Design, synthesis, and testing toward a 57-codon genome

Overcoming Challenges in Engineering the Genetic Code

(2016) M.J. Lajoie et al.   JOURNAL OF MOLECULAR BIOLOGY

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Incorporation of Unnatural Amino Acids in Response to the AGG Codon

(2015) Byeong Sung Lee et al.   ACS Chemical Biology

Codon Bias as a Means to Fine-Tune Gene Expression

(2015) Tessa E.F. Quax et al.   MOLECULAR CELL

Recoded organisms engineered to depend on synthetic amino acids

(2015) Alexis J. Rovner et al.   NATURE

Biocontainment of genetically modified organisms by synthetic protein design

(2015) Daniel J. Mandell et al.   NATURE

Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology

(2015) Jiqiang Ling et al.   NATURE REVIEWS MICROBIOLOGY

Reassignment of a rare sense codon to a non-canonical amino acid inEscherichia coli

(2015) Takahito Mukai et al.   NUCLEIC ACIDS RESEARCH

Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli

(2015) Joanne M. Ho et al.   ACS Synthetic Biology

Towards Reassigning the Rare AGG Codon inEscherichia coli

(2014) Yu Zeng et al.   CHEMBIOCHEM

Rational optimization of tolC as a powerful dual selectable marker for genome engineering

(2014) Christopher J. Gregg et al.   NUCLEIC ACIDS RESEARCH

Total Synthesis of a Functional Designer Eukaryotic Chromosome

(2014) N. Annaluru et al.   SCIENCE

Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing

(2014) T. Conway et al.   mBio

Recoding the Genetic Code with Selenocysteine

(2013) Markus J. Bröcker et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2013) Mian Zhou et al.   NATURE

Characterization of 582 natural and synthetic terminators and quantification of their design constraints

(2013) Ying-Ja Chen et al.   NATURE METHODS

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

Probing the Limits of Genetic Recoding in Essential Genes

(2013) M. J. Lajoie et al.   SCIENCE

Genomically Recoded Organisms Expand Biological Functions

(2013) M. J. Lajoie et al.   SCIENCE

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

(2013) D. B. Goodman et al.   SCIENCE

tRNA genes rapidly change in evolution to meet novel translational demands

(2013) Avihu H Yona et al.   eLife

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

(2012) Gene-Wei Li et al.   NATURE

Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca

(2012) K. Temme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

Adding New Chemistries to the Genetic Code

(2010) Chang C. Liu et al.   Annual Review of Biochemistry

De NovoGeneration of Mutually Orthogonal Aminoacyl-tRNA Synthetase/tRNA Pairs

(2010) Heinz Neumann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

(2009) Mark Welch et al.   PLoS One

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

(2008) D. G. Gibson et al.   SCIENCE