P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads

Programming Escherichia coli to function as a digital display

(2020) Jonghyeon Shin et al.   Molecular Systems Biology

Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph

(2020) Sarah E Bloch et al.   JOURNAL OF EXPERIMENTAL BOTANY

Comparison of Integrases Identifies Bxb1-GA Mutant as the Most Efficient Site-Specific Integrase System in Mammalian Cells

(2019) Barbara Jusiak et al.   ACS Synthetic Biology

High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription

(2019) Scott A. Scholz et al.   Cell Systems

Small-molecule control of antibody N-glycosylation in engineered mammalian cells

(2019) Michelle M. Chang et al.   Nature Chemical Biology

Programmable bacteria induce durable tumor regression and systemic antitumor immunity

(2019) Sreyan Chowdhury et al.   NATURE MEDICINE

Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface

(2019) Alexander D. Naydich et al.   mSystems

Control of nitrogen fixation in bacteria that associate with cereals

(2019) Min-Hyung Ryu et al.   Nature Microbiology

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

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

Burden-driven feedback control of gene expression

(2018) Francesca Ceroni et al.   NATURE METHODS

A multi-landing pad DNA integration platform for mammalian cell engineering

(2018) Leonid Gaidukov et al.   NUCLEIC ACIDS RESEARCH

An Automated Design Framework for Multicellular Recombinase Logic

(2018) Sarah Guiziou 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

Creating a functional single-chromosome yeast

(2018) Yangyang Shao et al.   NATURE

Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria

(2018) Vincent M Isabella et al.   NATURE BIOTECHNOLOGY

Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria

(2018) Jennifer A. N. Brophy et al.   Nature Microbiology

Dynamic control of endogenous metabolism with combinatorial logic circuits

(2018) Felix Moser et al.   Molecular Systems Biology

Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors

(2018) Adam J. Meyer et al.   Nature Chemical Biology

Rational Design of Evolutionarily Stable Microbial Kill Switches

(2017) Finn Stirling et al.   MOLECULAR CELL

Genetic circuit characterization and debugging using RNA‐seq

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

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

(2017) David T Riglar et al.   NATURE BIOTECHNOLOGY

Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

(2017) Apoorv Gupta et al.   NATURE BIOTECHNOLOGY

Engineering RGB color vision into Escherichia coli

(2017) Jesus Fernandez-Rodriguez et al.   Nature Chemical Biology

Bug mapping and fitness testing of chemically synthesized chromosome X

(2017) Yi Wu et al.   SCIENCE

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

(2017) Leslie A. Mitchell et al.   SCIENCE

“Perfect” designer chromosome V and behavior of a ring derivative

(2017) Ze-Xiong Xie et al.   SCIENCE

Digital logic circuits in yeast with CRISPR-dCas9 NOR gates

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

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

Quantitative Localization Microscopy Reveals a Novel Organization of a High-Copy Number Plasmid

(2016) Yong Wang et al.   BIOPHYSICAL JOURNAL

Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits

(2016) Kole T. Roybal et al.   CELL

Overloaded and stressed: whole-cell considerations for bacterial synthetic biology

(2016) Olivier Borkowski et al.   CURRENT OPINION IN MICROBIOLOGY

Creating Single-Copy Genetic Circuits

(2016) Jeong Wook Lee et al.   MOLECULAR CELL

Antisense transcription as a tool to tune gene expression

(2016) J. A. Brophy et al.   Molecular Systems Biology

Defining synonymous codon compression schemes by genome recoding

(2016) Kaihang Wang et al.   NATURE

Synchronized cycles of bacterial lysis for in vivo delivery

(2016) M. Omar Din et al.   NATURE

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

Hard-Wired Control of Bacterial Processes by Chromosomal Gene Location

(2016) Jelle Slager et al.   TRENDS IN MICROBIOLOGY

Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli

(2016) Marcelo C. Bassalo et al.   ACS Synthetic Biology

Coupling the CRISPR/Cas9 System with Lambda Red Recombineering Enables Simplified Chromosomal Gene Replacement in Escherichia coli

(2015) Michael E. Pyne et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System

(2015) Yu Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Isocost Lines Describe the Cellular Economy of Genetic Circuits

(2015) Andras Gyorgy et al.   BIOPHYSICAL JOURNAL

A Framework for Genetic Logic Synthesis

(2015) Prashant Vaidyanathan et al.   PROCEEDINGS OF THE IEEE

Programmable probiotics for detection of cancer in urine

(2015) Tal Danino et al.   Science Translational Medicine

Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability

(2015) Jesus Fernandez-Rodriguez et al.   ACS Synthetic Biology

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota

(2015) Mark Mimee et al.   Cell Systems

A Rule-Based Design Specification Language for Synthetic Biology

(2015) Ernst Oberortner et al.   ACM Journal on Emerging Technologies in Computing Systems

A rapid and reliable strategy for chromosomal integration of gene(s) with multiple copies

(2015) Pengfei Gu et al.   Scientific Reports

Mechanism of Transcriptional Bursting in Bacteria

(2014) Shasha Chong et al.   CELL

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

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

A platform for rapid prototyping of synthetic gene networks in mammalian cells

(2014) Xavier Duportet et al.   NUCLEIC ACIDS RESEARCH

Chromosome position effects on gene expression in Escherichia coli K-12

(2014) Jack A. Bryant et al.   NUCLEIC ACIDS RESEARCH

Programmable bacteria detect and record an environmental signal in the mammalian gut

(2014) Jonathan W. Kotula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Total Synthesis of a Functional Designer Eukaryotic Chromosome

(2014) N. Annaluru et al.   SCIENCE

Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition

(2014) Noah Davidsohn et al.   ACS Synthetic Biology

Generalized bacterial genome editing using mobile group II introns and Cre-lox

(2013) P. J. Enyeart et al.   Molecular Systems Biology

Genome-scale engineering for systems and synthetic biology

(2013) K. M. Esvelt et al.   Molecular Systems Biology

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

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

(2013) Vivek K Mutalik et al.   NATURE METHODS

Measurement and modeling of intrinsic transcription terminators

(2013) Guillaume Cambray et al.   NUCLEIC ACIDS RESEARCH

Implementation of stable and complex biological systems through recombinase-assisted genome engineering

(2013) Christine Nicole S. Santos et al.   Nature Communications

One-Step Cloning and Chromosomal Integration of DNA

(2013) François St-Pierre 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

Genetic programs constructed from layered logic gates in single cells

(2012) Tae Seok Moon et al.   NATURE

Ribozyme-based insulator parts buffer synthetic circuits from genetic context

(2012) Chunbo Lou et al.   NATURE BIOTECHNOLOGY

Regulatory consequences of gene translocation in bacteria

(2012) Dena H. S. Block et al.   NUCLEIC ACIDS RESEARCH

Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors

(2012) Felix Moser et al.   ACS Synthetic Biology

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Genetically engineered bacteria: An emerging tool for environmental remediation and future research perspectives

(2011) Jay Shankar Singh et al.   GENE

RNIE: genome-wide prediction of bacterial intrinsic terminators

(2011) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

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

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

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An experimentally anchored map of transcriptional start sites in the model cyanobacteriumSynechocystissp. PCC6803

(2011) Jan Mitschke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Baojun Wang et al.   Nature Communications

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

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

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

(2010) Alvin Tamsir et al.   NATURE

Site-specific chromosomal integration of large synthetic constructs

(2010) Thomas E. Kuhlman 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

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Group II Introns: Mobile Ribozymes that Invade DNA

(2010) A. M. Lambowitz et al.   Cold Spring Harbor Perspectives in Biology

Designing and engineering evolutionary robust genetic circuits

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Synthetic Genetic Edge Detection Program

(2009) Jeffrey J. Tabor et al.   CELL

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Protein Occupancy Landscape of a Bacterial Genome

(2009) Tiffany Vora et al.   MOLECULAR CELL

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Recombineering: a homologous recombination-based method of genetic engineering

(2009) Shyam K Sharan et al.   Nature Protocols

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

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

The Organization of the Bacterial Genome

(2008) Eduardo P.C. Rocha   Annual Review of Genetics

The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products

(2008) D. M. Stoebel et al.   GENETICS

The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse

(2008) T. Durfee et al.   JOURNAL OF BACTERIOLOGY

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

Regulated programmed lysis of recombinant Salmonella in host tissues to release protective antigens and confer biological containment

(2008) W. Kong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA