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

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

Roles for Synonymous Codon Usage in Protein Biogenesis

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

Nonoptimal codon usage influences protein structure in intrinsically disordered regions

(2015) Mian Zhou et al.   MOLECULAR MICROBIOLOGY

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

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

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective

(2014) Shelly Mahlab et al.   PLoS Computational Biology

The Effects of Codon Context on In Vivo Translation Speed

(2014) Fabienne F. V. Chevance et al.   PLoS Genetics

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

(2014) Justin Gardin et al.   eLife

Efficient translation initiation dictates codon usage at gene start

(2013) K. Bentele et al.   Molecular Systems Biology

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

(2013) Mian Zhou et al.   NATURE

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

(2013) Yao Xu et al.   NATURE

Identification of a Novel Synonymous Mutation in the Humanβ-Ureidopropionase GeneUPB1Affecting Pre-mRNA Splicing

(2013) J. Meijer et al.   NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS

Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

(2013) D. B. Goodman et al.   SCIENCE

A serine sensor for multicellularity in a bacterium

(2013) Arvind R Subramaniam et al.   eLife

Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

(2012) Matthieu Chartier et al.   BIOINFORMATICS

Intrinsically Disordered Proteins: From Sequence and Conformational Properties toward Drug Discovery

(2012) Nasrollah Rezaei-Ghaleh et al.   CHEMBIOCHEM

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

(2012) Milana Frenkel-Morgenstern et al.   Molecular Systems Biology

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

(2012) Gene-Wei Li et al.   NATURE

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

(2011) K. Megy et al.   NUCLEIC ACIDS RESEARCH

Increased incidence of rare codon clusters at 5' and 3' gene termini:implications for function

(2010) Thomas F Clarke et al.   BMC GENOMICS

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

A Synonymous Mutation in the CFTR Gene Causes Aberrant Splicing in an Italian Patient Affected by a Mild Form of Cystic Fibrosis

(2010) Valeria Faa′ et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Detecting Positive and Purifying Selection at Synonymous Sites in Yeast and Worm

(2010) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Synonymous codon usage influences the local protein structure observed

(2010) Rhodri Saunders et al.   NUCLEIC ACIDS RESEARCH

Forces that influence the evolution of codon bias

(2010) P. M. Sharp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Insights into protein folding mechanisms from large scale analysis of mutational effects

(2010) A. N. Naganathan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential Arginylation of Actin Isoforms Is Regulated by Coding Sequence-Dependent Degradation

(2010) F. Zhang et al.   SCIENCE

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

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

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

(2009) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Generic Algorithm to Predict the Speed of Translational Elongation: Implications for Protein Biogenesis

(2009) Gong Zhang et al.   PLoS One

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Biased codon usage in signal peptides: a role in protein export

(2009) Yaramah M. Zalucki et al.   TRENDS IN MICROBIOLOGY

Clustering of Codons with Rare Cognate tRNAs in Human Genes Suggests an Extra Level of Expression Regulation

(2009) Joanna L. Parmley et al.   PLoS Genetics

Preferred and avoided codon pairs in three domains of life

(2008) Age Tats et al.   BMC GENOMICS

Rare Codons Cluster

(2008) Thomas F. Clarke et al.   PLoS One

Predicting protein folding rates from geometric contact and amino acid sequence

(2008) Zheng Ouyang et al.   PROTEIN SCIENCE

A pause for thought along the co-translational folding pathway

(2008) Anton A. Komar   TRENDS IN BIOCHEMICAL SCIENCES