny et al.   NATURE

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

Nascent peptides that block protein synthesis in bacteria

(2013) C. J. Woolstenhulme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL