Creating custom synthetic genomes in Escherichia coli with REXER and GENESIS

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

Total synthesis of Escherichia coli with a recoded genome

(2019) Julius Fredens et al.   NATURE

Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality

(2019) Jonathan E. Venetz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria

(2019) Gaoyan Wang et al.   Nature Microbiology

Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA

(2017) Yu Heng Lau et al.   NUCLEIC ACIDS RESEARCH

Design of a synthetic yeast genome

(2017) Sarah M. Richardson et al.   SCIENCE

Defining synonymous codon compression schemes by genome recoding

(2016) Kaihang Wang et al.   NATURE

Design and synthesis of a minimal bacterial genome

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

Engineering complex biological systems in bacteria through recombinase-assisted genome engineering

(2014) Christine Nicole S Santos et al.   Nature Protocols

Simultaneous non-contiguous deletions using large synthetic DNA and site-specific recombinases

(2014) Radha Krishnakumar 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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae

(2008) Natalay Kouprina et al.   Nature Protocols