Joseph Bondy‐Denomy

Also affiliated with University of California, San Francisco, Quantitative BioSciences

Biochemistry, Genetics and Molecular BiologyEnvironmental Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 56 papers. Top paper: “Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements”.

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

Nucleic Acids Research(2024)10.1093/nar/gkae1171

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1.1DataRank · unranked

60 citations

Erin Huiting, Linlin Wei, Jie Ren, Matthew C. Johnson, Rémi Planel +5 more

Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements

Nature Communications(2020)10.1038/s41467-020-19415-3

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0DataRank · unranked

160 citations

Saadlee Shehreen, Nicole D. Marino, Robert D. Fagerlund, Chris M. Brown, Søren J. Sørensen +3 more

Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies

Nature Methods(2020)10.1038/s41592-020-0771-6

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0DataRank · unranked

258 citations

Rafael Pinilla‐Redondo, Bálint Csörgő, Joseph Bondy‐Denomy, Nicole D. Marino

Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer

Nature Microbiology(2020)10.1038/s41564-020-0692-2

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0DataRank · unranked

125 citations

Kathleen A. Christie, Beatriz A. Osuna, Rafael Pinilla‐Redondo, Benjamin P. Kleinstiver, Joseph Bondy‐Denomy +1 more

Machine-learning approach expands the repertoire of anti-CRISPR protein families

Nature Communications(2020)10.1038/s41467-020-17652-0

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0DataRank · unranked

111 citations

Allyson E. Park, Adair L. Borges, Sergey Shmakov, Kira S. Makarova, Yuri I. Wolf +3 more

Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression

Annual Review of Microbiology(2020)10.1146/annurev-micro-020518-120107

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0DataRank · unranked

101 citations

Shweta Karambelkar, Joseph Bondy‐Denomy, Blake Wiedenheft, Tanner Wiegand

Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes

Cell Host & Microbe(2020)10.1016/j.chom.2020.04.001

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0DataRank · unranked

94 citations

Shweta Karambelkar, Caroline Mahendra, Kathleen A. Christie, Bianca Garcı́a, Alan R. Davidson +4 more

Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor

Cell Host & Microbe(2020)10.1016/j.chom.2020.04.002

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0DataRank · unranked

71 citations

Shweta Karambelkar, Caroline Mahendra, Anne Sarbach, Matthew C. Johnson, Samuel Kilcher +2 more

Bacterial alginate regulators and phage homologs repress CRISPR–Cas immunity

Nature Microbiology(2020)10.1038/s41564-020-0691-3

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0DataRank · unranked

55 citations

Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy‐Denomy +1 more

Intracellular Organization by Jumbo Bacteriophages

Journal of Bacteriology(2020)10.1128/jb.00362-20

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0DataRank · unranked

28 citations

Joseph Bondy‐Denomy, Jingwen Guan

Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.23.916767

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0DataRank · unranked

12 citations

Sergey Shmakov, Kira S. Makarova, Yuri I. Wolf, Joseph Bondy‐Denomy, Eugene V. Koonin +1 more

Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.15.151498

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0DataRank · unranked

6 citations

Allyson E. Park, Adair L. Borges, Jenny Y. Zhang, Joseph Bondy‐Denomy, Lina M León

Distinct subcellular localization of a Type I CRISPR complex and the Cas3 nuclease in bacteria

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.29.318501

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0DataRank · unranked

3 citations

Adair L. Borges, Joseph Bondy‐Denomy, Sutharsan Govindarajan

Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa

Nucleic Acids Research(2021)10.1093/nar/gkab006

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0DataRank · unranked

81 citations

Allyson E. Park, Adair L. Borges, Jenny Y. Zhang, Joseph Bondy‐Denomy, Lina M León

Anti-CRISPRs go viral: The infection biology of CRISPR-Cas inhibitors

Cell Host & Microbe(2021)10.1016/j.chom.2020.12.007

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0DataRank · unranked

79 citations

Joseph Bondy‐Denomy, Yuping Li

Positioning Diverse Type IV Structures and Functions Within Class 1 CRISPR-Cas Systems

Frontiers in Microbiology(2021)10.3389/fmicb.2021.671522

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0DataRank · unranked

38 citations

Eric Laderman, Matt Armbrust, Thomson Hallmark, Dylan Keiser, Joseph Bondy‐Denomy +2 more

Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.27.445852

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0DataRank · unranked

1 citations

Matthew C. Johnson, Logan T. Hille, Benjamin P. Kleinstiver, Joseph Bondy‐Denomy, Alexander J. Meeske

Bacteriophage genome engineering with CRISPR–Cas13a

Nature Microbiology(2022)10.1038/s41564-022-01243-4

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0DataRank · unranked

104 citations

Agnès Oromí-Bosch, Senén D. Mendoza, Shweta Karambelkar, Joel Berry, Joseph Bondy‐Denomy +1 more

CRISPR-Cas12a targeting of ssDNA plays no detectable role in immunity

Nucleic Acids Research(2022)10.1093/nar/gkac462

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0DataRank · unranked

33 citations

Rafael Pinilla‐Redondo, Joseph Bondy‐Denomy, Nicole D. Marino

Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages

Molecular Cell(2022)10.1016/j.molcel.2022.05.002

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0DataRank · unranked

13 citations

Logan T. Hille, Benjamin P. Kleinstiver, Alexander J. Meeske, Joseph Bondy‐Denomy, Matthew C. Johnson

Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor

Nature Chemical Biology(2022)10.1038/s41589-022-01137-w

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0DataRank · unranked

13 citations

C. Gabel, Nicholas Noinaj, Joseph Bondy‐Denomy, Leifu Chang, Indranil Arun Mukherjee

Distinct Subcellular Localization of a Type I CRISPR Complex and the Cas3 Nuclease in Bacteria

Journal of Bacteriology(2022)10.1128/jb.00105-22

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0DataRank · unranked

13 citations

Adair L. Borges, Shweta Karambelkar, Joseph Bondy‐Denomy, Sutharsan Govindarajan

A family of novel immune systems targets early infection of nucleus-forming jumbo phages

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.17.508391

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0DataRank · unranked

23 citations

Jingwen Guan, Surabhi Hareendranath, Emily Crawford, David A. Agard, Kira S. Makarova +3 more

Translation-dependent downregulation of Cas12a mRNA by an anti-CRISPR protein

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.29.518452

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0DataRank · unranked

17 citations

Alexander Talaie, Héloïse Carion, Matthew C. Johnson, Zhang Yang, Sukrit Silas +3 more

The ϕPA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.06.487387

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0DataRank · unranked

7 citations

Axel F. Brilot, Melissa Mèndez-Moran, Minkyung Baek, Junrui Li, Claire Kokontis +5 more

Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.11.516204

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0DataRank · unranked

2 citations

Eric Laderman, Erin Huiting, Charles Zhang, Alan R. Davidson, Joseph Bondy‐Denomy +1 more

The ΦPA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice

Research Square(2022)10.21203/rs.3.rs-1531074/v1

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0DataRank · unranked

1 citations

Axel F. Brilot, Melissa Mèndez-Moran, Minkyung Baek, Junrui Li, Claire Kokontis +5 more

Bacteriophages inhibit and evade cGAS-like immune function in bacteria

Cell(2023)10.1016/j.cell.2022.12.041

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0DataRank · unranked

135 citations

Xueli Cao, Jie Ren, Januka S. Athukoralage, Zhaorong Luo, Sukrit Silas +7 more

Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems

Nucleic Acids Research(2023)10.1093/nar/gkad317

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0DataRank · unranked

68 citations

Eric Laderman, Erin Huiting, Chi Zhang, Alan R. Davidson, Joseph Bondy‐Denomy +1 more

Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides

Molecular Cell(2023)10.1016/j.molcel.2023.11.026

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0DataRank · unranked

51 citations

Yu Xiao, Erin Huiting, Xujun Cao, Dong Li, Jie Ren +8 more

The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice

Nature Communications(2023)10.1038/s41467-023-36526-9

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0DataRank · unranked

41 citations

Axel F. Brilot, Melissa Mèndez-Moran, Claire Kokontis, Minkyung Baek, Junrui Li +5 more

Defining the expanding mechanisms of phage-mediated activation of bacterial immunity

Current Opinion in Microbiology(2023)10.1016/j.mib.2023.102325

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0DataRank · unranked

34 citations

Joseph Bondy‐Denomy, Erin Huiting

Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping

Nature Communications(2023)10.1038/s41467-023-40724-w

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0DataRank · unranked

34 citations

Deepto Mozumdar, Claire Kokontis, Melissa Mèndez-Moran, Eliza Nieweglowska, Adrian Pelin +7 more

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

mSphere(2023)10.1128/msphere.00401-23

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0DataRank · unranked

5 citations

Anton Shkaruta, Noemí M. Guzmán, Jessica Andréani, Adair L. Borges, Joseph Bondy‐Denomy +5 more

Activation of programmed cell death and counter-defense functions of phage accessory genes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.06.535777

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0DataRank · unranked

11 citations

Héloïse Carion, Kira S. Makarova, Eric Laderman, David Sanchez Godinez, Matthew C. Johnson +6 more

Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.01.543220

N/A

0DataRank · unranked

7 citations

Yu Xiao, Erin Huiting, Xujun Cao, Dong Li, Jie Ren +6 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.15.567273

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0DataRank · unranked

7 citations

Yu Xiao, Weijia Xiong, Iana Fedorova, Yu Wang, Xi Liu +9 more

Diverse viral cas genes antagonize CRISPR immunity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.24.545427

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0DataRank · unranked

3 citations

Edith M Sawyer, Albina Kozlova, Madison C Williams, Shally R. Margolis, Luke Oriolt +4 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.22.562561

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0DataRank · unranked

2 citations

Marie J. Stoltzfus, Nicholas C Keith, Chad W. Euler, Joseph Bondy‐Denomy, Joshua W. Modell +1 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.22.541795

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0DataRank · unranked

1 citations

Anton Shkaruta, Noemí M. Guzmán, Jessica Andréani, Adair L. Borges, Joseph Bondy‐Denomy +5 more

Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.13.523954

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0DataRank · unranked

0 citations

Deepto Mozumdar, Claire Kokontis, Melissa Mèndez-Moran, Eliza Nieweglowska, Adrian Pelin +7 more

Single phage proteins sequester signals from TIR and cGAS-like enzymes

Nature(2024)10.1038/s41586-024-08122-4

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0DataRank · unranked

36 citations

Yu Xiao, Iana Fedorova, Weijia Xiong, Yu Wang, Xi Liu +9 more

Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection

Cell Host & Microbe(2024)10.1016/j.chom.2024.05.016

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0DataRank · unranked

29 citations

Andrea Fossati, Erica Stevenson, Jingwen Guan, Eliza Nieweglowska, Sanjana Rao +4 more

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

Cell Reports(2024)10.1016/j.celrep.2024.113849

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0DataRank · unranked

27 citations

Marie J. Stoltzfus, Nicholas C Keith, Chad W. Euler, Joseph Bondy‐Denomy, Joshua W. Modell +1 more

Diverse viral cas genes antagonize CRISPR immunity

Nature(2024)10.1038/s41586-024-07923-x

N/A

0DataRank · unranked

25 citations

Edith M Sawyer, Luke Oriolt, Albina Kozlova, Madison C Williams, Shally R. Margolis +4 more

Conserved jumbo phage factors required for protein import into a phage nucleus

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.27.586873

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0DataRank · unranked

5 citations

Timothy A. Klein, Sukrit Silas, Joseph Bondy‐Denomy, Claire Kokontis

Defining the constituents and functions of a lipid-based jumbo phage compartment

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.24.586471

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0DataRank · unranked

3 citations

Andrea Fossati, Erica Stevenson, Jingwen Guan, Eliza Nieweglowska, Sanjana Rao +4 more

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.26.609590

N/A

0DataRank · unranked

0 citations

Leah T. Roe, Yuping Li, Adair L. Borges, Jenny Y. Zhang, Palak Babbar +11 more

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

Cell(2025)10.1016/j.cell.2025.02.016

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0DataRank · unranked

23 citations

Linlin Guan, Isabelle Becher, Kira S. Makarova, Xueli Cao, Surabhi Hareendranath +13 more

Multi-interface licensing of protein import into a phage nucleus

Nature(2025)10.1038/s41586-024-08547-x

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0DataRank · unranked

16 citations

Timothy A. Klein, Sukrit Silas, Joseph Bondy‐Denomy, Claire Kokontis

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

Molecular Cell(2025)10.1016/j.molcel.2025.04.010

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0DataRank · unranked

15 citations

Héloïse Carion, Kira S. Makarova, Eric Laderman, Thomas C. Todeschini, Pradeep Kumar +6 more

Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity

Nature Communications(2025)10.1038/s41467-025-63056-3

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0DataRank · unranked

8 citations

Héloïse Carion, Kira S. Makarova, David Sanchez Godinez, Surabhi Haniyur, Lucy Volino +7 more

The complex developmental mechanisms of nucleus-forming jumbo phages

Current Opinion in Microbiology(2025)10.1016/j.mib.2025.102676

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0DataRank · unranked

3 citations

David A. Agard, Joseph Bondy‐Denomy, Deepto Mozumdar

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

mBio(2025)10.1128/mbio.01698-25

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0DataRank · unranked

4 citations

Leah T. Roe, Yuping Li, Adair L. Borges, Jenny Y. Zhang, Palak Babbar +11 more

A compact Cascade–Cas3 system for targeted genome engineering

Nature Methods(2020)10.1038/s41592-020-00980-w

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0DataRank · unranked

202 citations

Lina M León, Ilea J. Chau-Ly, Alejandro Vasquez-Rifo, Joel Berry, Caroline Mahendra +4 more

Chemical inhibition of a bacterial immune system

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.20.638879

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0DataRank · unranked

5 citations

Olivia K. Duncan, Dziugas Sabonis, Yun Shi, Gause Miraj, Iana Fedorova +13 more