A critical analysis of codon optimization in human therapeutics

VP Mauro, SA Chappell - Trends in molecular medicine, 2014 - cell.com
Codon optimization describes gene engineering approaches that use synonymous codon
changes to increase protein production. Applications for codon optimization include …

Engineering biological systems using automated biofoundries

R Chao, S Mishra, T Si, H Zhao - Metabolic Engineering, 2017 - Elsevier
Engineered biological systems such as genetic circuits and microbial cell factories have
promised to solve many challenges in the modern society. However, the artisanal processes …

Design of a synthetic yeast genome

SM Richardson, LA Mitchell, G Stracquadanio, K Yang… - Science, 2017 - science.org
We describe complete design of a synthetic eukaryotic genome, Sc2. 0, a highly modified
Saccharomyces cerevisiae genome reduced in size by nearly 8%, with 1.1 megabases of …

Repurposing CRISPR-Cas12b for mammalian genome engineering

F Teng, T Cui, G Feng, L Guo, K Xu, Q Gao, T Li, J Li… - Cell discovery, 2018 - nature.com
The prokaryotic CRISPR-Cas adaptive immune systems provide valuable resources to
develop genome editing tools, such as CRISPR-Cas9 and CRISPR-Cas12a/Cpf1. Recently …

Codon optimization with deep learning to enhance protein expression

H Fu, Y Liang, X Zhong, ZL Pan, L Huang, HL Zhang… - Scientific reports, 2020 - nature.com
Heterologous expression is the main approach for recombinant protein production ingenetic
synthesis, for which codon optimization is necessary. The existing optimization methods are …

Total synthesis of a functional designer eukaryotic chromosome

N Annaluru, H Muller, LA Mitchell, S Ramalingam… - science, 2014 - science.org
Rapid advances in DNA synthesis techniques have made it possible to engineer viruses,
biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a …

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

JS Dymond, SM Richardson, CE Coombes, T Babatz… - Nature, 2011 - nature.com
Recent advances in DNA synthesis technology have enabled the construction of novel
genetic pathways and genomic elements, furthering our understanding of system-level …

Engineering BioBrick vectors from BioBrick parts

RP Shetty, D Endy, TF Knight - Journal of biological engineering, 2008 - Springer
Background The underlying goal of synthetic biology is to make the process of engineering
biological systems easier. Recent work has focused on defining and developing standard …

GFP Reconstitution Across Synaptic Partners (GRASP) defines cell contacts and synapses in living nervous systems

EH Feinberg, MK VanHoven, A Bendesky, G Wang… - Neuron, 2008 - cell.com
The identification of synaptic partners is challenging in dense nerve bundles, where many
processes occupy regions beneath the resolution of conventional light microscopy. To …

OPTIMIZER: a web server for optimizing the codon usage of DNA sequences

P Puigbo, E Guzmán, A Romeu… - Nucleic acids …, 2007 - academic.oup.com
OPTIMIZER is an on-line application that optimizes the codon usage of a gene to increase
its expression level. Three methods of optimization are available: the 'one amino acid–one …