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Published Works
Rapid protein evolution by few-shot learning with a protein language model | Science | Kaiyi Jiang, Zhaoqing Yan, Matteo Di Bernardo, Samantha R. Sgrizzi, Lukas Villiger, Alisan Kayabolen, Byungji Kim, Josephine K. Carscadden, Masahiro Hiraizumi, Hiroshi Nishimasu, Jonathan S. Gootenberg, Omar O. Abudayyeh | 21/11/2024 | |
Programmable RNA writing with trans-splicing | bioRxiv | Schmitt-Ulms, C., Kayabolen, A., Manero-Carranza, M., Zhou, N., Donnelly, K., Nuccio, S.P., Kato, K., Nishimasu, H., Gootenberg, J.S.#, and Abudayyeh, O.O.# | 01/02/2024 | |
Advances in genome, epigenome, and transcriptome editing using CRISPR effectors, | Nature Reviews Molecular Cell Biology | Villiger, L., Joung, J., Koblan, L., Weissman, J.S., Abudayyeh, O.O.#, and Gootenberg, J.S.#. | 01/11/2023 | |
Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses | Science Advances | Jiang, K., Lim, J., Sgrizzi, S., Trinh, M., Kayabolen, A., Yutin, N., Koonin, E.V., Gootenberg, J.S.# Abudayyeh, O.O.# | 27/09/2023 | |
A Transcription Factor Atlas of Directed Differentiation | Cell | Joung, J., Ma, S., Tay, T., Geiger-Schuller, K.R., Kirchgatterer, P.C., Verdine, V.K., Guo, B., Arias-Garcia, M.A., Allen, W.E., Singh, A., Kuksenko, O., Abudayyeh, O.O., Gootenberg, J.S., Fu, Z., Macrae, R.K., Buenrostro, J.D., Regev, A., and Zhang, F. | 05/01/2023 | |
Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases. | Nature Biotechnology | Yarnall, Matthew T. N., Ioannidi, Eleonora I., Schmitt-Ulms, Cian, Krajeski, Rohan N., Lim, Justin, Villiger, Lukas, Zhou, Wenyuan, Jiang, Kaiyi, Roberts, Nathaniel, Zhang, Liyang, Vakulskas, Christopher A., Walker, John A., Kadina, Anastasia P., Zepeda, Adrianna E., Holden, Kevin, Abudayyeh, Omar O., Gootenberg, Jonathan S. | 24/11/2022 | |
A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance | The CRISPR Journal | Patchsung, Maturada, Homchan, Aimorn, Aphicho, Kanokpol, Suraritdechachai, Surased, Wanitchanon, Thanyapat, Pattama, Archiraya, Sappakhaw, Khomkrit, Meesawat, Piyachat, Wongsatit, Thanakrit, Athipanyasilp, Artittaya, Jantarug, Krittapas, Athipanyasilp, Niracha, Buahom, Juthamas, Visanpattanasin, Supapat, Niljianskul, Nootaree, Chaiyen, Pimchai, Tinikul, Ruchanok, Wichukchinda, Nuanjun, Mahasirimongkol, Surakameth, Sirijatuphat, Rujipas, Angkasekwinai, Nasikarn, Crone, Michael A, Freemont, Paul S, Joung, Julia, Ladha, Alim, Abudayyeh, Omar, Gootenberg, Jonathan, Zhang, Feng, Chewapreecha, Claire, Chanarat, Sittinan, Horthongkham, Navin, Pakotiprapha, Danaya, Uttamapinant, Chayasith. | 11/11/2022 | |
RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex | Science | Kato, K., Okazaki, S., Schmitt-Ulms, C., Jiang, K., Zhou, W., Ishikawa, J., Isayama, Y., Adachi, S., Nishizawa, T., Makarova, K.S., Koonin, E.V., Abudayyeh, O.O.#, Gootenberg, J.S.#, Nishamasu, H. | 03/11/2022 | |
RNA-activated protein cleavage with a CRISPR-associated endopeptidase | Science | Strecker J., Demircioglu, F.E., Li, D., Faure, G., Wilkinson, M.E., Gootenberg, J.S., Abudayyeh, O., Nishimasu, H., Macrae, R.K., and Zhang, F. | 03/11/2022 | |
Programmable eukaryotic protein expression with RNA sensors | Nature Biotechnology | Jiang K,Koob J,Chen XD,Krajeski RN,Zhang Y,Villiger L,Zhou W, Gootenberg JS, Chen F, Abudayyeh OO | 27/10/2022 | |
Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex | Cell | Kato, K., Zhou, W., Okazaki, S., Isayama, Y., Nishizawa, T., Gootenberg, J.S.#, Abudayyeh, O.O.#, Nishamasu, H. | 23/06/2022 | |
Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases | bioRxiv | Yarnall, Matthew T. N., Ioannidi, Eleonora I., Schmitt-Ulms, Cian, Krajeski, Rohan N., Lim, Justin, Villiger, Lukas, Zhou, Wenyuan, Jiang, Kaiyi, Roberts, Nathaniel, Zhang, Liyang, Vakulskas, Christopher A., Walker, John A., Kadina, Anastasia P., Zepeda, Adrianna E., Holden, Kevin, Abudayyeh, Omar O., Gootenberg, Jonathan S | 01/11/2021 | |
Programmable RNA targeting with the single-protein CRISPR effector Cas7-11 | Nature | Ozcan A,Krajeski R,Ioannidi E,Lee B,Gardner A,Makarova KS,Koonin EV,Abudayyeh OO,Gootenberg JS | 06/09/2021 | |
CRISPR-based diagnostics | Nat Biomed Eng | Kaminski MM,Abudayyeh OO,Gootenberg JS,Zhang F,Collins JJ | 30/06/2021 | |
A global metagenomic map of urban microbiomes and antimicrobial resistance | Cell | Danko D,Bezdan D,Afshin EE,Ahsanuddin S,Bhattacharya C,Butler DJ,Chng KR,Donnellan D,Hecht J,Jackson K,Kuchin K,Karasikov M,Lyons A,Mak L,Meleshko D,Mustafa H,Mutai B,Neches RY,Ng A,Nikolayeva O,Nikolayeva T,Png E,Ryon KA,Sanchez JL,Shaaban H,Sierra MA,Thomas D,Young B,Abudayyeh OO,Alicea J,Bhattacharyya M,Blekhman R,Castro-Nallar E,Cañas AM,Chatziefthimiou AD,Crawford RW,De Filippis F,Deng Y,Desnues C,Dias-Neto E,Dybwad M,Elhaik E,Ercolini D,Frolova A,Gankin D,Gootenberg JS,Graf AB,Green DC,Hajirasouliha I,Hastings JJA,Hernandez M,Iraola G,Jang S,Kahles A,Kelly FJ,Knights K,Kyrpides NC,Łabaj PP,Lee PKH,Leung MHY,Ljungdahl PO,Mason-Buck G,McGrath K,Meydan C,Mongodin EF,Moraes MO,Nagarajan N,Nieto-Caballero M,Noushmehr H,Oliveira M,Ossowski S,Osuolale OO,Özcan O,Paez-Espino D,Rascovan N,Richard H,Rätsch G,Schriml LM,Semmler T,Sezerman OU,Shi L,Shi T,Siam R,Song LH,Suzuki H,Court DS,Tighe SW,Tong X,Udekwu KI,Ugalde JA,Valentine B,Vassilev DI,Vayndorf EM,Velavan TP,Wu J,Zambrano MM,Zhu J,Zhu S,Mason CE,International MetaSUB Consortium | 24/06/2021 | |
CRISPR diagnostics | Science | Abudayyeh OO,Gootenberg JS | 28/05/2021 | |
Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay | PLoS One | Schermer B,Fabretti F,Damagnez M,Di Cristanziano V,Heger E,Arjune S,Tanner NA,Imhof T,Koch M,Ladha A,Joung J,Gootenberg JS,Abudayyeh OO,Burst V,Zhang F,Klein F,Benzing T,Müller RU | 02/11/2020 | |
Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing | N. Engl. J. Med. | Joung J,Ladha A,Saito M,Kim NG,Woolley AE,Segel M,Barretto RP,Ranu A,Macrae RK,Faure G, Ioannidi EI, Krajeski Rn, Bruneau R, Huang M, Yu XG, Li JZ, Walker BD, Hung DT, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. | 08/10/2020 | |
A Survey of Genome Editing Activity for 16 Cas12a Orthologs | Keio J. Med. | Zetsche B,Abudayyeh OO,Gootenberg JS,Scott DA,Zhang F | 25/09/2020 | |
Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA | Nat Biomed Eng | Patchsung M,Jantarug K,Pattama A,Aphicho K,Suraritdechachai S,Meesawat P,Sappakhaw K,Leelahakorn N,Ruenkam T,Wongsatit T,Athipanyasilp N,Eiamthong B,Lakkanasirorat B,Phoodokmai T,Niljianskul N,Pakotiprapha D,Chanarat S,Homchan A,Tinikul R,Kamutira P,Phiwkaow K,Soithongcharoen S,Kantiwiriyawanitch C,Pongsupasa V,Trisrivirat D,Jaroensuk J,Wongnate T,Maenpuen S,Chaiyen P,Kamnerdnakta S,Swangsri J,Chuthapisith S,Sirivatanauksorn Y,Chaimayo C,Sutthent R,Kantakamalakul W,Joung J,Ladha A,Jin X,Gootenberg JS,Abudayyeh OO,Zhang F,Horthongkham N,Uttamapinant C | 26/08/2020 | |
Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK | Mol. Ecol. Resour. | Baerwald MR,Goodbla AM,Nagarajan RP,Gootenberg JS,Abudayyeh OO,Zhang F,Schreier AD | 30/06/2020 | |
A 5-min RNA preparation method for COVID-19 detection with RT-qPCR | medRxiv | Ladha A,Joung J,Abudayyeh OO,Gootenberg JS,Zhang F | 08/05/2020 | |
A Protocol for Detection of COVID-19 Using CRISPR Diagnostics | White paper | Zhang F,Abudayyeh OO,Gootenberg JS | 31/01/2020 | |
Programmable Inhibition and Detection of RNA Viruses Using Cas13 | Mol. Cell | Freije CA,Myhrvold C,Boehm CK,Lin AE,Welch NL,Carter A,Metsky HC,Luo CY,Abudayyeh OO,Gootenberg JS,Yozwiak NL,Zhang F,Sabeti PC | 05/12/2019 | |
SHERLOCK: nucleic acid detection with CRISPR nucleases | Nat. Protoc. | Kellner MJ,Koob JG,Gootenberg JS,Abudayyeh OO,Zhang F | 23/09/2019 | |
A cytosine deaminase for programmable single-base RNA editing | Science | Abudayyeh OO,Gootenberg JS,Franklin B,Koob J,Kellner MJ,Ladha A,Joung J,Kirchgatterer P,Cox DBT,Zhang F | 11/07/2019 | |
Nucleic Acid Detection of Plant Genes Using CRISPR-Cas13 | CRISPR J | Abudayyeh OO,Gootenberg JS,Kellner MJ,Zhang F | 31/05/2019 | |
Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9 | Nat. Commun. | Hirano S,Abudayyeh OO,Gootenberg JS,Horii T,Ishitani R,Hatada I,Zhang F,Nishimasu H,Nureki O | 29/04/2019 | |
Chipping in on Diagnostics | CRISPR J | Abudayyeh OO,Gootenberg JS | 31/03/2019 | |
High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage | Cell Rep. | Slaymaker IM,Mesa P,Kellner MJ,Kannan S,Brignole E,Koob J,Feliciano PR,Stella S,Abudayyeh OO,Gootenberg JS,Strecker J,Montoya G,Zhang F | 26/03/2019 | |
Engineered CRISPR-Cas9 nuclease with expanded targeting space | Science | Nishimasu H,Shi X,Ishiguro S,Gao L,Hirano S,Okazaki S,Noda T,Abudayyeh OO,Gootenberg JS,Mori H,Oura S,Holmes B,Tanaka M,Seki M,Hirano H,Aburatani H,Ishitani R,Ikawa M,Yachie N,Zhang F,Nureki O | 21/09/2018 | |
Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells | Nat. Commun. | Tycko J,Barrera LA,Huston NC,Friedland AE,Wu X,Gootenberg JS,Abudayyeh OO,Myer VE,Wilson CJ,Hsu PD | 27/07/2018 | |
Field-deployable viral diagnostics using CRISPR-Cas13 | Science | Myhrvold C,Freije CA,Gootenberg JS,Abudayyeh OO,Metsky HC,Durbin AF,Kellner MJ,Tan AL,Paul LM,Parham LA,Garcia KF,Barnes KG,Chak B,Mondini A,Nogueira ML,Isern S,Michael SF,Lorenzana I,Yozwiak NL,MacInnis BL,Bosch I,Gehrke L,Zhang F,Sabeti PC | 27/04/2018 | |
Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6 | Science | Gootenberg JS,Abudayyeh OO,Kellner MJ,Joung J,Collins JJ,Zhang F | 27/04/2018 | |
RNA editing with CRISPR-Cas13 | Science | Cox DBT,Gootenberg JS,Abudayyeh OO,Franklin B,Kellner MJ,Joung J,Zhang F | 24/11/2017 | |
RNA targeting with CRISPR–Cas13 | Nature | Abudayyeh OO,Gootenberg JS,Essletzbichler P,Han S,Joung J,Belanto JJ,Verdine V,Cox DB,Kellner MJ,Regev A,Lander ES,Voytas DF,Ting AY,Zhang F | 04/10/2017 | |
Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States | Cell Systems | Kim JW,Abudayyeh OO,Yeerna H,Yeang CH,Stewart M,Jenkins RW,Kitajima S,Konieczkowski DJ,Medetgul-Ernar K,Cavazos T,Mah C,Ting S,Van Allen EM,Cohen O,Mcdermott J,Damato E,Aguirre AJ,Liang J,Liberzon A,Alexe G,Doench J,Ghandi M,Vazquez F,Weir BA,Tsherniak A,Subramanian A,Meneses-Cime K,Park J,Clemons P,Garraway LA,Thomas D,Boehm JS,Barbie DA,Hahn WC,Mesirov JP,Tamayo P | 23/08/2017 | |
Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood | Nature | Joung J,Engreitz JM,Konermann S,Abudayyeh OO,Verdine VK,Aguet F,Gootenberg JS,Sanjana NE,Wright JB,Fulco CP,Tseng YY,Yoon CH,Boehm JS,Lander ES,Zhang F | 17/08/2017 | |
Nucleic acid detection with CRISPR-Cas13a/C2c2 | Science | Gootenberg JS,Abudayyeh OO,Lee JW,Essletzbichler P,Dy AJ,Joung J,Verdine V,Donghia N,Daringer NM,Freije CA,Myhrvold C,Bhattacharyya RP,Livny J,Regev A,Koonin EV,Hung DT,Sabeti PC,Collins JJ,Zhang F | 13/04/2017 | |
Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening | Nat. Protoc. | Joung J,Konermann S,Gootenberg JS,Abudayyeh OO,Platt RJ,Brigham MD,Sanjana NE,Zhang F | 31/03/2017 | |
Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems | Mol. Cell | Yamada M,Watanabe Y,Gootenberg JS,Hirano H,Ran FA,Nakane T,Ishitani R,Zhang F,Nishimasu H,Nureki O | 16/03/2017 | |
Diversity and evolution of class 2 CRISPR-Cas systems | Nat. Rev. Microbiol. | Shmakov S,Smargon A,Scott D,Cox D,Pyzocha N,Yan W,Abudayyeh OO,Gootenberg JS,Makarova KS,Wolf YI,Severinov K,Zhang F,Koonin EV | 28/02/2017 | |
Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28 | Mol. Cell | Smargon AA,Cox DB,Pyzocha NK,Zheng K,Slaymaker IM,Gootenberg JS,Abudayyeh OA,Essletzbichler P,Shmakov S,Makarova KS,Koonin EV,Zhang F | 16/02/2017 | |
Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array | Nature | Zetsche B,Heidenreich M,Mohanraju P,et al. | 05/12/2016 | |
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector | Science | Abudayyeh OO,Gootenberg JS,Konermann S,Joung J,Slaymaker IM,Cox DB,Shmakov S,Makarova KS,Semenova E,Minakhin L,Severinov K,Regev A,Lander ES,Koonin EV,Zhang F | 05/08/2016 | |
Characterizing genomic alterations in cancer by complementary functional associations | Nat. Biotechnol. | Kim JW,Botvinnik OB,Abudayyeh O,Birger C,Rosenbluh J,Shrestha Y,Abazeed ME,Hammerman PS,DiCara D,Konieczkowski DJ,Johannessen CM,Liberzon A,Alizad-Rahvar AR,Alexe G,Aguirre A,Ghandi M,Greulich H,Vazquez F,Weir BA,Van Allen EM,Tsherniak A,Shao DD,Zack TI,Noble M,Getz G,Beroukhim R,Garraway LA,Ardakani M,Romualdi C,Sales G,Barbie DA,Boehm JS,Hahn WC,Mesirov JP,Tamayo P | 30/04/2016 | |
Structure and Engineering of Francisella novicida Cas9 | Cell | Hirano H,Gootenberg JS,Horii T,Abudayyeh OO,Kimura M,Hsu PD,Nakane T,Ishitani R,Hatada I,Zhang F,Nishimasu H,Nureki O | 25/02/2016 | |
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems | Mol. Cell | Shmakov S,Abudayyeh OO,Makarova KS,Wolf YI,Gootenberg JS,Semenova E,Minakhin L,Joung J,Konermann S,Severinov K,Zhang F,Koonin EV | 05/11/2015 | |
Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease | Nat. Biotechnol. | Dahlman JE,Abudayyeh OO,Joung J,Gootenberg JS,Zhang F,Konermann S | 31/10/2015 | |
Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system | Cell | Zetsche B,Gootenberg JS,Abudayyeh OO,Slaymaker IM,Makarova KS,Essletzbichler P,Volz SE,Joung J,van der Oost J,Regev A,Koonin EV,Zhang F | 22/10/2015 | |
In vivo genome editing using Staphylococcus aureus Cas9 | Nature | Ran FA,Cong L,Yan WX,Scott DA,Gootenberg JS,Kriz AJ,Zetsche B,Shalem O,Wu X,Makarova KS,Koonin EV,Sharp PA,Zhang F | 09/04/2015 | |
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex | Nature | Konermann S,Brigham MD,Trevino AE,Joung J,Abudayyeh OO,Barcena C,Hsu PD,Habib N,Gootenberg JS,Nishimasu H,Nureki O,Zhang F | 29/01/2015 | |
A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors | Cancer Discov. | Konieczkowski DJ,Johannessen CM,Abudayyeh O,Kim JW,Cooper ZA,Piris A,Frederick DT,Barzily-Rokni M,Straussman R,Haq R,Fisher DE,Mesirov JP,Hahn WC,Flaherty KT,Wargo JA,Tamayo P,Garraway LA | 30/06/2014 | |
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity | Cell | Ran FA,Hsu PD,Lin CY,Gootenberg JS,Konermann S,Trevino AE,Scott DA,Inoue A,Matoba S,Zhang Y,Zhang F | 12/09/2013 |
Title | Journal | Authors | Date | |
|---|---|---|---|---|
Rapid protein evolution by few-shot learning with a protein language model | Science | Kaiyi Jiang, Zhaoqing Yan, Matteo Di Bernardo, Samantha R. Sgrizzi, Lukas Villiger, Alisan Kayabolen, Byungji Kim, Josephine K. Carscadden, Masahiro Hiraizumi, Hiroshi Nishimasu, Jonathan S. Gootenberg, Omar O. Abudayyeh | 21/11/2024 | |
Programmable RNA writing with trans-splicing | bioRxiv | Schmitt-Ulms, C., Kayabolen, A., Manero-Carranza, M., Zhou, N., Donnelly, K., Nuccio, S.P., Kato, K., Nishimasu, H., Gootenberg, J.S.#, and Abudayyeh, O.O.# | 01/02/2024 | |
Advances in genome, epigenome, and transcriptome editing using CRISPR effectors, | Nature Reviews Molecular Cell Biology | Villiger, L., Joung, J., Koblan, L., Weissman, J.S., Abudayyeh, O.O.#, and Gootenberg, J.S.#. | 01/11/2023 | |
Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses | Science Advances | Jiang, K., Lim, J., Sgrizzi, S., Trinh, M., Kayabolen, A., Yutin, N., Koonin, E.V., Gootenberg, J.S.# Abudayyeh, O.O.# | 27/09/2023 | |
A Transcription Factor Atlas of Directed Differentiation | Cell | Joung, J., Ma, S., Tay, T., Geiger-Schuller, K.R., Kirchgatterer, P.C., Verdine, V.K., Guo, B., Arias-Garcia, M.A., Allen, W.E., Singh, A., Kuksenko, O., Abudayyeh, O.O., Gootenberg, J.S., Fu, Z., Macrae, R.K., Buenrostro, J.D., Regev, A., and Zhang, F. | 05/01/2023 | |
Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases. | Nature Biotechnology | Yarnall, Matthew T. N., Ioannidi, Eleonora I., Schmitt-Ulms, Cian, Krajeski, Rohan N., Lim, Justin, Villiger, Lukas, Zhou, Wenyuan, Jiang, Kaiyi, Roberts, Nathaniel, Zhang, Liyang, Vakulskas, Christopher A., Walker, John A., Kadina, Anastasia P., Zepeda, Adrianna E., Holden, Kevin, Abudayyeh, Omar O., Gootenberg, Jonathan S. | 24/11/2022 | |
A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance | The CRISPR Journal | Patchsung, Maturada, Homchan, Aimorn, Aphicho, Kanokpol, Suraritdechachai, Surased, Wanitchanon, Thanyapat, Pattama, Archiraya, Sappakhaw, Khomkrit, Meesawat, Piyachat, Wongsatit, Thanakrit, Athipanyasilp, Artittaya, Jantarug, Krittapas, Athipanyasilp, Niracha, Buahom, Juthamas, Visanpattanasin, Supapat, Niljianskul, Nootaree, Chaiyen, Pimchai, Tinikul, Ruchanok, Wichukchinda, Nuanjun, Mahasirimongkol, Surakameth, Sirijatuphat, Rujipas, Angkasekwinai, Nasikarn, Crone, Michael A, Freemont, Paul S, Joung, Julia, Ladha, Alim, Abudayyeh, Omar, Gootenberg, Jonathan, Zhang, Feng, Chewapreecha, Claire, Chanarat, Sittinan, Horthongkham, Navin, Pakotiprapha, Danaya, Uttamapinant, Chayasith. | 11/11/2022 | |
RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex | Science | Kato, K., Okazaki, S., Schmitt-Ulms, C., Jiang, K., Zhou, W., Ishikawa, J., Isayama, Y., Adachi, S., Nishizawa, T., Makarova, K.S., Koonin, E.V., Abudayyeh, O.O.#, Gootenberg, J.S.#, Nishamasu, H. | 03/11/2022 | |
RNA-activated protein cleavage with a CRISPR-associated endopeptidase | Science | Strecker J., Demircioglu, F.E., Li, D., Faure, G., Wilkinson, M.E., Gootenberg, J.S., Abudayyeh, O., Nishimasu, H., Macrae, R.K., and Zhang, F. | 03/11/2022 | |
Programmable eukaryotic protein expression with RNA sensors | Nature Biotechnology | Jiang K,Koob J,Chen XD,Krajeski RN,Zhang Y,Villiger L,Zhou W, Gootenberg JS, Chen F, Abudayyeh OO | 27/10/2022 | |
Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex | Cell | Kato, K., Zhou, W., Okazaki, S., Isayama, Y., Nishizawa, T., Gootenberg, J.S.#, Abudayyeh, O.O.#, Nishamasu, H. | 23/06/2022 | |
Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases | bioRxiv | Yarnall, Matthew T. N., Ioannidi, Eleonora I., Schmitt-Ulms, Cian, Krajeski, Rohan N., Lim, Justin, Villiger, Lukas, Zhou, Wenyuan, Jiang, Kaiyi, Roberts, Nathaniel, Zhang, Liyang, Vakulskas, Christopher A., Walker, John A., Kadina, Anastasia P., Zepeda, Adrianna E., Holden, Kevin, Abudayyeh, Omar O., Gootenberg, Jonathan S | 01/11/2021 | |
Programmable RNA targeting with the single-protein CRISPR effector Cas7-11 | Nature | Ozcan A,Krajeski R,Ioannidi E,Lee B,Gardner A,Makarova KS,Koonin EV,Abudayyeh OO,Gootenberg JS | 06/09/2021 | |
CRISPR-based diagnostics | Nat Biomed Eng | Kaminski MM,Abudayyeh OO,Gootenberg JS,Zhang F,Collins JJ | 30/06/2021 | |
A global metagenomic map of urban microbiomes and antimicrobial resistance | Cell | Danko D,Bezdan D,Afshin EE,Ahsanuddin S,Bhattacharya C,Butler DJ,Chng KR,Donnellan D,Hecht J,Jackson K,Kuchin K,Karasikov M,Lyons A,Mak L,Meleshko D,Mustafa H,Mutai B,Neches RY,Ng A,Nikolayeva O,Nikolayeva T,Png E,Ryon KA,Sanchez JL,Shaaban H,Sierra MA,Thomas D,Young B,Abudayyeh OO,Alicea J,Bhattacharyya M,Blekhman R,Castro-Nallar E,Cañas AM,Chatziefthimiou AD,Crawford RW,De Filippis F,Deng Y,Desnues C,Dias-Neto E,Dybwad M,Elhaik E,Ercolini D,Frolova A,Gankin D,Gootenberg JS,Graf AB,Green DC,Hajirasouliha I,Hastings JJA,Hernandez M,Iraola G,Jang S,Kahles A,Kelly FJ,Knights K,Kyrpides NC,Łabaj PP,Lee PKH,Leung MHY,Ljungdahl PO,Mason-Buck G,McGrath K,Meydan C,Mongodin EF,Moraes MO,Nagarajan N,Nieto-Caballero M,Noushmehr H,Oliveira M,Ossowski S,Osuolale OO,Özcan O,Paez-Espino D,Rascovan N,Richard H,Rätsch G,Schriml LM,Semmler T,Sezerman OU,Shi L,Shi T,Siam R,Song LH,Suzuki H,Court DS,Tighe SW,Tong X,Udekwu KI,Ugalde JA,Valentine B,Vassilev DI,Vayndorf EM,Velavan TP,Wu J,Zambrano MM,Zhu J,Zhu S,Mason CE,International MetaSUB Consortium | 24/06/2021 | |
CRISPR diagnostics | Science | Abudayyeh OO,Gootenberg JS | 28/05/2021 | |
Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay | PLoS One | Schermer B,Fabretti F,Damagnez M,Di Cristanziano V,Heger E,Arjune S,Tanner NA,Imhof T,Koch M,Ladha A,Joung J,Gootenberg JS,Abudayyeh OO,Burst V,Zhang F,Klein F,Benzing T,Müller RU | 02/11/2020 | |
Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing | N. Engl. J. Med. | Joung J,Ladha A,Saito M,Kim NG,Woolley AE,Segel M,Barretto RP,Ranu A,Macrae RK,Faure G, Ioannidi EI, Krajeski Rn, Bruneau R, Huang M, Yu XG, Li JZ, Walker BD, Hung DT, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. | 08/10/2020 | |
A Survey of Genome Editing Activity for 16 Cas12a Orthologs | Keio J. Med. | Zetsche B,Abudayyeh OO,Gootenberg JS,Scott DA,Zhang F | 25/09/2020 | |
Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA | Nat Biomed Eng | Patchsung M,Jantarug K,Pattama A,Aphicho K,Suraritdechachai S,Meesawat P,Sappakhaw K,Leelahakorn N,Ruenkam T,Wongsatit T,Athipanyasilp N,Eiamthong B,Lakkanasirorat B,Phoodokmai T,Niljianskul N,Pakotiprapha D,Chanarat S,Homchan A,Tinikul R,Kamutira P,Phiwkaow K,Soithongcharoen S,Kantiwiriyawanitch C,Pongsupasa V,Trisrivirat D,Jaroensuk J,Wongnate T,Maenpuen S,Chaiyen P,Kamnerdnakta S,Swangsri J,Chuthapisith S,Sirivatanauksorn Y,Chaimayo C,Sutthent R,Kantakamalakul W,Joung J,Ladha A,Jin X,Gootenberg JS,Abudayyeh OO,Zhang F,Horthongkham N,Uttamapinant C | 26/08/2020 | |
Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK | Mol. Ecol. Resour. | Baerwald MR,Goodbla AM,Nagarajan RP,Gootenberg JS,Abudayyeh OO,Zhang F,Schreier AD | 30/06/2020 | |
A 5-min RNA preparation method for COVID-19 detection with RT-qPCR | medRxiv | Ladha A,Joung J,Abudayyeh OO,Gootenberg JS,Zhang F | 08/05/2020 | |
A Protocol for Detection of COVID-19 Using CRISPR Diagnostics | White paper | Zhang F,Abudayyeh OO,Gootenberg JS | 31/01/2020 | |
Programmable Inhibition and Detection of RNA Viruses Using Cas13 | Mol. Cell | Freije CA,Myhrvold C,Boehm CK,Lin AE,Welch NL,Carter A,Metsky HC,Luo CY,Abudayyeh OO,Gootenberg JS,Yozwiak NL,Zhang F,Sabeti PC | 05/12/2019 | |
SHERLOCK: nucleic acid detection with CRISPR nucleases | Nat. Protoc. | Kellner MJ,Koob JG,Gootenberg JS,Abudayyeh OO,Zhang F | 23/09/2019 | |
A cytosine deaminase for programmable single-base RNA editing | Science | Abudayyeh OO,Gootenberg JS,Franklin B,Koob J,Kellner MJ,Ladha A,Joung J,Kirchgatterer P,Cox DBT,Zhang F | 11/07/2019 | |
Nucleic Acid Detection of Plant Genes Using CRISPR-Cas13 | CRISPR J | Abudayyeh OO,Gootenberg JS,Kellner MJ,Zhang F | 31/05/2019 | |
Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9 | Nat. Commun. | Hirano S,Abudayyeh OO,Gootenberg JS,Horii T,Ishitani R,Hatada I,Zhang F,Nishimasu H,Nureki O | 29/04/2019 | |
Chipping in on Diagnostics | CRISPR J | Abudayyeh OO,Gootenberg JS | 31/03/2019 | |
High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage | Cell Rep. | Slaymaker IM,Mesa P,Kellner MJ,Kannan S,Brignole E,Koob J,Feliciano PR,Stella S,Abudayyeh OO,Gootenberg JS,Strecker J,Montoya G,Zhang F | 26/03/2019 | |
Engineered CRISPR-Cas9 nuclease with expanded targeting space | Science | Nishimasu H,Shi X,Ishiguro S,Gao L,Hirano S,Okazaki S,Noda T,Abudayyeh OO,Gootenberg JS,Mori H,Oura S,Holmes B,Tanaka M,Seki M,Hirano H,Aburatani H,Ishitani R,Ikawa M,Yachie N,Zhang F,Nureki O | 21/09/2018 | |
Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells | Nat. Commun. | Tycko J,Barrera LA,Huston NC,Friedland AE,Wu X,Gootenberg JS,Abudayyeh OO,Myer VE,Wilson CJ,Hsu PD | 27/07/2018 | |
Field-deployable viral diagnostics using CRISPR-Cas13 | Science | Myhrvold C,Freije CA,Gootenberg JS,Abudayyeh OO,Metsky HC,Durbin AF,Kellner MJ,Tan AL,Paul LM,Parham LA,Garcia KF,Barnes KG,Chak B,Mondini A,Nogueira ML,Isern S,Michael SF,Lorenzana I,Yozwiak NL,MacInnis BL,Bosch I,Gehrke L,Zhang F,Sabeti PC | 27/04/2018 | |
Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6 | Science | Gootenberg JS,Abudayyeh OO,Kellner MJ,Joung J,Collins JJ,Zhang F | 27/04/2018 | |
RNA editing with CRISPR-Cas13 | Science | Cox DBT,Gootenberg JS,Abudayyeh OO,Franklin B,Kellner MJ,Joung J,Zhang F | 24/11/2017 | |
RNA targeting with CRISPR–Cas13 | Nature | Abudayyeh OO,Gootenberg JS,Essletzbichler P,Han S,Joung J,Belanto JJ,Verdine V,Cox DB,Kellner MJ,Regev A,Lander ES,Voytas DF,Ting AY,Zhang F | 04/10/2017 | |
Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States | Cell Systems | Kim JW,Abudayyeh OO,Yeerna H,Yeang CH,Stewart M,Jenkins RW,Kitajima S,Konieczkowski DJ,Medetgul-Ernar K,Cavazos T,Mah C,Ting S,Van Allen EM,Cohen O,Mcdermott J,Damato E,Aguirre AJ,Liang J,Liberzon A,Alexe G,Doench J,Ghandi M,Vazquez F,Weir BA,Tsherniak A,Subramanian A,Meneses-Cime K,Park J,Clemons P,Garraway LA,Thomas D,Boehm JS,Barbie DA,Hahn WC,Mesirov JP,Tamayo P | 23/08/2017 | |
Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood | Nature | Joung J,Engreitz JM,Konermann S,Abudayyeh OO,Verdine VK,Aguet F,Gootenberg JS,Sanjana NE,Wright JB,Fulco CP,Tseng YY,Yoon CH,Boehm JS,Lander ES,Zhang F | 17/08/2017 | |
Nucleic acid detection with CRISPR-Cas13a/C2c2 | Science | Gootenberg JS,Abudayyeh OO,Lee JW,Essletzbichler P,Dy AJ,Joung J,Verdine V,Donghia N,Daringer NM,Freije CA,Myhrvold C,Bhattacharyya RP,Livny J,Regev A,Koonin EV,Hung DT,Sabeti PC,Collins JJ,Zhang F | 13/04/2017 | |
Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening | Nat. Protoc. | Joung J,Konermann S,Gootenberg JS,Abudayyeh OO,Platt RJ,Brigham MD,Sanjana NE,Zhang F | 31/03/2017 | |
Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems | Mol. Cell | Yamada M,Watanabe Y,Gootenberg JS,Hirano H,Ran FA,Nakane T,Ishitani R,Zhang F,Nishimasu H,Nureki O | 16/03/2017 | |
Diversity and evolution of class 2 CRISPR-Cas systems | Nat. Rev. Microbiol. | Shmakov S,Smargon A,Scott D,Cox D,Pyzocha N,Yan W,Abudayyeh OO,Gootenberg JS,Makarova KS,Wolf YI,Severinov K,Zhang F,Koonin EV | 28/02/2017 | |
Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28 | Mol. Cell | Smargon AA,Cox DB,Pyzocha NK,Zheng K,Slaymaker IM,Gootenberg JS,Abudayyeh OA,Essletzbichler P,Shmakov S,Makarova KS,Koonin EV,Zhang F | 16/02/2017 | |
Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array | Nature | Zetsche B,Heidenreich M,Mohanraju P,et al. | 05/12/2016 | |
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector | Science | Abudayyeh OO,Gootenberg JS,Konermann S,Joung J,Slaymaker IM,Cox DB,Shmakov S,Makarova KS,Semenova E,Minakhin L,Severinov K,Regev A,Lander ES,Koonin EV,Zhang F | 05/08/2016 | |
Characterizing genomic alterations in cancer by complementary functional associations | Nat. Biotechnol. | Kim JW,Botvinnik OB,Abudayyeh O,Birger C,Rosenbluh J,Shrestha Y,Abazeed ME,Hammerman PS,DiCara D,Konieczkowski DJ,Johannessen CM,Liberzon A,Alizad-Rahvar AR,Alexe G,Aguirre A,Ghandi M,Greulich H,Vazquez F,Weir BA,Van Allen EM,Tsherniak A,Shao DD,Zack TI,Noble M,Getz G,Beroukhim R,Garraway LA,Ardakani M,Romualdi C,Sales G,Barbie DA,Boehm JS,Hahn WC,Mesirov JP,Tamayo P | 30/04/2016 | |
Structure and Engineering of Francisella novicida Cas9 | Cell | Hirano H,Gootenberg JS,Horii T,Abudayyeh OO,Kimura M,Hsu PD,Nakane T,Ishitani R,Hatada I,Zhang F,Nishimasu H,Nureki O | 25/02/2016 | |
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems | Mol. Cell | Shmakov S,Abudayyeh OO,Makarova KS,Wolf YI,Gootenberg JS,Semenova E,Minakhin L,Joung J,Konermann S,Severinov K,Zhang F,Koonin EV | 05/11/2015 | |
Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease | Nat. Biotechnol. | Dahlman JE,Abudayyeh OO,Joung J,Gootenberg JS,Zhang F,Konermann S | 31/10/2015 | |
Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system | Cell | Zetsche B,Gootenberg JS,Abudayyeh OO,Slaymaker IM,Makarova KS,Essletzbichler P,Volz SE,Joung J,van der Oost J,Regev A,Koonin EV,Zhang F | 22/10/2015 | |
In vivo genome editing using Staphylococcus aureus Cas9 | Nature | Ran FA,Cong L,Yan WX,Scott DA,Gootenberg JS,Kriz AJ,Zetsche B,Shalem O,Wu X,Makarova KS,Koonin EV,Sharp PA,Zhang F | 09/04/2015 | |
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex | Nature | Konermann S,Brigham MD,Trevino AE,Joung J,Abudayyeh OO,Barcena C,Hsu PD,Habib N,Gootenberg JS,Nishimasu H,Nureki O,Zhang F | 29/01/2015 | |
A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors | Cancer Discov. | Konieczkowski DJ,Johannessen CM,Abudayyeh O,Kim JW,Cooper ZA,Piris A,Frederick DT,Barzily-Rokni M,Straussman R,Haq R,Fisher DE,Mesirov JP,Hahn WC,Flaherty KT,Wargo JA,Tamayo P,Garraway LA | 30/06/2014 | |
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity | Cell | Ran FA,Hsu PD,Lin CY,Gootenberg JS,Konermann S,Trevino AE,Scott DA,Inoue A,Matoba S,Zhang Y,Zhang F | 12/09/2013 |
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