Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

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 …

SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities

E Martínez-García, T Aparicio… - Nucleic acids …, 2015 - academic.oup.com
Abstract The Standard European Vector Architecture 2.0 database (SEVA-DB 2.0,
http://seva. cnb. csic. es) is an improved and expanded version of the platform released in …

Sharing structure and function in biological design with SBOL 2.0

N Roehner, J Beal, K Clancy, B Bartley… - ACS synthetic …, 2016 - ACS Publications
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative
engineering of biological systems across different institutions and tools. SBOL is developed …

Tools and applications in synthetic biology

IC MacDonald, TL Deans - Advanced drug delivery reviews, 2016 - Elsevier
Advances in synthetic biology have enabled the engineering of cells with genetic circuits in
order to program cells with new biological behavior, dynamic gene expression, and logic …

Double dutch: a tool for designing combinatorial libraries of biological systems

N Roehner, EM Young, CA Voigt, DB Gordon… - ACS Synthetic …, 2016 - ACS Publications
Recently, semirational approaches that rely on combinatorial assembly of characterized
DNA components have been used to engineer biosynthetic pathways. In practice, however …

Toward the first data acquisition standard in synthetic biology

I Sainz de Murieta, M Bultelle, RI Kitney - ACS synthetic biology, 2016 - ACS Publications
This paper describes the development of a new data acquisition standard for synthetic
biology. This comprises the creation of a methodology that is designed to capture all the …

A framework for genetic logic synthesis

P Vaidyanathan, BS Der, S Bhatia… - Proceedings of the …, 2015 - ieeexplore.ieee.org
Digital electronic circuits have inspired synthetic biologists to program living cells with
synthetic decision-making circuits by creating multilevel genetic logic gates. In both genetic …

Generating systems biology markup language models from the synthetic biology open language

N Roehner, Z Zhang, T Nguyen, CJ Myers - ACS synthetic biology, 2015 - ACS Publications
In the context of synthetic biology, model generation is the automated process of
constructing biochemical models based on genetic designs. This paper discusses the use …

A converter from the systems biology markup language to the synthetic biology open language

T Nguyen, N Roehner, Z Zundel… - ACS synthetic biology, 2016 - ACS Publications
Standards are important to synthetic biology because they enable exchange and
reproducibility of genetic designs. This paper describes a procedure for converting between …