John van der OOST

The paper identifies novel biosynthetic gene clusters in marine sponge microbiomes associated with brominated alkaloids.

The paper systematically engineers and analyzes intrinsic terminators in bacteria, finding that an adenosine upstream of the terminator hairpin improves protein production and reduces read-through.

This study identifies distinct taxonomic groups of sponge symbionts with biosynthetic capacity for ether lipid production, supported by metagenomic analysis and lipidome confirmation.

This study investigates how titration of an active DnaA variant controls DNA replication in E. coli under different growth conditions, revealing limits and design principles for synthetic replication systems.

This study investigates DnaA titration on the E. coli chromosome and shows it controls free DnaA levels in a growth rate-dependent manner, preventing re-initiation during slow growth.

This study optimizes a genome editing system for Cupriavidus necator H16, achieving high editing efficiency using an improved SIBR-Cas system.

The paper demonstrates that plasmid conjugation can be used for in vivo laboratory evolution of Cas nucleases by enabling cleaving variants to spread through bacterial cultures.

This study shows DNA oligonucleotides can inhibit Cas9 activity in human cells and in vitro by targeting the guide RNA and requiring a PAM-loop for effective inhibition.

This study uses codon randomisation and machine learning to show that the first 8 codons of a gene strongly predict protein production levels in E. coli.

The paper constructs a synthetic RNA polymerase operon in E. coli, showing that adaptive evolution can restore growth after deleting native genes.

The paper introduces NAVIGATER, a method using TtAgo to enrich rare nucleic acid alleles, demonstrating 60-fold enrichment of KRAS G12D in pancreatic cancer blood samples.

This study characterizes CbAgo, a mesophilic prokaryotic Argonaute that enables DNA-guided DNA cleavage at moderate temperatures using specific siDNA guides.

The paper demonstrates multiplex gene editing in mammalian cells and mouse brains using a single CRISPR array processed by Cpf1 without requiring additional factors.