Joseph Bondy-Denomy, PhD

Associate Professor
Microbiology and Immunology
+1 415 514-1381
Research Overview: 

In the Bondy-Denomy lab, we study and discover bacterial immune systems that antagonize bacteriophages (bacterial viruses). These systems include CRISPR-Cas, restriction-modification, and numerous other anti-phage defenses that are related to human innate immunity including cGAS-STING. We are very interested in how anti-phage defense works and the ways that phages fight back to survive in this ever raging arms race.

Primary Thematic Area: 
Virology & Microbial Pathogenesis
Secondary Thematic Area: 
Research Summary: 
CRISPR-Cas immunity and anti-immunity
Mentorship Development: 

4/11/19    Acknowleding and Negotiating the Mentee-Mentor Tensions Inherent in the Research Lab (Mission Bay)
2/16/21    Three Truths and Three Tries: Facing and Overcoming Critical Social Justice Challenges at the Micro, Mezzo, and Macro Levels



The ?PA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice.

Nature communications

Nieweglowska ES, Brilot AF, M?ndez-Moran M, Kokontis C, Baek M, Li J, Cheng Y, Baker D, Bondy-Denomy J, Agard DA

Bacteriophages inhibit and evade cGAS-like immune function in bacteria.


Huiting E, Cao X, Ren J, Athukoralage JS, Luo Z, Silas S, An N, Carion H, Zhou Y, Fraser JS, Feng Y, Bondy-Denomy J

Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping.

bioRxiv : the preprint server for biology

Fossati A, Mozumdar D, Kokontis C, Nieweglowska E, Mendez M, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL

Bacteriophage genome engineering with CRISPR-Cas13a.

Nature microbiology

Guan J, Orom?-Bosch A, Mendoza SD, Karambelkar S, Berry JD, Bondy-Denomy J

Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor.

Nature chemical biology

Mukherjee IA, Gabel C, Noinaj N, Bondy-Denomy J, Chang L