Joseph Bondy-Denomy, PhD

Title(s)Associate Professor, Microbiology and Immunology
SchoolSchool of Medicine
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 Research 
    Collapse Research Activities and Funding
    Uncovering the mechanism and role of a widespread anti-CRISPR-Cas9 protein
    NIH R01GM127489Apr 9, 2018 - Mar 31, 2023
    Role: Principal Investigator
    Discovering New Roles for CRISPR-Cas in Bacterial Pathogenesis
    NIH DP5OD021344Sep 25, 2015 - Aug 31, 2021
    Role: Principal Investigator

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    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A single bacterial enzyme i(NHI)bits phage DNA replication. Cell Host Microbe. 2022 04 13; 30(4):417-419. Huiting E, Bondy-Denomy J. PMID: 35421333.
      View in: PubMed   Mentions:
    2. Distinct Subcellular Localization of a Type I CRISPR Complex and the Cas3 Nuclease in Bacteria. J Bacteriol. 2022 Apr 07; e0010522. Govindarajan S, Borges A, Karambelkar S, Bondy-Denomy J. PMID: 35389256.
      View in: PubMed   Mentions:
    3. Genetic Manipulation of a CAST of Characters in a Microbial Community. CRISPR J. 2022 02; 5(1):4-6. Mozumdar D, Csörgo B, Bondy-Denomy J, Mozumdar D, Csörgo B, Bondy-Denomy J. PMID: 35119310; PMCID: PMC9009589.
      View in: PubMed   Mentions:
    4. Publisher Correction: CRISPR inactivation by integration. Nat Microbiol. 2022 Jan; 7(1):181. Bondy-Denomy J. PMID: 34880417.
      View in: PubMed   Mentions:
    5. CRISPR inactivation by integration. Nat Microbiol. 2021 12; 6(12):1475-1476. Bondy-Denomy J. PMID: 34819641.
      View in: PubMed   Mentions:
    6. Positioning Diverse Type IV Structures and Functions Within Class 1 CRISPR-Cas Systems. Front Microbiol. 2021; 12:671522. Taylor HN, Laderman E, Armbrust M, Hallmark T, Keiser D, Bondy-Denomy J, Jackson RN. PMID: 34093491; PMCID: PMC8175902.
      View in: PubMed   Mentions:
    7. Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa. Nucleic Acids Res. 2021 02 26; 49(4):2114-2125. León LM, Park AE, Borges AL, Zhang JY, Bondy-Denomy J. PMID: 33544853; PMCID: PMC7913775.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    8. Anti-CRISPRs go viral: The infection biology of CRISPR-Cas inhibitors. Cell Host Microbe. 2021 05 12; 29(5):704-714. Li Y, Bondy-Denomy J. PMID: 33444542; PMCID: PMC8122014.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    9. A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa. Mol Cell. 2021 02 04; 81(3):571-583.e6. Shah M, Taylor VL, Bona D, Tsao Y, Stanley SY, Pimentel-Elardo SM, McCallum M, Bondy-Denomy J, Howell PL, Nodwell JR, Davidson AR, Moraes TF, Maxwell KL. PMID: 33412111.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    10. Intracellular Organization by Jumbo Bacteriophages. J Bacteriol. 2020 12 18; 203(2). Guan J, Bondy-Denomy J. PMID: 32868402; PMCID: PMC7950403.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    11. Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. Nat Commun. 2020 11 06; 11(1):5652. Pinilla-Redondo R, Shehreen S, Marino ND, Fagerlund RD, Brown CM, Sørensen SJ, Fineran PC, Bondy-Denomy J. PMID: 33159058; PMCID: PMC7648647.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    12. A compact Cascade-Cas3 system for targeted genome engineering. Nat Methods. 2020 12; 17(12):1183-1190. Csörgo B, León LM, Chau-Ly IJ, Vasquez-Rifo A, Berry JD, Mahendra C, Crawford ED, Lewis JD, Bondy-Denomy J. PMID: 33077967; PMCID: PMC7611934.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    13. Machine-learning approach expands the repertoire of anti-CRISPR protein families. Nat Commun. 2020 07 29; 11(1):3784. Gussow AB, Park AE, Borges AL, Shmakov SA, Makarova KS, Wolf YI, Bondy-Denomy J, Koonin EV. PMID: 32728052; PMCID: PMC7391736.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    14. Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression. Annu Rev Microbiol. 2020 09 08; 74:21-37. Wiegand T, Karambelkar S, Bondy-Denomy J, Wiedenheft B. PMID: 32503371; PMCID: PMC7712631.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    15. Author Correction: Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer. Nat Microbiol. 2020 Jun; 5(6):872. Mahendra C, Christie KA, Osuna BA, Pinilla-Redondo R, Kleinstiver BP, Bondy-Denomy J. PMID: 32327734.
      View in: PubMed   Mentions: 1     Fields:    
    16. Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes. Cell Host Microbe. 2020 07 08; 28(1):31-40.e9. Osuna BA, Karambelkar S, Mahendra C, Christie KA, Garcia B, Davidson AR, Kleinstiver BP, Kilcher S, Bondy-Denomy J. PMID: 32325050; PMCID: PMC7351598.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    17. Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor. Cell Host Microbe. 2020 07 08; 28(1):23-30.e5. Osuna BA, Karambelkar S, Mahendra C, Sarbach A, Johnson MC, Kilcher S, Bondy-Denomy J. PMID: 32325051; PMCID: PMC7351615.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    18. Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer. Nat Microbiol. 2020 04; 5(4):620-629. Mahendra C, Christie KA, Osuna BA, Pinilla-Redondo R, Kleinstiver BP, Bondy-Denomy J. PMID: 32218510; PMCID: PMC7194981.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    19. Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity. Nat Microbiol. 2020 05; 5(5):679-687. Borges AL, Castro B, Govindarajan S, Solvik T, Escalante V, Bondy-Denomy J. PMID: 32203410; PMCID: PMC7190418.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    20. Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies. Nat Methods. 2020 05; 17(5):471-479. Marino ND, Pinilla-Redondo R, Csörgo B, Bondy-Denomy J. PMID: 32203383; PMCID: PMC8510557.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimals
    21. Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol. 2020 Mar; 5(3):527. Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. PMID: 32047285; PMCID: PMC7608142.
      View in: PubMed   Mentions:    Fields:    
    22. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature. 2020 01; 577(7789):244-248. Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J. PMID: 31819262; PMCID: PMC6949375.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    23. A Type IV-A CRISPR-Cas System in Pseudomonas aeruginosa Mediates RNA-Guided Plasmid Interference In Vivo. CRISPR J. 2019 12; 2(6):434-440. Crowley VM, Catching A, Taylor HN, Borges AL, Metcalf J, Bondy-Denomy J, Jackson RN. PMID: 31809194; PMCID: PMC6919247.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    24. Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance. PLoS Negl Trop Dis. 2019 11; 13(11):e0007868. Hooda Y, Sajib MSI, Rahman H, Luby SP, Bondy-Denomy J, Santosham M, Andrews JR, Saha SK, Saha S. PMID: 31730615; PMCID: PMC6881056.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    25. CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog. Cell Host Microbe. 2019 Sep 11; 26(3):325-335.e5. Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. PMID: 31492655; PMCID: PMC6936622.
      View in: PubMed   Mentions: 10  Translation:HumansCells
    26. Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Cell. 2019 09 05; 178(6):1452-1464.e13. Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. PMID: 31474367; PMCID: PMC6754177.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    27. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol. 2019 11; 4(11):1895-1906. Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. PMID: 31332386; PMCID: PMC6813254.
      View in: PubMed   Mentions: 55     Fields:    Translation:Cells
    28. Cas13 Helps Bacteria Play Dead when the Enemy Strikes. Cell Host Microbe. 2019 07 10; 26(1):1-2. Mendoza SD, Bondy-Denomy J. PMID: 31295418; PMCID: PMC6842608.
      View in: PubMed   Mentions: 2  Translation:Cells
    29. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nat Commun. 2019 01 14; 10(1):194. Nakamura M, Srinivasan P, Chavez M, Carter MA, Dominguez AA, La Russa M, Lau MB, Abbott TR, Xu X, Zhao D, Gao Y, Kipniss NH, Smolke CD, Bondy-Denomy J, Qi LS. PMID: 30643127; PMCID: PMC6331597.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    30. Temperature-Responsive Competitive Inhibition of CRISPR-Cas9. Mol Cell. 2019 02 07; 73(3):601-610.e5. Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA. PMID: 30595438; PMCID: PMC6480404.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    31. Phage Morons Play an Important Role in Pseudomonas aeruginosa Phenotypes. J Bacteriol. 2018 11 15; 200(22). Tsao YF, Taylor VL, Kala S, Bondy-Denomy J, Khan AN, Bona D, Cattoir V, Lory S, Davidson AR, Maxwell KL. PMID: 30150232; PMCID: PMC6199475.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    32. A Unified Resource for Tracking Anti-CRISPR Names. CRISPR J. 2018 10; 1:304-305. Bondy-Denomy J, Davidson AR, Doudna JA, Fineran PC, Maxwell KL, Moineau S, Peng X, Sontheimer EJ, Wiedenheft B. PMID: 31021273.
      View in: PubMed   Mentions: 19     Fields:    
    33. Discovery of widespread type I and type V CRISPR-Cas inhibitors. Science. 2018 10 12; 362(6411):240-242. Marino ND, Zhang JY, Borges AL, Sousa AA, Leon LM, Rauch BJ, Walton RT, Berry JD, Joung JK, Kleinstiver BP, Bondy-Denomy J. PMID: 30190308; PMCID: PMC6520112.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    34. Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity. Cell. 2018 08 09; 174(4):917-925.e10. Borges AL, Zhang JY, Rollins MF, Osuna BA, Wiedenheft B, Bondy-Denomy J. PMID: 30033364; PMCID: PMC6086726.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    35. Protein Inhibitors of CRISPR-Cas9. ACS Chem Biol. 2018 02 16; 13(2):417-423. Bondy-Denomy J. PMID: 29251498; PMCID: PMC6049822.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    36. How bacteria control the CRISPR-Cas arsenal. Curr Opin Microbiol. 2018 04; 42:87-95. Leon LM, Mendoza SD, Bondy-Denomy J. PMID: 29169146; PMCID: PMC5899631.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    37. Pseudomonas aeruginosa defends against phages through type IV pilus glycosylation. Nat Microbiol. 2018 Jan; 3(1):47-52. Harvey H, Bondy-Denomy J, Marquis H, Sztanko KM, Davidson AR, Burrows LL. PMID: 29133883.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    38. The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs. Annu Rev Virol. 2017 09 29; 4(1):37-59. Borges AL, Davidson AR, Bondy-Denomy J. PMID: 28749735; PMCID: PMC6039114.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    39. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv. 2017 07; 3(7):e1701620. Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA. PMID: 28706995; PMCID: PMC5507636.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansCells
    40. Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity. Proc Natl Acad Sci U S A. 2017 06 27; 114(26):E5113-E5121. Rollins MF, Chowdhury S, Carter J, Golden SM, Wilkinson RA, Bondy-Denomy J, Lander GC, Wiedenheft B. PMID: 28438998; PMCID: PMC5495223.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    41. Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. Cell. 2017 03 23; 169(1):47-57.e11. 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. PMID: 28340349; PMCID: PMC5478280.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
    42. CRISPR control of virulence in Pseudomonas aeruginosa. Cell Res. 2017 02; 27(2):163-164. Wiedenheft B, Bondy-Denomy J. PMID: 28084330; PMCID: PMC5339854.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    43. Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. Cell. 2017 Jan 12; 168(1-2):150-158.e10. Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J. PMID: 28041849; PMCID: PMC5235966.
      View in: PubMed   Mentions: 126     Fields:    Translation:HumansCells
    44. 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. Høyland-Kroghsbo NM, Paczkowski J, Mukherjee S, Broniewski J, Westra E, Bondy-Denomy J, Bassler BL. PMID: 27849583; PMCID: PMC5224376.
      View in: PubMed   Mentions: 60     Fields:    Translation:Cells
    45. The solution structure of an anti-CRISPR protein. Nat Commun. 2016 10 11; 7:13134. Maxwell KL, Garcia B, Bondy-Denomy J, Bona D, Hidalgo-Reyes Y, Davidson AR. PMID: 27725669; PMCID: PMC5062604.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    46. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 2016 12; 10(12):2854-2866. Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL. PMID: 27258950; PMCID: PMC5148200.
      View in: PubMed   Mentions: 82     Fields:    Translation:Cells
    47. The diversity-generating benefits of a prokaryotic adaptive immune system. Nature. 2016 Apr 21; 532(7599):385-8. van Houte S, Ekroth AK, Broniewski JM, Chabas H, Ashby B, Bondy-Denomy J, Gandon S, Boots M, Paterson S, Buckling A, Westra ER. PMID: 27074511; PMCID: PMC4935084.
      View in: PubMed   Mentions: 77     Fields:    Translation:Cells
    48. Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen. Cell Microbiol. 2016 10; 18(10):1319-38. Rao C, Guyard C, Pelaz C, Wasserscheid J, Bondy-Denomy J, Dewar K, Ensminger AW. PMID: 26936325; PMCID: PMC5071653.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    49. 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. Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E. PMID: 26586803; PMCID: PMC4678832.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    50. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature. 2015 Oct 01; 526(7571):136-9. Bondy-Denomy J, Garcia B, Strum S, Du M, Rollins MF, Hidalgo-Reyes Y, Wiedenheft B, Maxwell KL, Davidson AR. PMID: 26416740; PMCID: PMC4935067.
      View in: PubMed   Mentions: 115     Fields:    Translation:Cells
    51. Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense. Curr Biol. 2015 Apr 20; 25(8):1043-9. Westra ER, van Houte S, Oyesiku-Blakemore S, Makin B, Broniewski JM, Best A, Bondy-Denomy J, Davidson A, Boots M, Buckling A. PMID: 25772450.
      View in: PubMed   Mentions: 79     Fields:    Translation:AnimalsCells
    52. 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. Pawluk A, Bondy-Denomy J, Cheung VH, Maxwell KL, Davidson AR. PMID: 24736222; PMCID: PMC3993853.
      View in: PubMed   Mentions: 97     Fields:    Translation:Cells
    53. When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. J Microbiol. 2014 Mar; 52(3):235-42. Bondy-Denomy J, Davidson AR. PMID: 24585054.
      View in: PubMed   Mentions: 58     Fields:    Translation:Cells
    54. To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol. 2014 Apr; 22(4):218-25. Bondy-Denomy J, Davidson AR. PMID: 24582529.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    55. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature. 2013 Jan 17; 493(7432):429-32. Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR. PMID: 23242138; PMCID: PMC4931913.
      View in: PubMed   Mentions: 234     Fields:    Translation:Cells
    56. Efficacy of bacteriophage treatment on Pseudomonas aeruginosa biofilms. J Endod. 2013 Mar; 39(3):364-9. Phee A, Bondy-Denomy J, Kishen A, Basrani B, Azarpazhooh A, Maxwell K. PMID: 23402508.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    57. 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. Cady KC, Bondy-Denomy J, Heussler GE, Davidson AR, O'Toole GA. PMID: 22885297; PMCID: PMC3486085.
      View in: PubMed   Mentions: 115     Fields:    Translation:Cells
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