Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly

The genome editing revolution

(2023) John van der Oost et al.   TRENDS IN BIOTECHNOLOGY

A swapped genetic code prevents viral infections and gene transfer

(2023) Akos Nyerges et al.   NATURE

Refactored genetic codes enable bidirectional genetic isolation

(2022) Jérôme F. Zürcher et al.   SCIENCE

Genetically programmed cell-based synthesis of non-natural peptide and depsipeptide macrocycles

(2022) Martin Spinck et al.   Nature Chemistry

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Creating custom synthetic genomes in Escherichia coli with REXER and GENESIS

(2021) Wesley E. Robertson et al.   Nature Protocols

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

(2021) Max G. Schubert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’

(2021) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Sense codon reassignment enables viral resistance and encoded polymer synthesis

(2021) Wesley E. Robertson et al.   SCIENCE

A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing

(2021) Yaojun Tong et al.   Nature Communications

Overcoming the Challenges of Megabase-Sized Plasmid Construction in Escherichia coli

(2020) Takahito Mukai et al.   ACS Synthetic Biology

Total synthesis of Escherichia coli with a recoded genome

(2019) Julius Fredens et al.   NATURE

Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly

(2019) Kaihang Wang et al.   SCIENCE

Creating a functional single-chromosome yeast

(2018) Yangyang Shao et al.   NATURE

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

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Design, synthesis, and testing toward a 57-codon genome

(2016) N. Ostrov et al.   SCIENCE

Design and synthesis of a minimal bacterial genome

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

Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery

(2014) E-Chiang Lee et al.   NATURE BIOTECHNOLOGY

Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering

(2014) Natalie J Ma et al.   Nature Protocols

Precise and in situ genetic humanization of 6 Mb of mouse immunoglobulin genes

(2014) L. E. Macdonald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

The structure of Escherichia coli ExoIX—implications for DNA binding and catalysis in flap endonucleases

(2013) Christopher S. Anstey-Gilbert et al.   NUCLEIC ACIDS RESEARCH

Genomically Recoded Organisms Expand Biological Functions

(2013) M. J. Lajoie et al.   SCIENCE

A direct characterization of human mutation based on microsatellites

(2012) James X Sun et al.   NATURE GENETICS

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools

(2012) Regina Z. Cer et al.   NUCLEIC ACIDS RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

(2008) D. G. Gibson et al.   SCIENCE