Genetic circuit design automation

Creating small transcription activating RNAs

(2015) James Chappell et al.   Nature Chemical Biology

SBOL Visual: A Graphical Language for Genetic Designs

(2015) Jacqueline Y. Quinn et al.   PLOS BIOLOGY

Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition

(2014) Andrew E Blanchard et al.   BMC Systems Biology

Toehold Switches: De-Novo-Designed Regulators of Gene Expression

(2014) Alexander A. Green et al.   CELL

A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase

(2014) T. H. Segall-Shapiro et al.   Molecular Systems Biology

Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks

(2014) A. A. Nielsen et al.   Molecular Systems Biology

Functional optimization of gene clusters by combinatorial design and assembly

(2014) Michael J Smanski et al.   NATURE BIOTECHNOLOGY

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

(2014) Michal Galdzicki et al.   NATURE BIOTECHNOLOGY

Large-scale de novo DNA synthesis: technologies and applications

(2014) Sriram Kosuri et al.   NATURE METHODS

Permanent genetic memory with >1-byte capacity

(2014) Lei Yang et al.   NATURE METHODS

Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models

(2014) Nicholas Roehner et al.   ACS Synthetic Biology

A Computational Method for Automated Characterization of Genetic Components

(2014) Boyan Yordanov et al.   ACS Synthetic Biology

Optimal Part and Module Selection for Synthetic Gene Circuit Design Automation

(2014) Linh Huynh et al.   ACS Synthetic Biology

Development and characterization of AND-gate dynamic controllers with a modular synthetic GAL1 core promoter inSaccharomyces cerevisiae

(2013) Wei Suong Teo et al.   BIOTECHNOLOGY AND BIOENGINEERING

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Designing a synthetic genetic circuit that enables cell density-dependent auto-regulatory lysis for macromolecule release

(2013) Tat-Ming Lo et al.   CHEMICAL ENGINEERING SCIENCE

Synthetic analog computation in living cells

(2013) Ramiz Daniel et al.   NATURE

Computational design of ligand-binding proteins with high affinity and selectivity

(2013) Christine E. Tinberg 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

Precise and reliable gene expression via standard transcription and translation initiation elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amplifying Genetic Logic Gates

(2013) J. Bonnet et al.   SCIENCE

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

(2013) D. B. Goodman et al.   SCIENCE

Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits

(2013) Sean C. Sleight et al.   ACS Synthetic Biology

Effects of Genetic Variation on the E. coli Host-Circuit Interface

(2013) Stefano Cardinale et al.   Cell Reports

Sequestration-based bistability enables tuning of the switching boundaries and design of a latch

(2012) David Chen et al.   Molecular Systems Biology

Genetic programs constructed from layered logic gates in single cells

(2012) Tae Seok Moon et al.   NATURE

Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids

(2012) Fuzhong Zhang et al.   NATURE BIOTECHNOLOGY

Ribozyme-based insulator parts buffer synthetic circuits from genetic context

(2012) Chunbo Lou et al.   NATURE BIOTECHNOLOGY

Rationally designed families of orthogonal RNA regulators of translation

(2012) Vivek K Mutalik et al.   Nature Chemical Biology

Genome-scale promoter engineering by coselection MAGE

(2012) Harris H Wang et al.   NATURE METHODS

Rewritable digital data storage in live cells via engineered control of recombination directionality

(2012) J. Bonnet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering robust control of two-component system phosphotransfer using modular scaffolds

(2012) W. R. Whitaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AutoBioCAD: Full Biodesign Automation of Genetic Circuits

(2012) Guillermo Rodrigo et al.   ACS Synthetic Biology

Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks

(2012) Fusun Yaman et al.   ACS Synthetic Biology

Specification and Simulation of Synthetic Multicelled Behaviors

(2012) Seunghee S. Jang et al.   ACS Synthetic Biology

Computational Modeling of Synthetic Microbial Biofilms

(2012) Timothy J. Rudge et al.   ACS Synthetic Biology

Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors

(2012) Felix Moser et al.   ACS Synthetic Biology

Parts plus pipes: Synthetic biology approaches to metabolic engineering

(2011) Patrick M. Boyle et al.   METABOLIC ENGINEERING

Predicting the strength of UP-elements and full-length E. coli σE promoters

(2011) Virgil A. Rhodius et al.   NUCLEIC ACIDS RESEARCH

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

(2011) Jacob Beal et al.   PLoS One

Synthetic Biology Moving into the Clinic

(2011) W. C. Ruder et al.   SCIENCE

Automatic Design of Digital Synthetic Gene Circuits

(2011) Mario A. Marchisio et al.   PLoS Computational Biology

Engineering Static and Dynamic Control of Synthetic Pathways

(2010) William J. Holtz et al.   CELL

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

(2010) Alvin Tamsir et al.   NATURE

Five hard truths for synthetic biology

(2010) Roberta Kwok   NATURE

A synchronized quorum of genetic clocks

(2010) Tal Danino et al.   NATURE

Designing customized cell signalling circuits

(2010) Wendell A. Lim   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

iBioSim: a tool for the analysis and design of genetic circuits

(2009) C. J. Myers et al.   BIOINFORMATICS

A tunable synthetic mammalian oscillator

(2009) Marcel Tigges et al.   NATURE

Diversity-based, model-guided construction of synthetic gene networks with predicted functions

(2009) Tom Ellis et al.   NATURE BIOTECHNOLOGY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

The second wave of synthetic biology: from modules to systems

(2009) Priscilla E. M. Purnick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Writing DNA with GenoCADTM

(2009) M. J. Czar et al.   NUCLEIC ACIDS RESEARCH

Measuring the activity of BioBrick promoters using an in vivo reference standard

(2009) Jason R Kelly et al.   Journal of Biological Engineering

TinkerCell: modular CAD tool for synthetic biology

(2009) Deepak Chandran et al.   Journal of Biological Engineering

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY

Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

(2008) Timothy S. Ham et al.   PLoS One