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Joseph Bondy-Denomy, PhD

TitleAssistant Professor
InstitutionUniversity of California San Francisco
DepartmentMicrobiology and Immunology
Address600 16th St
San Francisco CA 94158
Phone415-514-1381
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    Collapse Biography 
    Collapse Education and Training
    University of Waterloo, Waterloo, ONBSc08/2008Biology, Microbiology
    University of Toronto, Toronto, ONPhD11/2014Molecular Genetics

    Collapse Overview 
    Collapse Overview
    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.


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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Marino ND, Zhang JY, Borges AL, Sousa AA, Leon LM, Rauch BJ, Walton RT, Berry JD, Joung JK, Kleinstiver BP, Bondy-Denomy J. Discovery of widespread Type I and Type V CRISPR-Cas inhibitors. Science. 2018 Sep 06. PMID: 30190308.
      View in: PubMed
    2. Tsao YF, Taylor VL, Kala S, Bondy-Denomy J, Khan AN, Bona D, Cattoir V, Lory S, Davidson AR, Maxwell KL. Phage morons play important roles in controlling Pseudomonas aeruginosa phenotypes. J Bacteriol. 2018 Aug 27. PMID: 30150232.
      View in: PubMed
    3. Borges AL, Zhang JY, Rollins MF, Osuna BA, Wiedenheft B, Bondy-Denomy J. Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity. Cell. 2018 Jul 18. PMID: 30033364.
      View in: PubMed
    4. Bondy-Denomy J. Protein Inhibitors of CRISPR-Cas9. ACS Chem Biol. 2018 Feb 16; 13(2):417-423. PMID: 29251498.
      View in: PubMed
    5. Leon LM, Mendoza SD, Bondy-Denomy J. How bacteria control the CRISPR-Cas arsenal. Curr Opin Microbiol. 2017 Nov 21; 42:87-95. PMID: 29169146.
      View in: PubMed
    6. Harvey H, Bondy-Denomy J, Marquis H, Sztanko KM, Davidson AR, Burrows LL. Pseudomonas aeruginosa defends against phages through type IV pilus glycosylation. Nat Microbiol. 2018 Jan; 3(1):47-52. PMID: 29133883.
      View in: PubMed
    7. Borges AL, Davidson AR, Bondy-Denomy J. The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs. Annu Rev Virol. 2017 Sep 29; 4(1):37-59. PMID: 28749735.
      View in: PubMed
    8. Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv. 2017 Jul; 3(7):e1701620. PMID: 28706995.
      View in: PubMed
    9. Rollins MF, Chowdhury S, Carter J, Golden SM, Wilkinson RA, Bondy-Denomy J, Lander GC, Wiedenheft B. Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity. Proc Natl Acad Sci U S A. 2017 Jun 27; 114(26):E5113-E5121. PMID: 28438998.
      View in: PubMed
    10. Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, Nosaka L, Bondy-Denomy J, Maxwell KL, Davidson AR, Fischer ER, Lander GC, Wiedenheft B. Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. Cell. 2017 Mar 23; 169(1):47-57.e11. PMID: 28340349.
      View in: PubMed
    11. Wiedenheft B, Bondy-Denomy J. CRISPR control of virulence in Pseudomonas aeruginosa. Cell Res. 2017 Feb; 27(2):163-164. PMID: 28084330.
      View in: PubMed
    12. Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J. Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. Cell. 2017 Jan 12; 168(1-2):150-158.e10. PMID: 28041849.
      View in: PubMed
    13. Høyland-Kroghsbo NM, Paczkowski J, Mukherjee S, Broniewski J, Westra E, Bondy-Denomy J, Bassler BL. Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system. Proc Natl Acad Sci U S A. 2017 01 03; 114(1):131-135. PMID: 27849583.
      View in: PubMed
    14. Maxwell KL, Garcia B, Bondy-Denomy J, Bona D, Hidalgo-Reyes Y, Davidson AR. The solution structure of an anti-CRISPR protein. Nat Commun. 2016 Oct 11; 7:13134. PMID: 27725669.
      View in: PubMed
    15. Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 2016 12; 10(12):2854-2866. PMID: 27258950.
      View in: PubMed
    16. van Houte S, Ekroth AK, Broniewski JM, Chabas H, Ashby B, Bondy-Denomy J, Gandon S, Boots M, Paterson S, Buckling A, Westra ER. The diversity-generating benefits of a prokaryotic adaptive immune system. Nature. 2016 Apr 21; 532(7599):385-8. PMID: 27074511.
      View in: PubMed
    17. Rao C, Guyard C, Pelaz C, Wasserscheid J, Bondy-Denomy J, Dewar K, Ensminger AW. Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen. Cell Microbiol. 2016 Oct; 18(10):1319-38. PMID: 26936325.
      View in: PubMed
    18. Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery. Nucleic Acids Res. 2015 Dec 15; 43(22):10848-60. PMID: 26586803.
      View in: PubMed
    19. Bondy-Denomy J, Garcia B, Strum S, Du M, Rollins MF, Hidalgo-Reyes Y, Wiedenheft B, Maxwell KL, Davidson AR. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature. 2015 Oct 01; 526(7571):136-9. PMID: 26416740; PMCID: PMC4935067 [Available on 10/01/16].
      View in: PubMed, PubMed Central
    20. Westra ER, van Houte S, Oyesiku-Blakemore S, Makin B, Broniewski JM, Best A, Bondy-Denomy J, Davidson A, Boots M, Buckling A. Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense. Curr Biol. 2015 Apr 20; 25(8):1043-9. PMID: 25772450.
      View in: PubMed
    21. Pawluk A, Bondy-Denomy J, Cheung VH, Maxwell KL, Davidson AR. A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. MBio. 2014 Apr 15; 5(2):e00896. PMID: 24736222; PMCID: PMC3993853.
      View in: PubMed, PubMed Central
    22. Bondy-Denomy J, Davidson AR. When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. J Microbiol. 2014 Mar; 52(3):235-42. PMID: 24585054.
      View in: PubMed
    23. Bondy-Denomy J, Davidson AR. To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol. 2014 Apr; 22(4):218-25. PMID: 24582529.
      View in: PubMed
    24. Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature. 2013 Jan 17; 493(7432):429-32. PMID: 23242138; PMCID: PMC4931913.
      View in: PubMed, PubMed Central
    25. Phee A, Bondy-Denomy J, Kishen A, Basrani B, Azarpazhooh A, Maxwell K. Efficacy of bacteriophage treatment on Pseudomonas aeruginosa biofilms. J Endod. 2013 Mar; 39(3):364-9. PMID: 23402508.
      View in: PubMed
    26. Cady KC, Bondy-Denomy J, Heussler GE, Davidson AR, O'Toole GA. The CRISPR/Cas adaptive immune system of Pseudomonas aeruginosa mediates resistance to naturally occurring and engineered phages. J Bacteriol. 2012 Nov; 194(21):5728-38. PMID: 22885297; PMCID: PMC3486085.
      View in: PubMed, PubMed Central
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