A swapped genetic code prevents viral infections and gene transfer

Mechanistic insights into tRNA cleavage by a contact-dependent growth inhibitor protein and translation factors

(2022) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

(2022) Adair L. Borges et al.   Nature Microbiology

Systematic strategies for developing phage resistant Escherichia coli strains

(2022) Xuan Zou et al.   Nature Communications

Multiplex base editing to convert TAG into TAA codons in the human genome

(2022) Yuting Chen et al.   Nature Communications

Refactored genetic codes enable bidirectional genetic isolation

(2022) Jérôme F. Zürcher et al.   SCIENCE

Experimental validation that human microbiome phages use alternative genetic coding

(2022) Samantha L. Peters et al.   Nature Communications

Role of a cryptic tRNA gene operon in survival under translational stress

(2021) Javier Santamaría-Gómez et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

(2021) Patricia P Chan et al.   NUCLEIC ACIDS RESEARCH

Sense codon reassignment enables viral resistance and encoded polymer synthesis

(2021) Wesley E. Robertson et al.   SCIENCE

Degradation of host translational machinery drives tRNA acquisition in viruses

(2021) Joy Y. Yang et al.   Cell Systems

Synthetic auxotrophy remains stable after continuous evolution and in coculture with mammalian cells

(2021) Aditya M. Kunjapur et al.   Science Advances

Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection

(2021) Enea Maffei et al.   PLOS BIOLOGY

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

Resurrection of a global, metagenomically defined Gokushovirus

(2020) Paul C Kirchberger et al.   eLife

Viral contamination in biologic manufacture and implications for emerging therapies

(2020) Paul W. Barone et al.   NATURE BIOTECHNOLOGY

Automated design of thousands of nonrepetitive parts for engineering stable genetic systems

(2020) Ayaan Hossain et al.   NATURE BIOTECHNOLOGY

An Amino Acid-Swapped Genetic Code

(2020) Tomoshige Fujino et al.   ACS Synthetic Biology

How To Quantify a Genetic Firewall? A Polarity‐Based Metric for Genetic Code Engineering

(2020) Markus Schmidt et al.   CHEMBIOCHEM

Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes

(2019) Sergio Morgado et al.   Viruses-Basel

Total synthesis of Escherichia coli with a recoded genome

(2019) Julius Fredens et al.   NATURE

Rapid evolution of reduced susceptibility against a balanced dual-targeting antibiotic through stepping-stone mutations

(2019) Petra Szili et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Adaptive evolution of genomically recodedEscherichia coli

(2018) Timothy M. Wannier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering posttranslational proofreading to discriminate nonstandard amino acids

(2018) Aditya M. Kunjapur et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Essential Genome of Escherichia coli K-12

(2018) Emily C. A. Goodall et al.   mBio

Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere

(2018) Jônatas Abrahão et al.   Nature Communications

Bacteriophage-resistant industrial fermentation strains: from the cradle to CRISPR/Cas9

(2018) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Functionality of tRNAs encoded in a mobile genetic element from an acidophilic bacterium

(2017) Pamela Alamos et al.   RNA Biology

Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis

(2017) Kinga Umenhoffer et al.   ACS Synthetic Biology

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, synthesis, and testing toward a 57-codon genome

(2016) N. Ostrov et al.   SCIENCE

The Genome Project-Write

(2016) J. D. Boeke et al.   SCIENCE

Phage on tap–a quick and efficient protocol for the preparation of bacteriophage laboratory stocks

(2016) Natasha Bonilla et al.   PeerJ

Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements

(2016) Natalie Jing Ma et al.   Cell Systems

Recoded organisms engineered to depend on synthetic amino acids

(2015) Alexis J. Rovner et al.   NATURE

Biocontainment of genetically modified organisms by synthetic protein design

(2015) Daniel J. Mandell et al.   NATURE

tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily

(2015) Ru-Juan Liu et al.   NUCLEIC ACIDS RESEARCH

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Genomically Recoded Organisms Expand Biological Functions

(2013) M. J. Lajoie et al.   SCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification

(2011) Z. D. Miles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

tRNADB-CE 2011: tRNA gene database curated manually by experts

(2010) T. Abe et al.   NUCLEIC ACIDS RESEARCH

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Simple Method for Plating Escherichia coli Bacteriophages Forming Very Small Plaques or No Plaques under Standard Conditions

(2008) J. M. Los et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry

(2008) L. Kall et al.   BIOINFORMATICS

Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage

(2008) V. S. Brok-Volchanskaya et al.   NUCLEIC ACIDS RESEARCH