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



Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense.

Cell reports

Workman RE, Stoltzfus MJ, Keith NC, Euler CW, Bondy-Denomy J, Modell JW

Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides.

Molecular cell

Cao X, Xiao Y, Huiting E, Cao X, Li D, Ren J, Fedorova I, Wang H, Guan L, Wang Y, Li L, Bondy-Denomy J, Feng Y

Cas9 degradation in human cells using phage anti-CRISPR proteins.

PLoS biology

Meacham Z, de Tacca LA, Bondy-Denomy J, Rabuka D, Schelle M

Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile.


Muzyukina P, Shkaruta A, Guzman NM, Andreani J, Borges AL, Bondy-Denomy J, Maikova A, Semenova E, Severinov K, Soutourina O

Single phage proteins sequester TIR- and cGAS-generated signaling molecules.

bioRxiv : the preprint server for biology

Li D, Xiao Y, Xiong W, Fedorova I, Wang Y, Liu X, Huiting E, Ren J, Gao Z, Zhao X, Cao X, Zhang Y, Bondy-Denomy J, Feng Y