Joseph Bondy‐Denomy

This study identifies a tripartite mechanism involving Imp7 and Imp1 that licenses RNA polymerase import into the phage nucleus, showing that nuclear compartment assembly precedes transcriptional and replicative programs.

The paper identifies a DNA repair mechanism in phages that allows them to resist CRISPR-Cas and R-M systems by repairing nuclease-induced breaks via a ligase-dependent process.

This study develops a phage transposon sequencing (TnSeq) platform to identify essential genes in bacteriophages, finding ~110 fitness-conferring genes in a jumbo phage model.

The paper shows that CBASS effector CapV limits phage production without reducing cell viability in Pseudomonas aeruginosa by interfering with phage capsid assembly.

The paper identifies surface receptor masking and internal defenses as barriers to phage therapy in Pseudomonas aeruginosa clinical isolates and presents strategies to overcome these barriers through phage engineering.

The paper shows how phages evade bacterial immune systems by using allelic variation and an anti-defense hotspot, revealing a similarity to a human protein.

This study identifies chemical inhibitors that block a bacterial immune system, enhancing phage therapy efficacy against resistant strains.

This study shows that Pseudomonas aeruginosa inactivates its type I R-M system via proteolysis at high temperatures, leading to prolonged genomic hypomethylation and a memory effect lasting over 60 generations.

The paper identifies how Gabija, a bacterial anti-phage system, discriminates self from non-self DNA by targeting phages that antagonize the host RecBCD complex.

This study characterizes AcrIF11, an ADP-ribosyltransferase that inhibits CRISPR-Cas systems with high potency and specificity, and shows its reversibility through macrodomain enzymes.

The paper identifies ENDPaCF1, a novel defense system in Pseudomonas aeruginosa, which targets hypermodified phage DNA through an endonuclease domain fused to an inactive Endonuclease III, revealing its role in antiphage immunity.

The paper identifies conserved phage factors required for protein import into a phage nucleus and characterizes their interactions and roles in selectivity.

The paper develops AntiDefenseFinder to detect anti-defense systems in prokaryotes, phages, and MGEs, identifying 47,981 systems and revealing their distribution and evolutionary dynamics.

The paper identifies a lipid-based compartment in early phage infection that protects phage DNA and supports early transcription and translation.

The paper identifies two highly conserved core defense hotspots in Pseudomonas aeruginosa containing numerous anti-phage systems, including a newly discovered system called Shango.

This study uses co-fractionation mass spectrometry to map host-pathogen and pathogen-pathogen interactions in jumbophages infecting Pseudomonas aeruginosa, revealing over 6000 interactions and novel viral components.

The paper challenges the validity of AcrVIA1-7 as type VI-A CRISPR anti-CRISPR proteins due to inconsistencies in bioinformatics and experimental results.

This paper develops a minimal CRISPR-Cas3 system for efficient genome engineering, enabling large deletions in bacterial genomes.