Joseph Bondy-Denomy, PhD

Associate Professor
Microbiology and Immunology
[email protected]
+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: 
Immunology
Research Summary: 
CRISPR-Cas immunity and anti-immunity
Mentorship Development: 

4/2019 - Acknowleding and Negotiating the Mentee-Mentor Tensions Inherent in the Research Lab (Mission Bay)
2/2021 - Three Truths and Three Tries: Facing and Overcoming Critical Social Justice Challenges at the Micro, Mezzo, and Macro Levels
6/2022 - Career Conversations
11/2022 - Faculty Development Program: Supervising People Who Aren't You: Mentoring/Managing Different Work Styles

Websites

Publications: 

Activation of bacterial programmed cell death by phage inhibitors of host immunity.

Molecular cell

Silas S, Carion H, Makarova KS, Laderman ES, Todeschini T, Kumar P, Johnson M, Bocek M, Nobrega FL, Koonin EV, Bondy-Denomy J

Jumbo phage killer immune system targets early infection of nucleus-forming phages.

Cell

Yuping L, Guan L, Becher I, Makarova KS, Cao X, Hareendranath S, Guan J, Stein F, Yang S, Boergel A, Lapouge K, Remans K, Agard D, Savitski M, Typas A, Koonin EV, Feng Y, Bondy-Denomy J

Chemical inhibition of a bacterial immune system 1.

bioRxiv : the preprint server for biology

Zang Z, Duncan OK, Sabonis D, Shi Y, Miraj G, Fedorova I, Le S, Deng J, Zhu Y, Cai Y, Zhang C, Arya G, Duerkop BA, Liang H, Bondy-Denomy J, Ve T, Tamulaitiene G, Gerdt JP

Multi-interface licensing of protein import into a phage nucleus.

Nature

Kokontis C, Klein TA, Silas S, Bondy-Denomy J

Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements.

Nucleic acids research

Tesson F, Huiting E, Wei L, Ren J, Johnson M, Planel R, Cury J, Feng Y, Bondy-Denomy J, Bernheim A