Large-scale de novo DNA synthesis: technologies and applications

Programming biological operating systems: genome design, assembly and activation

(2014) Daniel G Gibson   NATURE METHODS

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

(2014) Y. Ivarsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid and Reliable DNA Assembly via Ligase Cycling Reaction

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

One-Pot Assembly of a Hetero-dimeric DNA Origami from Chip-Derived Staples and Double-Stranded Scaffold

(2013) Alexandria N. Marchi et al.   ACS Nano

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

(2013) Ilaria Mogno et al.   GENOME RESEARCH

PhIP-Seq characterization of autoantibodies from patients with multiple sclerosis, type 1 diabetes and rheumatoid arthritis

(2013) H. Benjamin Larman et al.   JOURNAL OF AUTOIMMUNITY

High-throughput Analysis ofin vivoProtein Stability

(2013) Ikjin Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Synthesis of DNA/RNA and Their Analogs via Phosphoramidite and H-Phosphonate Chemistries

(2013) Subhadeep Roy et al.   MOLECULES

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

(2013) Nick Goldman et al.   NATURE

Genomic mining of prokaryotic repressors for orthogonal logic gates

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

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

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

Quantitative estimation of activity and quality for collections of functional genetic elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

Measurement and modeling of intrinsic transcription terminators

(2013) Guillaume Cambray et al.   NUCLEIC ACIDS RESEARCH

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

(2013) M. A. White 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

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

(2013) D. Melamed et al.   RNA

Probing the Limits of Genetic Recoding in Essential Genes

(2013) M. J. Lajoie et al.   SCIENCE

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

(2013) D. B. Goodman et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics

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

Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA

(2013) Sandrine Geniez et al.   SYMBIOSIS

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

The expanding scope of DNA sequencing

(2012) Jay Shendure et al.   NATURE BIOTECHNOLOGY

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

(2012) Jerrod J Schwartz et al.   NATURE METHODS

‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules

(2012) Hwangbeom Kim et al.   NUCLEIC ACIDS RESEARCH

SLiCE: a novel bacterial cell extract-based DNA cloning method

(2012) Yongwei Zhang et al.   NUCLEIC ACIDS RESEARCH

Whole-Genome Synthesis and Characterization of Viable S13-Like Bacteriophages

(2012) Yuchen Liu et al.   PLoS One

Complex effects of nucleotide variants in a mammalian cis-regulatory element

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

Construction of a rationally designed antibody platform for sequencing-assisted selection

(2012) H. B. Larman 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

Next-Generation Digital Information Storage in DNA

(2012) G. M. Church et al.   SCIENCE

Three-Dimensional Structures Self-Assembled from DNA Bricks

(2012) Y. Ke et al.   SCIENCE

A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads

(2012) S. M. Douglas et al.   SCIENCE

A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast

(2012) Paul R. Jaschke et al.   VIROLOGY

When It Rains, It Pores

(2012) Sriram Kosuri et al.   ACS Synthetic Biology

Refactored M13 Bacteriophage as a Platform for Tumor Cell Imaging and Drug Delivery

(2012) Debadyuti Ghosh et al.   ACS Synthetic Biology

The rise of a digital immune system

(2012) Michael C Schatz et al.   GigaScience

Hot Spots for Allosteric Regulation on Protein Surfaces

(2011) Kimberly A. Reynolds et al.   CELL

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

(2011) Jessica S. Dymond et al.   NATURE

CCL2 recruits inflammatory monocytes to facilitate breast-tumour metastasis

(2011) Bin-Zhi Qian et al.   NATURE

Autoantigen discovery with a synthetic human peptidome

(2011) H Benjamin Larman et al.   NATURE BIOTECHNOLOGY

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

(2011) Jiayuan Quan et al.   NATURE BIOTECHNOLOGY

Error correction of microchip synthesized genes using Surveyor nuclease

(2011) Ishtiaq Saaem et al.   NUCLEIC ACIDS RESEARCH

A Modular Cloning System for Standardized Assembly of Multigene Constructs

(2011) Ernst Weber et al.   PLoS One

Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples

(2011) Daniel P. Depledge et al.   PLoS One

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

(2011) L. Qian et al.   SCIENCE

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

In situ Synthesis of DNA Microarray on Functionalized Cyclic Olefin Copolymer Substrate

(2010) Ishtiaq Saaem et al.   ACS Applied Materials & Interfaces

Synthetic Poliovirus and Other Designer Viruses: What Have We Learned from Them?

(2010) Eckard Wimmer et al.   Annual Review of Microbiology

A Fluorescence Selection Method for Accurate Large-Gene Synthesis

(2010) Hwangbeom Kim et al.   CHEMBIOCHEM

Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames

(2010) Malin Allert et al.   JOURNAL OF MOLECULAR BIOLOGY

High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing

(2010) Mark Matzas et al.   NATURE BIOTECHNOLOGY

Live attenuated influenza virus vaccines by computer-aided rational design

(2010) Steffen Mueller et al.   NATURE 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

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

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

DNA as a universal substrate for chemical kinetics

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

Synthetic design of strong promoters

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

An inactivated West Nile Virus vaccine derived from a chemically synthesized cDNA system

(2010) Klaus K. Orlinger et al.   VACCINE

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations

(2009) J. B. Li et al.   GENOME RESEARCH

Synthesis of Methyl Halides from Biomass Using Engineered Microbes

(2009) Travis S. Bayer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons

(2009) C. C. Burns et al.   JOURNAL OF VIROLOGY

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Genome engineering

(2009) Peter A Carr et al.   NATURE BIOTECHNOLOGY

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

(2009) Kun Zhang et al.   NATURE METHODS

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates

(2009) Hareem T. Maune et al.   Nature Nanotechnology

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

(2009) Daniel G. Gibson   NUCLEIC ACIDS RESEARCH

Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways

(2009) Jiayuan Quan et al.   PLoS One

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Folding DNA into Twisted and Curved Nanoscale Shapes

(2009) H. Dietz et al.   SCIENCE

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE

Enrichment of sequencing targets from the human genome by solution hybridization

(2009) Ryan Tewhey et al.   GENOME BIOLOGY

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

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

Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice

(2008) M. M. Becker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE

Gene synthesis demystified

(2008) Michael J. Czar et al.   TRENDS IN BIOTECHNOLOGY