David Bikard

The paper quantifies the fitness gain of DGR diversification compared to standard mutagenesis and identifies when DGR activation is evolutionarily favored.

The paper identifies and characterizes defence hotspots in P2-like phages and P4-like satellites, revealing rapid modular evolution of antiviral systems through gene swapping and recombination.

This paper characterizes OLD, an abortive immunity protein, revealing its structure and activation mechanism in response to phage replication and DNA defects in RecBCD-compromised cells.

The paper develops a method to improve DGRec mutagenesis efficiency by recoding templates and using an LSTM model to predict mutational profiles.

This study uses CRISPRi to identify genetic factors affecting E. coli adaptation across diets, inflammation, and strains in a mouse model.

This study uses CRISPRi to identify metabolic vulnerabilities of UPEC in urine, highlighting ALS II as a druggable target.

The paper identifies additional tRNA targets of the AriB nuclease in the PARIS system and shows that phage-encoded tRNAs can inhibit this defense.

This study investigates the incomplete lytic cycle of hankyphage, a Bacteroides bacteriophage, revealing defective virion formation and incomplete DNA packaging.

This paper introduces DGRec, a method using DGRs to enable targeted hyper-mutagenesis in E. coli, creating diverse variants that allow evasion of phage infection.

This paper develops a CRISPR-based therapy targeting Shiga toxin genes in STEC infections, showing efficacy in reducing bacterial load and mitigating disease in animal models.

The paper fine-tunes a CRISPRi screen in Vibrio cholerae to enable pooled genome-wide screening with minimal cytotoxicity and identifies 368 essential genes.

The paper identifies anti-phage defence systems encoded by sedentary chromosomal integron cassettes in Vibrio cholerae, showing 16 cassettes provide phage resistance.

The paper shows toxin-antitoxin systems regulate cassette recombination dynamics in chromosomal integrons by killing cells when excision rates are too high.

The paper designs novel Cas9 PAM-interacting domains using a combination of evolutionary modeling, physics-based scoring, and machine learning, identifying functional variants with up to 20% sequence divergence from the wild-type.

This paper develops a method to edit bacterial genes in the gut using a phage-derived particle, achieving high editing efficiency and stable maintenance of modified bacteria.

The paper introduces two scoring functions to assess the quality of secondary structures in generated protein sequences and shows improved detection of non-functional sequences.

This paper uses variational autoencoders to generate functional protein variants of bacterial luciferase, showing high success rates in retaining activity despite significant sequence changes.

This study assesses gene essentiality across diverse E. coli strains and growth conditions, revealing that essentiality varies independently of phylogeny and is influenced by mobile genetic elements.

The paper investigates epistatic interactions between CRISPR and Cas clusters in prokaryotes, finding that multiple CRISPRs can co-occur to enhance immune system effectiveness.

The paper identifies sequence determinants of CRISPR-Cas9 efficiency in E. coli through a genome-wide screen and develops a sequence-based model to predict cleavage efficiency.

This paper introduces an engineered CRISPR-Cas9 system that enables precise, tunable, and multiplexed repression of bacterial genes by controlling guide RNA complementarity.