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1

The CRISPR/Cas Adaptive Immune System of Pseudomonas aeruginosa Mediates Resistance to Naturally Occurring and Engineered Phages

Cady, K. C., Bondy-Denomy, J., Heussler, G. E., Davidson, A. R., O'Toole, G. A.

Journal:

Journal of Bacteriology

Year:

2012

Language:

english

File:

PDF, 3.62 MB

english, 2012

2

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

Bondy-Denomy, Joe, Pawluk, April, Maxwell, Karen L., Davidson, Alan R.

Journal:

Year:

2012

Language:

english

File:

PDF, 475 KB

english, 2012

3

To acquire or resist: the complex biological effects of CRISPR–Cas systems

Bondy-Denomy, Joseph, Davidson, Alan R.

Journal:

Trends in Microbiology

Year:

2014

Language:

english

File:

PDF, 366 KB

english, 2014

4

Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription

Stanley, Sabrina Y., Borges, Adair L., Chen, Kuei-Ho, Swaney, Danielle L., Krogan, Nevan J., Bondy-Denomy, Joseph, Davidson, Alan R.

Journal:

Year:

2019

Language:

english

File:

PDF, 7.37 MB

english, 2019

5

CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog

Soto-Perez, Paola, Bisanz, Jordan E., Berry, Joel D., Lam, Kathy N., Bondy-Denomy, Joseph, Turnbaugh, Peter J.

Journal:

Cell Host & Microbe

Year:

2019

Language:

english

File:

PDF, 3.24 MB

english, 2019

6

Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earthâs biomes

Roux, Simon, Krupovic, Mart, Daly, Rebecca A., Borges, Adair L., Nayfach, Stephen, Schulz, Frederik, Sharrar, Allison, Matheus Carnevali, Paula B., Cheng, Jan-Fang, Ivanova, Natalia N., Bondy-Denomy,

Journal:

Nature Microbiology

Year:

2020

Language:

english

File:

PDF, 747 KB

english, 2020

7

Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression

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

Journal:

Annual Review of Microbiology

Year:

2020

File:

PDF, 2.86 MB

2020

8

When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness

Bondy-Denomy, Joseph, Davidson, Alan R.

Journal:

Journal of Microbiology

Year:

2014

Language:

english

File:

PDF, 373 KB

english, 2014

9

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins

Bondy-Denomy, Joseph, Garcia, Bianca, Strum, Scott, Du, Mingjian, Rollins, MaryClare F., Hidalgo-Reyes, Yurima, Wiedenheft, Blake, Maxwell, Karen L., Davidson, Alan R.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.64 MB

english, 2015

10

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Rauch, Benjamin J., Silvis, Melanie R., Hultquist, Judd F., Waters, Christopher S., McGregor, Michael J., Krogan, Nevan J., Bondy-Denomy, Joseph

Journal:

Year:

2017

Language:

english

File:

PDF, 3.68 MB

english, 2017

11

Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex

Chowdhury, Saikat, Carter, Joshua, Rollins, MaryClare F., Golden, Sarah M., Jackson, Ryan N., Hoffmann, Connor, Nosaka, Lyn’Al, Bondy-Denomy, Joseph, Maxwell, Karen L., Davidson, Alan R., Fischer, Eli

Journal:

Year:

2017

Language:

english

File:

PDF, 6.59 MB

english, 2017

12

Disabling Cas9 by an anti-CRISPR DNA mimic

Shin, Jiyung, Jiang, Fuguo, Liu, Jun-Jie, Bray, Nicolas L., Rauch, Benjamin J., Baik, Seung Hyun, Nogales, Eva, Bondy-Denomy, Joseph, Corn, Jacob E., Doudna, Jennifer A.

Journal:

Science Advances

Year:

2017

Language:

english

File:

PDF, 5.79 MB

english, 2017

13

Cas13 Helps Bacteria Play Dead when the Enemy Strikes

Mendoza, Senén D., Bondy-Denomy, Joseph

Journal:

Cell Host & Microbe

Year:

2019

Language:

english

File:

PDF, 398 KB

english, 2019

14

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

Gussow, Ayal B., Park, Allyson E., Borges, Adair L., Shmakov, Sergey A., Makarova, Kira S., Wolf, Yuri I., Bondy-Denomy, Joseph, Koonin, Eugene V.

Journal:

Nature Communications

Year:

2020

File:

PDF, 843 KB

2020

15

Efficacy of Bacteriophage Treatment on Pseudomonas aeruginosa Biofilms

Phee, Alysen, Bondy-Denomy, Joe, Kishen, Anil, Basrani, Bettina, Azarpazhooh, Amir, Maxwell, Karen

Journal:

Journal of Endodontics

Year:

2013

Language:

english

File:

PDF, 316 KB

english, 2013

16

A New Group of Phage Anti-CRISPR Genes Inhibits the Type I-E CRISPR-Cas System of Pseudomonas aeruginosa

Pawluk, A., Bondy-Denomy, J., Cheung, V. H. W., Maxwell, K. L., Davidson, A. R.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.74 MB

english, 2014

17

Myxoma Virus Oncolysis of Primary and Metastatic B16F10 Mouse Tumors In Vivo

Stanford, Marianne M, Shaban, Mae, Barrett, John W, Werden, Steven J, Gilbert, Philippe-Alexandre, Bondy-Denomy, Joe, MacKenzie, Lisa, Graham, Kevin C, Chambers, Ann F, McFadden, Grant

Journal:

Molecular Therapy

Year:

2008

Language:

english

File:

PDF, 469 KB

english, 2008

18

Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense

Westra, Edze R., van Houte, Stineke, Oyesiku-Blakemore, Sam, Makin, Ben, Broniewski, Jenny M., Best, Alex, Bondy-Denomy, Joseph, Davidson, Alan, Boots, Mike, Buckling, Angus

Journal:

Current Biology

Year:

2015

Language:

english

File:

PDF, 723 KB

english, 2015

19

Foreign DNA acquisition by the I-F CRISPR–Cas system requires all components of the interference machinery

Vorontsova, Daria, Datsenko, Kirill A., Medvedeva, Sofia, Bondy-Denomy, Joseph, Savitskaya, Ekaterina E., Pougach, Ksenia, Logacheva, Maria, Wiedenheft, Blake, Davidson, Alan R., Severinov, Konstantin

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.28 MB

english, 2015

20

The diversity-generating benefits of a prokaryotic adaptive immune system

van Houte, Stineke, Ekroth, Alice K. E., Broniewski, Jenny M., Chabas, Hélène, Ben Ashby,, Bondy-Denomy, Joseph, Gandon, Sylvain, Boots, Mike, Paterson, Steve, Buckling, Angus, Westra, Edze R.

Journal:

Year:

2016

Language:

english

File:

PDF, 725 KB

english, 2016

21

Prophages mediate defense against phage infection through diverse mechanisms

Bondy-Denomy, Joseph, Qian, Jason, Westra, Edze R, Buckling, Angus, Guttman, David S, Davidson, Alan R, Maxwell, Karen L

Journal:

The ISME Journal

Year:

2016

Language:

english

File:

PDF, 1.07 MB

english, 2016

22

Active and Adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen.

Rao, Chitong, Guyard, Cyril, Pelaz, Carmen, Wasserscheid, Jessica, Bondy-Denomy, Joseph, Dewar, Ken, Ensminger, Alexander W.

Journal:

Cellular Microbiology

Year:

2016

Language:

english

File:

PDF, 2.98 MB

english, 2016

23

The solution structure of an anti-CRISPR protein

Maxwell, Karen L., Garcia, Bianca, Bondy-Denomy, Joseph, Bona, Diane, Hidalgo-Reyes, Yurima, Davidson, Alan R.

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 809 KB

english, 2016

24

Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system

Høyland-Kroghsbo, Nina M., Paczkowski, Jon, Mukherjee, Sampriti, Broniewski, Jenny, Westra, Edze, Bondy-Denomy, Joseph, Bassler, Bonnie L.

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 770 KB

english, 2016

25

CRISPR control of virulence in Pseudomonas aeruginosa

Wiedenheft, Blake, Bondy-Denomy, Joseph

Journal:

Year:

2017

Language:

english

File:

PDF, 902 KB

english, 2017

26

Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity

Rollins, MaryClare F., Chowdhury, Saikat, Carter, Joshua, Golden, Sarah M., Wilkinson, Royce A., Bondy-Denomy, Joseph, Lander, Gabriel C., Wiedenheft, Blake

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.26 MB

english, 2017

27

The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs

Borges, Adair L., Davidson, Alan R., Bondy-Denomy, Joseph

Journal:

Annual Review of Virology

Year:

2017

Language:

english

File:

PDF, 1.61 MB

english, 2017

28

Pseudomonas aeruginosa defends against phages through type IV pilus glycosylation

Harvey, Hanjeong, Bondy-Denomy, Joseph, Marquis, Hélène, Sztanko, Kristina M., Davidson, Alan R., Burrows, Lori L.

Journal:

Nature Microbiology

Year:

2017

Language:

english

File:

PDF, 1.77 MB

english, 2017

29

How bacteria control the CRISPR-Cas arsenal

Leon, Lina M, Mendoza, Senén D, Bondy-Denomy, Joseph

Journal:

Current Opinion in Microbiology

Year:

2018

Language:

english

File:

PDF, 662 KB

english, 2018

30

Protein inhibitors of CRISPR-Cas9

Bondy-Denomy, Joseph

Journal:

ACS Chemical Biology

Year:

2017

Language:

english

File:

PDF, 869 KB

english, 2017

31

CRISPR-Cas-Mediated Phage Resistance Enhances Horizontal Gene Transfer by Transduction

Watson, Bridget N. J., Staals, Raymond H. J., Fineran, Peter C., Bondy-Denomy, Joseph, Gilmore, Michael S.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.90 MB

english, 2018

32

Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity

Borges, Adair L., Zhang, Jenny Y., Rollins, MaryClare F., Osuna, Beatriz A., Wiedenheft, Blake, Bondy-Denomy, Joseph

Journal:

Year:

2018

Language:

english

File:

PDF, 3.08 MB

english, 2018

33

Phage morons play important roles in controlling Pseudomonas aeruginosa phenotypes

Tsao, Yu-Fan, Taylor, Véronique L., Kala, Smriti, Bondy-Denomy, Joseph, Khan, Alima N., Bona, Diane, Cattoir, Vincent, Lory, Stephen, Davidson, Alan R., Maxwell, Karen L.

Journal:

Journal of Bacteriology

Year:

2018

Language:

english

File:

PDF, 1.25 MB

english, 2018

34

A Unified Resource for Tracking Anti-CRISPR Names

Bondy-Denomy, Joseph, Davidson, Alan R., Doudna, Jennifer A., Fineran, Peter C., Maxwell, Karen L., Moineau, Sylvain, Peng, Xu, Sontheimer, Eric J., Wiedenheft, Blake

Journal:

The CRISPR Journal

Year:

2018

Language:

english

File:

PDF, 92 KB

english, 2018

35

Temperature-Responsive Competitive Inhibition of CRISPR-Cas9

Jiang, Fuguo, Liu, Jun-Jie, Osuna, Beatriz A., Xu, Michael, Berry, Joel D., Rauch, Benjamin J., Nogales, Eva, Bondy-Denomy, Joseph, Doudna, Jennifer A.

Journal:

Year:

2018

Language:

english

File:

PDF, 3.88 MB

english, 2018

36

Molecular mechanism of azithromycin resistance among typhoidal Salmonella stains in Bangladesh identified through passive pediatric surveillance

Hooda, Yogesh, Sajib, Mohammad S. I., Rahman, Hafizur, Luby, Stephen P., Bondy-Denomy, Joseph, Santosham, Mathuram, Andrews, Jason R., Saha, Samir K., Saha, Senjuti, Azman, Andrew S.

Journal:

PLoS Neglected Tropical Diseases

Year:

2019

Language:

english

File:

PDF, 4.50 MB

english, 2019

37

Molecular mechanism of azithromycin resistance among typhoidal Salmonella stains in Bangladesh identified through passive pediatric surveillance

Hooda, Yogesh, Sajib, Mohammad S. I., Rahman, Hafizur, Luby, Stephen P., Bondy-Denomy, Joseph, Santosham, Mathuram, Andrews, Jason R., Saha, Samir K., Saha, Senjuti, Azman, Andrew S.

Journal:

PLoS Neglected Tropical Diseases

Year:

2019

File:

PDF, 4.50 MB

2019

38

A Type IV-A CRISPR-Cas System in Pseudomonas aeruginosa Mediates RNA-Guided Plasmid Interference In Vivo

Crowley, Valerie M., Catching, Adam, Taylor, Hannah N., Borges, Adair L., Metcalf, Josie, Bondy-Denomy, Joseph, Jackson, Ryan N.

Journal:

The CRISPR Journal

Year:

2019

File:

PDF, 445 KB

2019

39

A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases

Mendoza, Senén D., Nieweglowska, Eliza S., Govindarajan, Sutharsan, Leon, Lina M., Berry, Joel D., Tiwari, Anika, Chaikeeratisak, Vorrapon, Pogliano, Joe, Agard, David A., Bondy-Denomy, Joseph

Journal:

Year:

2019

File:

PDF, 5.78 MB

2019

40

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

Marino, Nicole D., Pinilla-Redondo, Rafael, CsÃ¶rgÅ, BÃ¡lint, Bondy-Denomy, Joseph

Journal:

Year:

2020

Language:

english

File:

PDF, 1.75 MB

english, 2020

41

Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer

Mahendra, Caroline, Christie, Kathleen A., Osuna, Beatriz A., Pinilla-Redondo, Rafael, Kleinstiver, Benjamin P., Bondy-Denomy, Joseph

Journal:

Nature Microbiology

Year:

2020

Language:

english

File:

PDF, 5.97 MB

english, 2020

42

Bacterial alginate regulators and phage homologs repress CRISPRâCas immunity

Borges, Adair L., Castro, Bardo, Govindarajan, Sutharsan, Solvik, Tina, Escalante, Veronica, Bondy-Denomy, Joseph

Journal:

Nature Microbiology

Year:

2020

Language:

english

File:

PDF, 3.35 MB

english, 2020

43

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

Osuna, Beatriz A., Karambelkar, Shweta, Mahendra, Caroline, Sarbach, Anne, Johnson, Matthew C., Kilcher, Samuel, Bondy-Denomy, Joseph

Journal:

Cell Host & Microbe

Year:

2020

File:

PDF, 2.77 MB

2020

44

Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes

Osuna, Beatriz A., Karambelkar, Shweta, Mahendra, Caroline, Christie, Kathleen A., Garcia, Bianca, Davidson, Alan R., Kleinstiver, Benjamin P., Kilcher, Samuel, Bondy-Denomy, Joseph

Journal:

Cell Host & Microbe

Year:

2020

File:

PDF, 3.01 MB

2020

45

Author Correction: Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer

Mahendra, Caroline, Christie, Kathleen A., Osuna, Beatriz A., Pinilla-Redondo, Rafael, Kleinstiver, Benjamin P., Bondy-Denomy, Joseph

Journal:

Nature Microbiology

Year:

2020

File:

PDF, 547 KB

2020

46

Intracellular Organization by Jumbo Bacteriophages

Guan, Jingwen, Bondy-Denomy, Joseph

Journal:

Journal of Bacteriology

Year:

2020

File:

PDF, 1.09 MB

2020

47

A compact CascadeâCas3 system for targeted genome engineering

CsÃ¶rgÅ, BÃ¡lint, LeÃ³n, Lina M., Chau-Ly, Ilea J., Vasquez-Rifo, Alejandro, Berry, Joel D., Mahendra, Caroline, Crawford, Emily D., Lewis, Jennifer D., Bondy-Denomy, Joseph

Journal:

Year:

2020

File:

PDF, 5.77 MB

2020

48

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

Pinilla-Redondo, Rafael, Shehreen, Saadlee, Marino, Nicole D., Fagerlund, Robert D., Brown, Chris M., SÃ¸rensen, SÃ¸ren J., Fineran, Peter C., Bondy-Denomy, Joseph

Journal:

Nature Communications

Year:

2020

File:

PDF, 1.03 MB

2020