
Associate Professor
M_Microbiology and Immunology
+1 415 514-1381
Custom People Group
In the Bondy-Denomy lab, we study CRISPR-Cas bacterial immune systems in an effort to understand their role in antagonizing viruses called bacteriophages. We are very interested in how CRISPR works and the ways that phages inhibit and evade CRISPR-Cas function.
Publications
Chemical inhibition of a bacterial immune system 1.
bioRxiv : the preprint server for biology
Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements.
Nucleic acids research
AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid.
bioRxiv : the preprint server for biology
Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements.
bioRxiv : the preprint server for biology
Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.
Cell host & microbe
Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense.
Cell reports
Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides.
Molecular cell
Single phage proteins sequester TIR- and cGAS-generated signaling molecules.
bioRxiv : the preprint server for biology
Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.
Nature communications
Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems.
Nucleic acids research
F-Type Pyocins Are Diverse Noncontractile Phage Tail-Like Weapons for Killing Pseudomonas aeruginosa.
Journal of bacteriology
Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides.
bioRxiv : the preprint server for biology
Defining the expanding mechanisms of phage-mediated activation of bacterial immunity.
Current opinion in microbiology
Ten Years of Anti-CRISPR Research.
Journal of molecular biology
Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping.
bioRxiv : the preprint server for biology
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice.
Nature communications
Bacteriophage genome engineering with CRISPR-Cas13a.
Nature microbiology
Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor.
Nature chemical biology
CRISPR-Cas12a targeting of ssDNA plays no detectable role in immunity.
Nucleic acids research
A single bacterial enzyme i(NHI)bits phage DNA replication.
Cell host & microbe
Distinct Subcellular Localization of a Type I CRISPR Complex and the Cas3 Nuclease in Bacteria.
Journal of bacteriology
Genetic Manipulation of a CAST of Characters in a Microbial Community.
The CRISPR journal
Publisher Correction: CRISPR inactivation by integration.
Nature microbiology
CRISPR inactivation by integration.
Nature microbiology
Positioning Diverse Type IV Structures and Functions Within Class 1 CRISPR-Cas Systems.
Frontiers in microbiology
Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa.
Nucleic acids research
Anti-CRISPRs go viral: The infection biology of CRISPR-Cas inhibitors.
Cell host & microbe
Intracellular Organization by Jumbo Bacteriophages.
Journal of bacteriology
Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements.
Nature communications
Machine-learning approach expands the repertoire of anti-CRISPR protein families.
Nature communications
Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression.
Annual review of microbiology
Author Correction: Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer.
Nature microbiology
Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor.
Cell host & microbe
Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes.
Cell host & microbe
Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer.
Nature microbiology
Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity.
Nature microbiology
Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.
Nature microbiology
A Type IV-A CRISPR-Cas System in Pseudomonas aeruginosa Mediates RNA-Guided Plasmid Interference In Vivo.
The CRISPR journal
Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance.
PLoS neglected tropical diseases
CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.
Cell host & microbe
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.
Nature microbiology
Cas13 Helps Bacteria Play Dead when the Enemy Strikes.
Cell host & microbe
Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells.
Nature communications
Phage Morons Play an Important Role in Pseudomonas aeruginosa Phenotypes.
Journal of bacteriology
A Unified Resource for Tracking Anti-CRISPR Names.
The CRISPR journal
Discovery of widespread type I and type V CRISPR-Cas inhibitors.
Science (New York, N.Y.)
Protein Inhibitors of CRISPR-Cas9.
ACS chemical biology
How bacteria control the CRISPR-Cas arsenal.
Current opinion in microbiology
Pseudomonas aeruginosa defends against phages through type IV pilus glycosylation.
Nature microbiology
The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs.
Annual review of virology
Disabling Cas9 by an anti-CRISPR DNA mimic.
Science advances
Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity.
Proceedings of the National Academy of Sciences of the United States of America
CRISPR control of virulence in Pseudomonas aeruginosa.
Cell research
Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system.
Proceedings of the National Academy of Sciences of the United States of America
The solution structure of an anti-CRISPR protein.
Nature communications
Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen.
Cellular microbiology
Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery.
Nucleic acids research
Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense.
Current biology : CB
When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness.
Journal of microbiology (Seoul, Korea)
To acquire or resist: the complex biological effects of CRISPR-Cas systems.
Trends in microbiology
Efficacy of bacteriophage treatment on Pseudomonas aeruginosa biofilms.
Journal of endodontics