High-throughput functional variant screens via in vivo production of single-stranded DNA

Characterizing the portability of phage-encoded homologous recombination proteins

(2021) Gabriel T. Filsinger et al.   Nature Chemical Biology

CRISPR /Cas9 recombineering‐mediated deep mutational scanning of essential genes in Escherichia coli

(2020) Alaksh Choudhury et al.   Molecular Systems Biology

Improved bacterial recombineering by parallelized protein discovery

(2020) Timothy M. Wannier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex Generation, Tracking, and Functional Screening of Substitution Mutants Using a CRISPR/Retron System

(2020) Hyeonseob Lim et al.   ACS Synthetic Biology

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation

(2019) Phil Oberacker et al.   PLOS BIOLOGY

High-Order Epistasis in Catalytic Power of Dihydrofolate Reductase Gives Rise to a Rugged Fitness Landscape in the Presence of Trimethoprim Selection

(2019) Yusuf Talha Tamer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Retrons and their applications in genome engineering

(2019) Anna J Simon et al.   NUCLEIC ACIDS RESEARCH

High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast

(2018) Xiaoge Guo et al.   NATURE BIOTECHNOLOGY

Multiplexed precision genome editing with trackable genomic barcodes in yeast

(2018) Kevin R Roy et al.   NATURE BIOTECHNOLOGY

Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER

(2018) Brandon G Wong et al.   NATURE BIOTECHNOLOGY

Precise Cas9 targeting enables genomic mutation prevention

(2018) Alejandro Chavez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli

(2018) Suhyung Cho et al.   ACS Synthetic Biology

Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing

(2018) Eilon Sharon et al.   CELL

Retroelement-based genome editing and evolution

(2018) Anna J. Simon et al.   ACS Synthetic Biology

Design of a synthetic yeast genome

(2017) Sarah M. Richardson et al.   SCIENCE

Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform

(2017) Jeremy M. Rock et al.   Nature Microbiology

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing

(2016) Justin Jee et al.   NATURE

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

(2016) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and synthesis of a minimal bacterial genome

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

Spatiotemporal microbial evolution on antibiotic landscapes

(2016) M. Baym et al.   SCIENCE

High-throughput bacterial functional genomics in the sequencing era

(2015) Andrew N Gray et al.   CURRENT OPINION IN MICROBIOLOGY

Synthetic biosensors for precise gene control and real-time monitoring of metabolites

(2015) Jameson K. Rogers et al.   NUCLEIC ACIDS RESEARCH

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

(2014) Mads T. Bonde et al.   NUCLEIC ACIDS RESEARCH

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

(2014) F. Farzadfard et al.   SCIENCE

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

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

Genomically Recoded Organisms Expand Biological Functions

(2013) M. J. Lajoie et al.   SCIENCE

Recovery of Phenotypes Obtained by Adaptive Evolution through Inverse Metabolic Engineering

(2012) Kuk-Ki Hong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering

(2012) M. J. Lajoie et al.   NUCLEIC ACIDS RESEARCH

Improving Lambda Red Genome Engineering in Escherichia coli via Rational Removal of Endogenous Nucleases

(2012) Joshua A. Mosberg et al.   PLoS One

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Probing Cellular Processes with Oligo-Mediated Recombination and Using the Knowledge Gained to Optimize Recombineering

(2011) James A. Sawitzke et al.   JOURNAL OF MOLECULAR BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Lambda Red Recombineering in Escherichia coli Occurs Through a Fully Single-Stranded Intermediate

(2010) J. A. Mosberg et al.   GENETICS

Escherichia coli rpoB Mutants Have Increased Evolvability in Proportion to Their Fitness Defects

(2010) J. E. Barrick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides

(2010) Joseph R Warner et al.   NATURE BIOTECHNOLOGY

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE