Challenges and obstacles related to solving the codon bias riddles: Figure 1

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

New Universal Rules of Eukaryotic Translation Initiation Fidelity

(2013) Hadas Zur et al.   PLoS Computational Biology

RFMapp: ribosome flow model application

(2012) H. Zur et al.   BIOINFORMATICS

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

(2012) Hadas Zur et al.   EMBO REPORTS

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

(2012) Gene-Wei Li et al.   NATURE

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

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

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

(2011) Nicholas T. Ingolia et al.   CELL

Understanding the contribution of synonymous mutations to human disease

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

Mathematical descriptions of biochemical networks: Stability, stochasticity, evolution

(2011) Simon Rosenfeld   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

(2011) Shlomi Reuveni et al.   PLoS Computational 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

Real-time tRNA transit on single translating ribosomes at codon resolution

(2010) Sotaro Uemura et al.   NATURE

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

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

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

Translation efficiency is determined by both codon bias and folding energy

(2010) Tamir Tuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Betulin Is a Potent Anti-Tumor Agent that Is Enhanced by Cholesterol

(2009) Franziska B. Mullauer et al.   PLoS One

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates

(2008) Jianli Lu et al.   JOURNAL OF MOLECULAR BIOLOGY