Principles of genetic circuit design

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

Designable DNA-binding domains enable construction of logic circuits in mammalian cells

(2014) Rok Gaber et al.   Nature Chemical Biology

Rapid and Reliable DNA Assembly via Ligase Cycling Reaction

(2014) Stefan de Kok et al.   ACS Synthetic Biology

CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

(2013) Rotem Sorek et al.   Annual Review of Biochemistry

Translational Cross Talk in Gene Networks

(2013) William H. Mather et al.   BIOPHYSICAL JOURNAL

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

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

(2013) Hans-Jörg Frasch et al.   CURRENT OPINION IN BIOTECHNOLOGY

Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression

(2013) Alec AK Nielsen et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

A wise consistency: engineering biology for conformity, reliability, predictability

(2013) Adam Paul Arkin   CURRENT OPINION IN CHEMICAL BIOLOGY

Design of orthogonal genetic switches based on a crosstalk map of  s, anti- s, and promoters

(2013) V. A. Rhodius et al.   Molecular Systems Biology

Synthetic analog computation in living cells

(2013) Ramiz Daniel et al.   NATURE

Engineering dynamic pathway regulation using stress-response promoters

(2013) Robert H Dahl et al.   NATURE BIOTECHNOLOGY

Synthetic circuits integrating logic and memory in living cells

(2013) Piro Siuti et al.   NATURE BIOTECHNOLOGY

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Directed evolution of genetic parts and circuits by compartmentalized partnered replication

(2013) Jared W Ellefson et al.   NATURE BIOTECHNOLOGY

Genomic mining of prokaryotic repressors for orthogonal logic gates

(2013) Brynne C Stanton et al.   Nature Chemical Biology

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

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

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

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder 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

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes

(2013) Annemarie H Becker et al.   Nature Protocols

Advanced genetic tools for plant biotechnology

(2013) Wusheng Liu et al.   NATURE REVIEWS GENETICS

Two- and three-input TALE-based AND logic computation in embryonic stem cells

(2013) Florian Lienert et al.   NUCLEIC ACIDS RESEARCH

Measurement and modeling of intrinsic transcription terminators

(2013) Guillaume Cambray et al.   NUCLEIC ACIDS RESEARCH

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

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites

(2013) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants

(2013) D. L. Shis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Functional Roles of Pulsing in Genetic Circuits

(2013) J. H. Levine et al.   SCIENCE

Protein folding and de novo protein design for biotechnological applications

(2013) George A. Khoury et al.   TRENDS IN BIOTECHNOLOGY

In Situ Overlap and Sequence Synthesis During DNA Assembly

(2013) Bernhard Paetzold et al.   ACS Synthetic Biology

Genetically Programmable Pathogen Sense and Destroy

(2013) Saurabh Gupta et al.   ACS Synthetic Biology

Modular Design of a Synthetic Payload Delivery Device

(2013) Jin H. Huh et al.   ACS Synthetic Biology

Synthetic Gene Circuit-Mediated Monitoring of Endogenous Metabolites: Identification of GAL11 as a Novel Multicopy Enhancer of S-Adenosylmethionine Level in Yeast

(2013) Taichi Umeyama et al.   ACS Synthetic Biology

SBROME: A Scalable Optimization and Module Matching Framework for Automated Biosystems Design

(2013) Linh Huynh et al.   ACS Synthetic Biology

Fluorescent Proteins and in Vitro Genetic Organization for Cell-Free Synthetic Biology

(2013) Roberta Lentini et al.   ACS Synthetic Biology

Randomized BioBrick Assembly: A Novel DNA Assembly Method for Randomizing and Optimizing Genetic Circuits and Metabolic Pathways

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

A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language

(2013) Nicholas Roehner et al.   ACS Synthetic Biology

SoxR as a Single-Cell Biosensor for NADPH-Consuming Enzymes in Escherichia coli

(2013) Solvej Siedler et al.   ACS Synthetic Biology

Engineering the esaR Promoter for Tunable Quorum Sensing-Dependent Gene Expression

(2013) Jasmine Shong et al.   ACS Synthetic Biology

Promoter Element Arising from the Fusion of Standard BioBrick Parts

(2013) Andrew I. Yao et al.   ACS Synthetic Biology

Antimicrobial Peptides Targeting Gram-negative Pathogens, Produced and Delivered by Lactic Acid Bacteria

(2013) Katherine Volzing et al.   ACS Synthetic Biology

Probing Cell-Free Gene Expression Noise in Femtoliter Volumes

(2013) David K. Karig et al.   ACS Synthetic Biology

Analysis and Design of a Genetic Circuit for Dynamic Metabolic Engineering

(2013) Nikolaos Anesiadis et al.   ACS Synthetic Biology

Expanding the Boolean Logic of the Prokaryotic Transcription Factor XylR by Functionalization of Permissive Sites with a Protease-Target Sequence

(2013) Belen Calles et al.   ACS Synthetic Biology

Refactoring the Silent Spectinabilin Gene Cluster Using a Plug-and-Play Scaffold

(2013) Zengyi Shao et al.   ACS Synthetic Biology

Pigeon: A Design Visualizer for Synthetic Biology

(2013) Swapnil Bhatia et al.   ACS Synthetic Biology

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas

(2013) Fahim Farzadfard et al.   ACS Synthetic Biology

Retroactivity Controls the Temporal Dynamics of Gene Transcription

(2013) Shridhar Jayanthi et al.   ACS Synthetic Biology

Tuning Response Curves for Synthetic Biology

(2013) Jordan Ang et al.   ACS Synthetic Biology

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

Taking Control over Control: Use of Product Sensing in Single Cells to Remove Flux Control at Key Enzymes in Biosynthesis Pathways

(2013) Georg Schendzielorz et al.   ACS Synthetic Biology

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

(2013) Stefano Cardinale et al.   Cell Reports

2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts

(2013) Mariana Leguia et al.   Journal of Biological Engineering

Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems

(2012) Stefano Cardinale et al.   Biotechnology Journal

Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features

(2012) Joo-Hyun Seo et al.   BMC GENOMICS

Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency

(2012) Sang Woo Seo et al.   METABOLIC ENGINEERING

New technologies in developing recombinant attenuated Salmonella vaccine vectors

(2012) Shifeng Wang et al.   MICROBIAL PATHOGENESIS

Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System

(2012) Dipali G. Sashital et al.   MOLECULAR CELL

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

(2012) David Chen et al.   Molecular Systems Biology

A regulatory role for repeated decoy transcription factor binding sites in target gene expression

(2012) Tek-Hyung Lee 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

RNA processing enables predictable programming of gene expression

(2012) Lei Qi 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

An adaptor from translational to transcriptional control enables predictable assembly of complex regulation

(2012) Chang C Liu et al.   NATURE METHODS

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Direct comparison of small RNA and transcription factor signaling

(2012) Razika Hussein et al.   NUCLEIC ACIDS RESEARCH

Engineering naturally occurring trans -acting non-coding RNAs to sense molecular signals

(2012) Lei Qi et al.   NUCLEIC ACIDS RESEARCH

Sequence dependence of transcription factor-mediated DNA looping

(2012) Stephanie Johnson et al.   NUCLEIC ACIDS RESEARCH

A tunable zinc finger-based framework for Boolean logic computation in mammalian cells

(2012) Jason J. Lohmueller et al.   NUCLEIC ACIDS RESEARCH

Engineering synthetic TAL effectors with orthogonal target sites

(2012) Abhishek Garg et al.   NUCLEIC ACIDS RESEARCH

Modular control of multiple pathways using engineered orthogonal T7 polymerases

(2012) Karsten Temme et al.   NUCLEIC ACIDS RESEARCH

cis-Expression QTL Analysis of Established Colorectal Cancer Risk Variants in Colon Tumors and Adjacent Normal Tissue

(2012) Lenora W. M. Loo et al.   PLoS One

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

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

Food-Grade Bacteria Expressing Elafin Protect Against Inflammation and Restore Colon Homeostasis

(2012) J.-P. Motta et al.   Science Translational Medicine

AutoBioCAD: Full Biodesign Automation of Genetic Circuits

(2012) Guillermo Rodrigo et al.   ACS Synthetic Biology

Tetracycline-Regulated Expression Implemented through Transcriptional Activation Combined with Proximal and Distal Repression

(2012) Ryan W. S. Peacock et al.   ACS Synthetic Biology

A Data-Driven Framework for Identifying Nonlinear Dynamic Models of Genetic Parts

(2012) Kirubhakaran Krishnanathan et al.   ACS Synthetic Biology

Engineered Microbes for Therapeutic Applications

(2012) Jeff Hasty   ACS Synthetic Biology

Engineered E. coli That Detect and Respond to Gut Inflammation through Nitric Oxide Sensing

(2012) Eric J. Archer et al.   ACS Synthetic Biology

Automated Design of Genetic Toggle Switches with Predetermined Bistability

(2012) Shuobing Chen et al.   ACS Synthetic Biology

Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks

(2012) Fusun Yaman et al.   ACS Synthetic Biology

In Vivo Gene Expression Dynamics of Tumor-Targeted Bacteria

(2012) Tal Danino et al.   ACS Synthetic Biology

Genetic Circuits in Salmonella typhimurium

(2012) Arthur Prindle et al.   ACS Synthetic Biology

An in vitro Autogene

(2012) Eric A. Davidson et al.   ACS Synthetic Biology

A Synthetic Post-transcriptional Controller To Explore the Modular Design of Gene Circuits

(2012) Francesca Ceroni et al.   ACS Synthetic Biology

Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis

(2012) Jeffrey A. Dietrich et al.   ACS Synthetic Biology

Real-Time mRNA Measurement during an in Vitro Transcription and Translation Reaction Using Binary Probes

(2012) Henrike Niederholtmeyer et al.   ACS Synthetic Biology

Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors

(2012) Felix Moser et al.   ACS Synthetic Biology

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

(2012) Robert C. Brewster et al.   PLoS Computational Biology

Temperature dependence of ssrA-tag mediated protein degradation

(2012) Oliver Purcell et al.   Journal of Biological Engineering

Engineering Biological Systems with Synthetic RNA Molecules

(2011) Joe C. Liang et al.   MOLECULAR CELL

Develop reusable and combinable designs for transcriptional logic gates

(2011) Jian Zhan et al.   Molecular Systems Biology

Queueing up for enzymatic processing: correlated signaling through coupled degradation

(2011) N. A. Cookson et al.   Molecular Systems Biology

A system for the continuous directed evolution of biomolecules

(2011) Kevin M. Esvelt et al.   NATURE

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

Regulation of transcription by unnatural amino acids

(2011) Chang C Liu et al.   NATURE BIOTECHNOLOGY

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

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

Coarse-Grained Dynamics of Protein Synthesis in a Cell-Free System

(2011) Eyal Karzbrun et al.   PHYSICAL REVIEW LETTERS

A molecular framework for the inhibition of Arabidopsis root growth in response to boron toxicity

(2011) FELIPE AQUEA et al.   PLANT CELL AND ENVIRONMENT

Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway

(2011) Mauricio S. Antunes et al.   PLoS One

Synthetic Biology Moving into the Clinic

(2011) W. C. Ruder et al.   SCIENCE

Biosensors and their applications in microbial metabolic engineering

(2011) Fuzhong Zhang et al.   TRENDS IN MICROBIOLOGY

Identification and microbial production of a terpene-based advanced biofuel

(2011) Pamela P. Peralta-Yahya et al.   Nature Communications

Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology

(2011) Baojun Wang et al.   Nature Communications

Ultrasensitive Synthetic Protein Regulatory Networks Using Mixed Decoys

(2011) Michelle S. Lu et al.   ACS Synthetic Biology

j5 DNA Assembly Design Automation Software

(2011) Nathan J. Hillson et al.   ACS Synthetic Biology

Feedback Control of Protein Expression in Mammalian Cells by Tunable Synthetic Translational Inhibition

(2011) James A. Stapleton et al.   ACS Synthetic Biology

An E. coli Cell-Free Expression Toolbox: Application to Synthetic Gene Circuits and Artificial Cells

(2011) Jonghyeon Shin et al.   ACS Synthetic Biology

Rapid optimization of gene dosage in E. coli using DIAL strains

(2011) Joshua T Kittleson et al.   Journal of Biological Engineering

Prokaryotic gene clusters: A rich toolbox for synthetic biology

(2010) Michael Fischbach et al.   Biotechnology Journal

Engineering Static and Dynamic Control of Synthetic Pathways

(2010) William J. Holtz et al.   CELL

Synthetic gene networks in mammalian cells

(2010) Wilfried Weber et al.   CURRENT OPINION IN BIOTECHNOLOGY

Programming cells: towards an automated ‘Genetic Compiler’

(2010) Kevin Clancy et al.   CURRENT OPINION IN BIOTECHNOLOGY

Construction of a Genetic Multiplexer to Toggle between Chemosensory Pathways in Escherichia coli

(2010) Tae Seok Moon et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantification of the physiochemical constraints on the export of spider silk proteins by Salmonella type III secretion

(2010) Daniel M Widmaier et al.   Microbial Cell Factories

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch

(2010) Chunbo Lou et al.   Molecular Systems Biology

Distributed biological computation with multicellular engineered networks

(2010) Sergi Regot et al.   NATURE

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

(2010) Alvin Tamsir et al.   NATURE

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms

(2010) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

Designing customized cell signalling circuits

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

A synthetic low-frequency mammalian oscillator

(2010) Marcel Tigges et al.   NUCLEIC ACIDS RESEARCH

Design, construction and characterization of a set of insulated bacterial promoters

(2010) J. H. Davis et al.   NUCLEIC ACIDS RESEARCH

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators

(2010) J. M. Callura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber

(2010) X.-X. Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Designing and engineering evolutionary robust genetic circuits

(2010) Sean C Sleight et al.   Journal of Biological Engineering

Forward engineering of synthetic bio-logical AND gates

(2009) Kavita Iyer Ramalingam et al.   BIOCHEMICAL ENGINEERING JOURNAL

Protein sequestration generates a flexible ultrasensitive response in a genetic network

(2009) Nicolas E Buchler et al.   Molecular Systems Biology

Engineering the Salmonella type III secretion system to export spider silk monomers

(2009) Daniel M Widmaier et al.   Molecular Systems Biology

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

The second wave of synthetic biology: from modules to systems

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

Oscillatory dynamics in a simple gene regulatory network mediated by small RNAs

(2009) Jianwei Shen et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes

(2009) Carola Engler et al.   PLoS One

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Synthetic Gene Networks That Count

(2009) A. E. Friedland et al.   SCIENCE

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

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

Small RNAs Establish Delays and Temporal Thresholds in Gene Expression

(2008) Stefan Legewie et al.   BIOPHYSICAL JOURNAL

Engineering stochasticity in gene expression

(2008) Jeffrey J. Tabor et al.   Molecular BioSystems

Modular cell biology: retroactivity and insulation

(2008) Domitilla Del Vecchio et al.   Molecular Systems Biology

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