Joseph Bondy-Denomy, PhD
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Title(s) | Associate Professor, Microbiology and Immunology |
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School | School of Medicine |
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Address | 600 16th St San Francisco CA 94158
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Phone | 415-514-1381 |
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vCard | Download vCard |
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Biography University of Waterloo, Waterloo, ON | BSc | 08/2008 | Biology, Microbiology | University of Toronto, Toronto, ON | PhD | 11/2014 | Molecular Genetics |
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.
Research ORNG Applications Bibliographic
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A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa. Mol Cell. 2021 Jan 04.
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: Fields:
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Intracellular Organization by Jumbo Bacteriophages. J Bacteriol. 2020 Dec 18; 203(2).
Guan J, Bondy-Denomy J. PMID: 32868402.
View in: PubMed Mentions: Fields:
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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.
View in: PubMed Mentions: Fields: Translation: Cells
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A compact Cascade-Cas3 system for targeted genome engineering. Nat Methods. 2020 Dec; 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.
View in: PubMed Mentions: 2 Fields:
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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.
View in: PubMed Mentions: Fields: Translation: Cells
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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.
View in: PubMed Mentions: 5 Fields:
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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: Fields:
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Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes. . 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.
View in: PubMed Mentions:
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Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor. . 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.
View in: PubMed Mentions:
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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.
View in: PubMed Mentions: 6 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 3 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 8 Fields: Translation: HumansAnimals
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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.
View in: PubMed Mentions: Fields:
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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.
View in: PubMed Mentions: 10 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 5 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 12 Fields: Translation: HumansCells
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CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog. . 2019 Sep 11; 26(3):325-335.e5.
Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. PMID: 31492655.
View in: PubMed Mentions:
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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.
View in: PubMed Mentions: 10 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 26 Fields: Translation: Cells
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Cas13 Helps Bacteria Play Dead when the Enemy Strikes. . 2019 07 10; 26(1):1-2.
Mendoza SD, Bondy-Denomy J. PMID: 31295418.
View in: PubMed Mentions:
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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.
View in: PubMed Mentions: 19 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 13 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 8 Fields: Translation: AnimalsCells
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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: 12 Fields:
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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.
View in: PubMed Mentions: 28 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 17 Fields: Translation: Cells
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Protein Inhibitors of CRISPR-Cas9. ACS Chem Biol. 2018 02 16; 13(2):417-423.
Bondy-Denomy J. PMID: 29251498.
View in: PubMed Mentions: 10 Fields: Translation: HumansCells
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How bacteria control the CRISPR-Cas arsenal. Curr Opin Microbiol. 2018 04; 42:87-95.
Leon LM, Mendoza SD, Bondy-Denomy J. PMID: 29169146.
View in: PubMed Mentions: 2 Fields: Translation: Cells
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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: 7 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 33 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 55 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 24 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 47 Fields: Translation: Cells
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CRISPR control of virulence in Pseudomonas aeruginosa. Cell Res. 2017 02; 27(2):163-164.
Wiedenheft B, Bondy-Denomy J. PMID: 28084330.
View in: PubMed Mentions: Fields: Translation: AnimalsCells
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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.
View in: PubMed Mentions: 91 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 45 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 20 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 45 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 55 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 8 Fields: Translation: AnimalsCells
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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.
View in: PubMed Mentions: 31 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 97 Fields: Translation: Cells
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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: 62 Fields: Translation: AnimalsCells
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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.
View in: PubMed Mentions: 77 Fields: Translation: Cells
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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: 51 Fields: Translation: Cells
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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: 36 Fields: Translation: Cells
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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.
View in: PubMed Mentions: 188 Fields: Translation: Cells
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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: 10 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 101 Fields: Translation: Cells
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Year | Publications |
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2012 | 3 | 2014 | 3 | 2015 | 3 | 2016 | 6 | 2017 | 7 | 2018 | 6 | 2019 | 8 | 2020 | 12 | 2021 | 1 |
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Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
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This graph shows the number and percent of publications by field.
Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications.
Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
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