Scaling up genetic circuit design for cellular computing: advances and prospects

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology

(2018) Arturo Casini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineered promoters enable constant gene expression at any copy number in bacteria

(2018) Thomas H Segall-Shapiro et al.   NATURE BIOTECHNOLOGY

Toward an orthogonal central dogma

(2018) Chang C Liu et al.   Nature Chemical Biology

Metabolic division of labor in microbial systems

(2018) Ryan Tsoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic Turing patterns in a synthetic bacterial population

(2018) David Karig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rewritable multi-event analog recording in bacterial and mammalian cells

(2018) Weixin Tang et al.   SCIENCE

Programming self-organizing multicellular structures with synthetic cell-cell signaling

(2018) Satoshi Toda et al.   SCIENCE

Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors

(2018) Ye Chen et al.   Nature Communications

An Automated Design Framework for Multicellular Recombinase Logic

(2018) Sarah Guiziou et al.   ACS Synthetic Biology

Single Day Construction of Multigene Circuits with 3G Assembly

(2018) Andrew D. Halleran et al.   ACS Synthetic Biology

Engineering the Ultrasensitive Transcription Factors by Fusing a Modular Oligomerization Domain

(2018) Junran Hou et al.   ACS Synthetic Biology

Orthogonality and Burdens of Heterologous AND Gate Gene Circuits in E. coli

(2018) Qijun Liu et al.   ACS Synthetic Biology

Predicting gene expression in massively parallel reporter assays: A comparative study

(2017) Anat Kreimer et al.   HUMAN MUTATION

Multi-dimensional studies of synthetic genetic promoters enabled by microfluidic impact printing

(2017) Jinzhen Fan et al.   LAB ON A CHIP

On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening

(2017) Joshua Heinemann et al.   LAB ON A CHIP

Genetic circuit characterization and debugging using RNA‐seq

(2017) Thomas E Gorochowski et al.   Molecular Systems Biology

CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria

(2017) Seth L. Shipman et al.   NATURE

Complex cellular logic computation using ribocomputing devices

(2017) Alexander A. Green et al.   NATURE

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

(2017) David T Riglar et al.   NATURE BIOTECHNOLOGY

Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells

(2017) Benjamin H Weinberg et al.   NATURE BIOTECHNOLOGY

Synthetic microbial consortia enable rapid assembly of pure translation machinery

(2017) Fernando Villarreal et al.   Nature Chemical Biology

Designed cell consortia as fragrance-programmable analog-to-digital converters

(2017) Marius Müller et al.   Nature Chemical Biology

Programmable full-adder computations in communicating three-dimensional cell cultures

(2017) David Ausländer et al.   NATURE METHODS

Genetic programs can be compressed and autonomously decompressed in live cells

(2017) Nicolas Lapique et al.   Nature Nanotechnology

Multiplex recording of cellular events over time on CRISPR biological tape

(2017) Ravi U. Sheth et al.   SCIENCE

Design of synthetic epigenetic circuits featuring memory effects and reversible switching based on DNA methylation

(2017) Johannes A. H. Maier et al.   Nature Communications

Digital logic circuits in yeast with CRISPR-dCas9 NOR gates

(2017) Miles W. Gander et al.   Nature Communications

Reconfigurable Analog Signal Processing by Living Cells

(2017) Daniel D. Lewis et al.   ACS Synthetic Biology

Genetic Design via Combinatorial Constraint Specification

(2017) Swapnil P. Bhatia et al.   ACS Synthetic Biology

A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria

(2017) Hung-Ju Chang et al.   ACS Synthetic Biology

CRISPR-Cas Expands Dynamic Range of Gene Expression From T7RNAP Promoters

(2017) Sean R. McCutcheon et al.   Biotechnology Journal

Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks

(2017) Enoch Yeung et al.   Cell Systems

An integrative circuit–host modelling framework for predicting synthetic gene network behaviours

(2017) Chen Liao et al.   Nature Microbiology

Reducing DNA context dependence in bacterial promoters

(2017) Swati B. Carr et al.   PLoS One

Sparse network identifiability via Compressed Sensing

(2016) David Hayden et al.   AUTOMATICA

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors

(2016) Leonardo Morsut et al.   CELL

Development and substrate specificity screening of an in vivo biosensor for the detection of biomass derived aromatic chemical building blocks

(2016) Leopoldo F. M. Machado et al.   CHEMICAL COMMUNICATIONS

Recognizing and engineering digital-like logic gates and switches in gene regulatory networks

(2016) Robert W Bradley et al.   CURRENT OPINION IN MICROBIOLOGY

Addressing biological uncertainties in engineering gene circuits

(2016) Carolyn Zhang et al.   Integrative Biology

Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets

(2016) M. Schwarz-Schilling et al.   Integrative Biology

Tools and Principles for Microbial Gene Circuit Engineering

(2016) Robert W. Bradley et al.   JOURNAL OF MOLECULAR BIOLOGY

Control theory meets synthetic biology

(2016) Domitilla Del Vecchio et al.   Journal of the Royal Society Interface

Creating Single-Copy Genetic Circuits

(2016) Jeong Wook Lee et al.   MOLECULAR CELL

A population‐based temporal logic gate for timing and recording chemical events

(2016) Victoria Hsiao et al.   Molecular Systems Biology

Orthogonal intercellular signaling for programmed spatial behavior

(2016) P. K. Grant et al.   Molecular Systems Biology

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration

(2016) Lauren B. A. Woodruff et al.   NUCLEIC ACIDS RESEARCH

RNA-based gene circuits for cell regulation

(2016) Peter KARAGIANNIS et al.   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Design and synthesis of a minimal bacterial genome

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

Genetic circuit design automation

(2016) A. A. K. Nielsen et al.   SCIENCE

Synthetic recombinase-based state machines in living cells

(2016) N. Roquet et al.   SCIENCE

Synthetic Evolution of Metabolic Productivity Using Biosensors

(2016) Thomas C. Williams et al.   TRENDS IN BIOTECHNOLOGY

Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications

(2016) Gang Wu et al.   TRENDS IN BIOTECHNOLOGY

Synthetic mixed-signal computation in living cells

(2016) Jacob R. Rubens et al.   Nature Communications

Characterization of Intrinsic Properties of Promoters

(2016) Timothy J. Rudge et al.   ACS Synthetic Biology

Toward the First Data Acquisition Standard in Synthetic Biology

(2016) Iñaki Sainz de Murieta et al.   ACS Synthetic Biology

A Parts Database with Consensus Parameter Estimation for Synthetic Circuit Design

(2016) Linh Huynh et al.   ACS Synthetic Biology

A Synthetic Multicellular Memory Device

(2016) Arturo Urrios et al.   ACS Synthetic Biology

A Droplet Microfluidic Platform for Automating Genetic Engineering

(2016) Philip C. Gach et al.   ACS Synthetic Biology

Sharing Structure and Function in Biological Design with SBOL 2.0

(2016) Nicholas Roehner et al.   ACS Synthetic Biology

The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology

(2016) Jonathan Garamella et al.   ACS Synthetic Biology

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

(2016) Javier Macia et al.   PLoS Computational Biology

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Mammalian synthetic circuits with RNA binding proteins for RNA-only delivery

(2015) Liliana Wroblewska et al.   NATURE BIOTECHNOLOGY

Creating small transcription activating RNAs

(2015) James Chappell et al.   Nature Chemical Biology

Modular construction of mammalian gene circuits using TALE transcriptional repressors

(2015) Yinqing Li et al.   Nature Chemical Biology

Engineering an allosteric transcription factor to respond to new ligands

(2015) Noah D Taylor et al.   NATURE METHODS

Quantifying cellular capacity identifies gene expression designs with reduced burden

(2015) Francesca Ceroni et al.   NATURE METHODS

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

Using synthetic RNAs as scaffolds and regulators

(2015) Cameron Myhrvold et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Designer cell signal processing circuits for biotechnology

(2015) Robert W. Bradley et al.   New Biotechnology

Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities

(2015) Baojun Wang et al.   NUCLEIC ACIDS RESEARCH

Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law

(2015) M. Carbonell-Ballestero et al.   NUCLEIC ACIDS RESEARCH

Using synthetic RNAs as scaffolds and regulators

(2015) Cameron Myhrvold et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology

(2015) Liqiang Wang et al.   Scientific Reports

A Versatile Microfluidic Device for Automating Synthetic Biology

(2015) Steve C. C. Shih et al.   ACS Synthetic Biology

Orthogonal Modular Gene Repression in Escherichia coli Using Engineered CRISPR/Cas9

(2015) Andriy Didovyk et al.   ACS Synthetic Biology

Sealable Femtoliter Chamber Arrays for Cell-free Biology

(2015) Sarah Elizabeth Norred et al.   Jove-Journal of Visualized Experiments

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

(2014) Alexander A. Green et al.   CELL

Paper-Based Synthetic Gene Networks

(2014) Keith Pardee et al.   CELL

Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules

(2014) Baojun Wang et al.   CHEMICAL COMMUNICATIONS

Synthetic analog and digital circuits for cellular computation and memory

(2014) Oliver Purcell et al.   CURRENT OPINION IN BIOTECHNOLOGY

Integration of microfluidics into the synthetic biology design flow

(2014) Haiyao Huang et al.   LAB ON A CHIP

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

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

Toehold gene switches make big footprints

(2014) Simon Ausländer et al.   NATURE

CRISPR transcriptional repression devices and layered circuits in mammalian cells

(2014) Samira Kiani et al.   NATURE METHODS

Principles of genetic circuit design

(2014) Jennifer A N Brophy et al.   NATURE METHODS

Permanent genetic memory with >1-byte capacity

(2014) Lei Yang et al.   NATURE METHODS

Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development

(2014) Chris J. Paddon et al.   NATURE REVIEWS MICROBIOLOGY

Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks

(2014) Baojun Wang et al.   NUCLEIC ACIDS RESEARCH

A split intein T7 RNA polymerase for transcriptional AND-logic

(2014) Yolanda Schaerli et al.   NUCLEIC ACIDS RESEARCH

Analog synthetic biology

(2014) R. Sarpeshkar   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

Environmental Sensing of Heavy Metals Through Whole Cell Microbial Biosensors: A Synthetic Biology Approach

(2014) Lara Tess Bereza-Malcolm et al.   ACS Synthetic Biology

Optimal Part and Module Selection for Synthetic Gene Circuit Design Automation

(2014) Linh Huynh et al.   ACS Synthetic Biology

Systematic Transfer of Prokaryotic Sensors and Circuits to Mammalian Cells

(2014) Brynne C. Stanton et al.   ACS Synthetic Biology

Rewiring cell signalling through chimaeric regulatory protein engineering

(2013) Baojun Wang et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

(2013) Lei S. Qi et al.   CELL

Changes in Cell Morphology Are Coordinated with Cell Growth through the TORC1 Pathway

(2013) Alexi I. Goranov et al.   CURRENT 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 circuits integrating logic and memory in living cells

(2013) Piro Siuti et al.   NATURE BIOTECHNOLOGY

Genomic mining of prokaryotic repressors for orthogonal logic gates

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

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

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

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

(2013) Joseph P. Torella et al.   NUCLEIC ACIDS RESEARCH

One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy

(2013) Arturo Casini et al.   NUCLEIC ACIDS RESEARCH

Multi-Input Regulation and Logic with T7 Promoters in Cells and Cell-Free Systems

(2013) Sukanya Iyer et al.   PLoS One

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

The Spinach RNA Aptamer as a Characterization Tool for Synthetic Biology

(2013) Georgios Pothoulakis et al.   ACS Synthetic Biology

Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System

(2013) Zachary Z. Sun et al.   ACS Synthetic Biology

A survey of enabling technologies in synthetic biology

(2013) Linda J Kahl et al.   Journal of Biological Engineering

Whole-cell MALDI-TOF Mass Spectrometry is an Accurate and Rapid Method to Analyze Different Modes of Macrophage Activation

(2013) Richard Ouedraogo et al.   Jove-Journal of Visualized Experiments

THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS

(2013) Gerd HG Moe-Behrens   Computational and Structural Biotechnology Journal

A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals

(2012) Baojun Wang et al.   BIOSENSORS & BIOELECTRONICS

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

(2012) Stefano Cardinale et al.   Biotechnology Journal

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

(2012) Ahmad S. Khalil et al.   CELL

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

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

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

Genetic switchboard for synthetic biology applications

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

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

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Distributed computation: the new wave of synthetic biology devices

(2012) Javier Macía et al.   TRENDS IN BIOTECHNOLOGY

Customizing cell signaling using engineered genetic logic circuits

(2012) Baojun Wang et al.   TRENDS IN MICROBIOLOGY

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

Computational design approaches and tools for synthetic biology

(2011) James T. MacDonald et al.   Integrative Biology

Small-molecule displacement of a cryptic degron causes conditional protein degradation

(2011) Kimberly M Bonger et al.   Nature Chemical Biology

Expression optimization and synthetic gene networks in cell-free systems

(2011) David K. Karig et al.   NUCLEIC ACIDS RESEARCH

A Modular Cloning System for Standardized Assembly of Multigene Constructs

(2011) Ernst Weber et al.   PLoS One

GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules

(2011) Alejandro Sarrion-Perdigones et al.   PLoS One

Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells

(2011) Z. Xie et al.   SCIENCE

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

(2011) Baojun Wang et al.   Nature Communications

Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo

(2011) A. Golightly et al.   Interface Focus

Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes

(2010) Bryan P Tracy et al.   CURRENT OPINION IN BIOTECHNOLOGY

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Experiential Engineering Through iGEM—An Undergraduate Summer Competition in Synthetic Biology

(2010) Rudolph Mitchell et al.   Journal of Science Education and Technology

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

Five hard truths for synthetic biology

(2010) Roberta Kwok   NATURE

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Designing and engineering evolutionary robust genetic circuits

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

A Synthetic Genetic Edge Detection Program

(2009) Jeffrey J. Tabor et al.   CELL

Computational design tools for synthetic biology

(2009) Mario A Marchisio et al.   CURRENT OPINION IN BIOTECHNOLOGY

Designing and encoding models for synthetic biology

(2009) L. Endler et al.   Journal of the Royal Society Interface

Towards programming languages for genetic engineering of living cells

(2009) M. Pedersen et al.   Journal of the Royal Society Interface

Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity

(2009) Jean-Christophe Baret et al.   LAB ON A CHIP

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

Microfluidic devices for measuring gene network dynamics in single cells

(2009) Matthew R. Bennett et al.   NATURE REVIEWS GENETICS

Writing DNA with GenoCADTM

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

Engineering transcription factors with novel DNA-binding specificity using comparative genomics

(2009) Tasha A. Desai 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

SynBioSS: the synthetic biology modeling suite

(2008) Anthony D. Hill et al.   BIOINFORMATICS

Optimization of Enzymatic Biochemical Logic for Noise Reduction and Scalability: How Many Biocomputing Gates Can Be Interconnected in a Circuit?

(2008) Vladimir Privman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Engineering Complex Riboswitch Regulation by Dual Genetic Selection

(2008) Vandana Sharma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

Modularity defined

(2008) Herbert M Sauro   Molecular Systems Biology

Modular cell biology: retroactivity and insulation

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

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE

Genetic design: rising above the sequence

(2008) Jonathan A. Goler et al.   TRENDS IN BIOTECHNOLOGY

Engineering BioBrick vectors from BioBrick parts

(2008) Reshma P Shetty et al.   Journal of Biological Engineering