Synthetic biology advances and applications in the biotechnology industry: a perspective

Characterization of a novel lytic bacteriophage from an industrial Escherichia coli fermentation process and elimination of virulence using a heterologous CRISPR–Cas9 system

(2018) Mathew C. Halter et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Synthetic biology of polyketide synthases

(2018) Satoshi Yuzawa et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Rewiring T-cell responses to soluble factors with chimeric antigen receptors

(2018) ZeNan L Chang et al.   Nature Chemical Biology

Programming gene and engineered-cell therapies with synthetic biology

(2018) Tasuku Kitada et al.   SCIENCE

A set of synthetic versatile genetic control elements for the efficient expression of genes in Actinobacteria

(2018) Lilya Horbal et al.   Scientific Reports

Molecular beacons to identify gifted microbes for genome mining

(2017) Richard H Baltz   JOURNAL OF ANTIBIOTICS

Synthetic biology, genome mining, and combinatorial biosynthesis of NRPS-derived antibiotics: a perspective

(2017) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli

(2017) Liya Liang et al.   METABOLIC ENGINEERING

Development of a CRISPR/Cas9-mediated gene-editing tool in Streptomyces rimosus

(2017) Haiyan Jia et al.   MICROBIOLOGY-SGM

Digital-to-biological converter for on-demand production of biologics

(2017) Kent S Boles et al.   NATURE BIOTECHNOLOGY

CRISPR–Cas9 strategy for activation of silent Streptomyces biosynthetic gene clusters

(2017) Mingzi M Zhang et al.   Nature Chemical Biology

Twin-primer non-enzymatic DNA assembly: an efficient and accurate multi-part DNA assembly method

(2017) Jing Liang et al.   NUCLEIC ACIDS RESEARCH

Design of a synthetic yeast genome

(2017) Sarah M. Richardson et al.   SCIENCE

Molecular remission of infant B-ALL after infusion of universal TALEN gene-edited CAR T cells

(2017) Waseem Qasim et al.   Science Translational Medicine

CARs: Synthetic Immunoreceptors for Cancer Therapy and Beyond

(2017) ZeNan L. Chang et al.   TRENDS IN MOLECULAR MEDICINE

Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system

(2017) Jiazhang Lian et al.   Nature Communications

CRISPR-Mediated Integration of Large Gene Cassettes Using AAV Donor Vectors

(2017) Rasmus O. Bak et al.   Cell Reports

A transatlantic perspective on 20 emerging issues in biological engineering

(2017) Bonnie C Wintle et al.   eLife

Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals

(2017) Shuobo Shi et al.   Frontiers in Microbiology

Options for Synthetic DNA Order Screening, Revisited

(2017) Diane DiEuliis et al.   mSphere

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors

(2016) Leonardo Morsut et al.   CELL

Sugar Synthesis from CO2 in Escherichia coli

(2016) Niv Antonovsky et al.   CELL

Principles for designing synthetic microbial communities

(2016) Nathan I Johns et al.   CURRENT OPINION IN MICROBIOLOGY

Synthetic biology routes to bio-artificial intelligence

(2016) Darren N. Nesbeth et al.   Essays in Biochemistry

Gifted microbes for genome mining and natural product discovery

(2016) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Biomanufacturing: history and perspective

(2016) Yi-Heng Percival Zhang et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Natural product discovery: past, present, and future

(2016) Leonard Katz et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

High Efficiency CRISPR/Cas9-mediated Gene Editing in Primary Human T-cells Using Mutant Adenoviral E4orf6/E1b55k “Helper” Proteins

(2016) Kamila S Gwiazda et al.   MOLECULAR THERAPY

Rewriting yeast central carbon metabolism for industrial isoprenoid production

(2016) Adam L. Meadows et al.   NATURE

Harnessing the power of microbial autotrophy

(2016) Nico J. Claassens et al.   NATURE REVIEWS MICROBIOLOGY

The Genome Project-Write

(2016) J. D. Boeke et al.   SCIENCE

Genetic circuit design automation

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

Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production

(2016) Satoshi Yuzawa et al.   ACS Synthetic Biology

Development of Next Generation Synthetic Biology Tools for Use in Streptomyces venezuelae

(2016) Ryan M. Phelan et al.   ACS Synthetic Biology

T Cells Expressing CD19/CD20 Bispecific Chimeric Antigen Receptors Prevent Antigen Escape by Malignant B Cells

(2016) E. Zah et al.   Cancer Immunology Research

CRMAGE: CRISPR Optimized MAGE Recombineering

(2016) Carlotta Ronda et al.   Scientific Reports

Highly efficient editing of the actinorhodin polyketide chain length factor gene in Streptomyces coelicolor M145 using CRISPR/Cas9-CodA(sm) combined system

(2015) Hu Zeng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Editorial: Yeast synthetic biology: new tools to unlock cellular function

(2015)   FEMS YEAST RESEARCH

Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes

(2015) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Engineering Escherichia coli for methanol conversion

(2015) Jonas E.N. Müller et al.   METABOLIC ENGINEERING

Multiplexed tracking of combinatorial genomic mutations in engineered cell populations

(2015) Ramsey I Zeitoun et al.   NATURE BIOTECHNOLOGY

The structural biology of biosynthetic megaenzymes

(2015) Kira J Weissman   Nature Chemical Biology

Efficient Gene Editing in Primary Human T Cells

(2015) Yvonne Y. Chen   TRENDS IN IMMUNOLOGY

A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform

(2015) Howon Lee et al.   Nature Communications

Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters

(2015) Wenjun Jiang et al.   Nature Communications

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly

(2015) Michael E. Lee et al.   ACS Synthetic Biology

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

(2015) Yaojun Tong et al.   ACS Synthetic Biology

Systematic Identification of a Panel of Strong Constitutive Promoters from Streptomyces albus

(2015) Yunzi Luo et al.   ACS Synthetic Biology

Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals

(2015) Benjamin M. Zeldes et al.   Frontiers in Microbiology

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Programming biological operating systems: genome design, assembly and activation

(2014) Daniel G Gibson   NATURE METHODS

Large-scale de novo DNA synthesis: technologies and applications

(2014) Sriram Kosuri et al.   NATURE METHODS

Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing

(2014) Bogumil J Karas et al.   Nature Protocols

Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A

(2014) Kazuya Yamanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Modular Extracellular Sensor Architecture for Engineering Mammalian Cell-based Devices

(2014) Nichole M. Daringer et al.   ACS Synthetic Biology

Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides

(2014) Mads T. Bonde et al.   ACS Synthetic Biology

High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System

(2014) Ryan E. Cobb et al.   ACS Synthetic Biology

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

(2013) Lei S. Qi et al.   CELL

Optimizing Retroviral Gene Expression for Effective Therapies

(2013) Michael N. Antoniou et al.   HUMAN GENE THERAPY

DNA assembly techniques for next-generation combinatorial biosynthesis of natural products

(2013) Ryan E. Cobb et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Microbial genome mining for accelerated natural products discovery: is a renaissance in the making?

(2013) Brian O. Bachmann et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Design, construction and characterisation of a synthetic promoter library for fine-tuned gene expression in actinomycetes

(2013) Theresa Siegl et al.   METABOLIC ENGINEERING

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics

(2013) P. R. Dormitzer et al.   Science Translational Medicine

PD-1- and CTLA-4-Based Inhibitory Chimeric Antigen Receptors (iCARs) Divert Off-Target Immunotherapy Responses

(2013) V. D. Fedorov et al.   Science Translational Medicine

Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster

(2013) Yunzi Luo et al.   Nature Communications

TanCAR: A Novel Bispecific Chimeric Antigen Receptor for Cancer Immunotherapy

(2013) Zakaria Grada et al.   Molecular Therapy-Nucleic Acids

TALE nucleases: tailored genome engineering made easy

(2012) Claudio Mussolino et al.   CURRENT OPINION IN BIOTECHNOLOGY

DNA synthesis, assembly and applications in synthetic biology

(2012) Siying Ma et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

(2012) Fuzhong Zhang et al.   NATURE BIOTECHNOLOGY

Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting

(2012) Jun Fu et al.   NATURE BIOTECHNOLOGY

Combinatorial antigen recognition with balanced signaling promotes selective tumor eradication by engineered T cells

(2012) Christopher C Kloss et al.   NATURE BIOTECHNOLOGY

Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules

(2012) Jerrod J Schwartz et al.   NATURE METHODS

Genome-scale promoter engineering by coselection MAGE

(2012) Harris H Wang et al.   NATURE METHODS

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

Combinatorial Biosynthesis of Cyclic Lipopeptide Antibiotics: A Model for Synthetic Biology To Accelerate the Evolution of Secondary Metabolite Biosynthetic Pathways

(2012) Richard H. Baltz   ACS Synthetic Biology

A brief review of DNA and RNA chemical synthesis: Figure 1

(2011) Marvin H. Caruthers   BIOCHEMICAL SOCIETY TRANSACTIONS

Streptomyces temperate bacteriophage integration systems for stable genetic engineering of actinomycetes (and other organisms)

(2011) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Parallel on-chip gene synthesis and application to optimization of protein expression

(2011) Jiayuan Quan et al.   NATURE BIOTECHNOLOGY

Genetic engineering of human pluripotent cells using TALE nucleases

(2011) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Error correction of microchip synthesized genes using Surveyor nuclease

(2011) Ishtiaq Saaem et al.   NUCLEIC ACIDS RESEARCH

Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters

(2010) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

(2010) Sriram Kosuri et al.   NATURE BIOTECHNOLOGY

Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides

(2010) Joseph R Warner et al.   NATURE BIOTECHNOLOGY

Chemical synthesis of the mouse mitochondrial genome

(2010) Daniel G Gibson et al.   NATURE METHODS

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides

(2010) Alex Y. Borovkov et al.   NUCLEIC ACIDS RESEARCH

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

(2010) Emily M. LeProust et al.   NUCLEIC ACIDS RESEARCH

TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain

(2010) Ting Li et al.   NUCLEIC ACIDS RESEARCH

Specific insertions of zinc finger domains into Gag-Pol yield engineered retroviral vectors with selective integration properties

(2010) Kwang-il Lim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

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

Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides

(2009) Daniel G. Gibson   NUCLEIC ACIDS RESEARCH

Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories

(2008) Takanori Tsuji et al.   ELECTROPHORESIS

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

(2008) Zengyi Shao et al.   NUCLEIC ACIDS RESEARCH

One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome

(2008) D. G. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA