publications

Scientific/Medical Publications (*denotes co-first authorship)

  1. Cox, D.B.T*, Gootenberg, J.S.*, Abudayyeh, O.O*, Franklin, B., Kellner, M.J., Joung, J., and Zhang, F. “RNA editing with CRISPR-Cas13,” Science, October 2017.
  2. Kim, J.W., Abudayyeh, O.O., Yeerna, H., Yeang, C.H., Stewart, M., Jenkins, J., Kitajima, S., Konieczkowski, D., Medetgul-Ernar, K., Cavazos, T., Mah, C., Ting, S., Van Allen, E., Cohen, O., Mcdermott J., Damato, E., Aguirre, A., Liang, J., Liberzon, A., Alexe, G., Doench, J., Ghandi, M., Vazquez, F., Weir, B., Tsherniak, A., Subramanian A., Meneses-Cime, K., Park, J., Clemons, P., Garraway, L., Thomas, D., ,Boehm, J., Barbie, D., Hahn, W.C., Mesirov, J., and Tamayo, P. “Decomposing oncogenic transcriptional signatures to generate maps of divergent cellular states,” Cell Systems, August 2017.
  3. Abudayyeh, O.O.*, Gootenberg, J.S.*, Essletzbichler, P., Han, S., Joung, J., Belanto, J., Verdine, V., Cox, D.B.T., Regev, A., Lander, E.S., Voytas, D.F., Ting, A.Y., and Zhang, F. “RNA targeting with CRISPR-Cas13a,” Nature, in press August 2017.
  4. Joung, J., Konermann, S., Abudayyeh, O., Gootenberg, J., Sanjana, N., Wright, J., Engreitz, J., Fulco, C., Lander, E., Zhang, F., “Genome-scale CRISPR-Cas9 LincRNA activation screen identifies novel vemurafenib resistance mediators,” Nature, August, 2017.
  5. Zetsche, B., Strecker, J., Abudayyeh, O.O, Gootenberg, J.S., Scott, D.A., and Zhang, F. “A survey of genome editing activity for 16 Cpf1 orthologs,” bioRxiv, May 2017.
  6. Gootenberg, J.S.*, Abudayyeh, O.O.*, Lee, J.W., Essletzbichler, P., Dy, A., Joung, J., Verdine, V., Donghia, N., Daringer, N.M., Freije, C.A., Myhrvold, C., Bhattacharyya, R.P., Livny, J., Regev, A., Koonin, E.V., Hung, D.T., Sabeti, P.S., Collins, J.J., Zhang, F., “Nucleic acid detection with CRISPR-Cas13a/C2c2,” Science, April 2017.
  7. Joung, J., Konermann, S., Gootenberg, J., Abudayyeh, O., Platt, R., Brigham, M., Sanjana, N., Zhang, F., “Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening,” Nature Protocols. March, 2017.
  8. Shmakov, S., Smargon, A., Scott, D., Cox, D., Pyzocha, N., Yan, W., Abudayyeh, O., Gootenberg, J., Makarova, K., Wolf, Y., Severinov, K., Zhang, F., Koonin, E., “Diversity and evolution of Class 2 CRISPR-Cas systems,” Nature Reviews Microbiology, January 2017.
  9. Smargon, A., Cox, D., Pyzocha, N., Zheng, K., Slaymaker, I., Gootenberg, J., Abudayyeh, O., Essletzbichler, P., Shmakov, S., Makarova, K., Koonin, E., Zhang, F., “Cas13b is a Type VI-B CRISPR-Associated RNA-guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28,” Molecular Cell, January 2017.
  10. Zetsche, B., Heidenreich,M., Mohanraju,P., Fedorova, I., Kneppers, J., DeGennaro, E., Winblad,N., Choudhury, S., Abudayyeh, O., Gootenberg, J., Wu, W., Scott, D., Severinov, K., Oost, J., and Zhang, F., “Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array,” Nature Biotechnology, December, 2016.
  11. Abudayyeh, O.*, Gootenberg, J.*, Konermann, S.*, Joung, J., Slaymaker, Ian., Cox, D., Shmakov, S., Makarova, K., Semenova, E., Minakhin, L., Severinov, K., Regev, A., Lander, E., Koonin, E., Zhang, F., “C2c2 is a single component programmable RNA-guided RNA-targeting CRISPR effector,” Science, June 2016.
  12. Botvinnik, O., B., Kim, W., Abudayyeh, , Birger, C., Rosenbluh, J., Shrestha, Y., Abazeed, M., Hammerman,P.,  Konieczkowski, D. J., Johannessen, C., Alexe, G., Aguirre, A., Ghandi, M., Kryukov, G., Greulich, H.,Vazquez, F., Weir, B. A., Van Allen, E., Liberzon, A., DiCara, D., Tsherniak, A., Shao, D., D., Zack, T. I., Noble, M., Getz, G., Beroukhim, R., Garraway, L. A., Meyerson, M., Barbie, D. A., Boehm, J., Hahn, W. C.,  Mesirov, J. P., and Tamayo, P., “Mapping Genomic Alterations to Functional Profiles of Pathway Activation, Gene Dependency, and Drug Sensitivity,” Nature Biotechnology, April 2016.
  13. Hirano, H., Gootenberg, J., Horii, T., Abudayyeh, O., Kimura, M., Hsu, P., Nakane, T., Ishitani, R., Hatada, Izuho, Zhang, F., Nishamasu, H., and Nureki, O. “Structure and Engineering of Francisella novicida Cas9,” Cell, February 2016.
  14. Shmakov, S.*, Abudayyeh, O.O.*, Makarova, K., Wolf, Y., Gootenberg, J., Semenova, E., Minakhin, L., Joung, J., Konermann, S., Severinov, K., Zhang, F., and Koonin, E. “Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems,” Molecular Cell, October 2015.
  15. Dahlman, JE*, Abudayyeh, O.O.*, Joung J, Gootenberg JS, Zhang F, Konermann S. “Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease,” Nature Biotechnology, October 2015.
  16. Zetsche B, Gootenberg JS, Abudayyeh O, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. “Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System,” Cell, September 2015.
  17. Silvana Konermann, S., Brigham, M., Trevino, A., Abudayyeh, O., Barcena, C., Hsu, P., Gootenberg, J., Nishimasu, H., Nureki, O., and Zhan, F., “Structure-guided engineering of a CRISPR-Cas9 complex for genome-scale gene activation,” Nature, December 2014.
  18. Konieczkowski, D. Johannessen, C., Abudayyeh, O., Kim, J.W., Cooper, Z., Piris, A., Frederick, D.T., Barzily-Rokni, M., Straussman, R., Mesirov, J., Hahn, W., Flaherty, K., Tamayo, P., Wargo, J., and Garraway, L. “A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors,” Cancer Discovery, April 2014.
  19. Kwong, G., von Maltzahn, G., Murugappan, G., Abudayyeh, O., Mo, S., Papayannopoulos, I., Sverdio, D., and Bhatia, S., “‘Synthetic biomarkers’ for highly multiplexed urinary profiling of protease activities in vivo,” Nature Biotechnology, December 2012.
  20. Hogan, N. C., Talei-Franzesi, G., Abudayyeh, O., Taberner, A., Constantine-Paton, M., and Hunter, I., “Low-cost, Flexible Polymer Arrays for Long-Term Neuronal Culture,” Paper in the Proceedings of the EMBC 2012: The 34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, San Diego, CA, August, 2012.

Other Publications

Abudayyeh, O., “Playing with fire? Linking Intelligence to Our Genetics,” Harvard Med Stud Rev 1(1): e5. March 2, 2014. (http://www.hmsreview.org/2014/03/02/opinion-playing-with-fire-linking-intelligence-to-our-genetics/)

Abudayyeh, O., Becwith, N., Frange, A., and Kumar, J. “Introducing the Harvard Medical Student Review,” Harvard Med Stud Rev 1(1): e1. March 2, 2014. (http://www.hmsreview.org/2014/03/02/introducing-the-harvard-medical-review/)

Abudayyeh, O., “Higher education finally embraces the digital age,” Article in USA TODAY – College, February 14, 2013. (http://www.usatodayeducate.com/staging/index.php/ccp/higher-education-finally-embraces-the-digital-age.)

Invited Talks

2017                “What if CRISPR could not only treat disease, but detect it too?” at TEDMED 2017, Palm Springs, CA

2017                “Harnessing new CRISPR systems for human health,” Lecture Seminar at the Karolinska Institutet, Stockholm, Sweden

2017               “Harnessing novel RNA-targeting CRISPR systems for diagnostics and transcriptome engineering,” Discovery on Target Conference, Boston, MA

2017               “Harnessing novel RNA-targeting CRISPR systems for diagnostics and transcriptome engineering,” Molecular Biology Seminar Series, University of Pennsylvania Genetics Department, Philadelphia, PA

2017               “Harnessing new CRISPR systems for diagnostics,” NIH-NIAID Enterovirus Workshop, Rockville, MD

2017               “An RNA Toolbox: Discovery and Applications of RNA-Targeting CRISPR Systems,” CRISPR Genome Editing Congress, Boston, MA

2016               “CRISPR/Cas,” MAV 2016: The 2nd Symposium on Molecular Aspects of Virology,

Mexico City, Mexico

2016               Finding Novel Genome Editing Tools in the CRISPR Diversity: From Cas9 to Cpf1 and Beyond,” The 4th Annual Re-writing Genomes: A New Era in Genome Engineering, University of California, Berkeley, CA

2016               Plant Genome Stability and Change 2016: Fifth International Conference on Molecular and Cellular Mechanisms Underlying the stability, Variability, and Modification of Plant Genome, Hayama, Kanagawa, Japan

2016               The Forefront of Genome Engineering in Plants, Tokyo, Japan

2016               Medical and Population Genetics Program Meeting, Broad Institute, Cambridge, MA

2016               “Functional Characterization of Novel Class 2 CRISPR-Cas Systems,” Plant CRISPR Workshop: CRISPR/Cas-mediated Plant Genome Editing: From Design to Analysis, Crop Bioengineering Consortium, Iowa State University, Ames, IA

2016               The 5th Annual SynBio Center @MIT Symposium, MIT, Cambridge, MA

2015               “Applications of CRISPR/Cas9 and Discovery of New CRISPR Systems,” e:Med Systems Medicine Conference, Heidelberg, Germany

 

 

Lectures/workshops

2017               Lecturer, Course 2970: Applications of CRISPR/Cas9 technology: genome editing and beyond

Karolinska Institutet, Stockholm, Sweden

Topic: “Introduction to CRISPR and discovery of novel systems with applications for human health and biotechnology”

2017               Guest lecturer, Genome Engineering 5.0 Workshop

Broad Institute, Cambridge, MA

Topic: “Introduction to novel RNA-guided RNA-targeting CRISPR systems”

2017               Guest lecturer, Methods in Neuroscience

(Professor Jean-Jacques R. Soghomonian)

Medical School, Boston University, Boston, MA

“Nuclease-based gene targetting methods-CRISPR-Cas9”

2017               Guest lecturer, Chemical Biology 2200: Introduction to Chemical Biology (Professor Ralph Mazitschek)

Harvard Medical School, Harvard University, Boston, MA

Topic: “Genome editing with CRISPR-Cas9”

2016               Guest lecturer, 9.123/20.203 Neurotechnology in Action (Professor Alan Jasanoff)

Massachusetts Institute of Technology, Cambridge, MA

Topic: “CRISPR and Next-Generation Sequencing”

2016               Guest lecturer, Broad Workshop: CRISPR in a Nutshell

Broad Institute, Cambridge, MA

Topic: “C2c2 is a novel RNA-guided RNA-targeting enzyme”

2016               Guest lecturer, Genome Engineering 4.0 Workshop

Broad Institute, Cambridge, MA

Topic: “Functional characterization of novel Class 2 CRISPR-Cas systems”

 Conference Presentations

  1. Kwong, G., von Maltzahn, G., Abudayyeh, O., Mo, S., and Bhatia, S., “Synthetic Nanoparticle-chaperoned Urinary “biomarkers” for Noninvasive Cancer Diagnostics,” Proceedings of the Symposium LL: Biomimetic Engineering of Micro- and Nanoparticles, Materials Research Society, San Francisco, CA, April, 2011.
  2. Brinas, R., Sundgren, A., Abudayyeh, O., Aknin Q., Young, H., Sanford, M., Barchi, J., “Modulation of the macrophage immune response using gold nanoparticles bearing tumor-associated carbohydrate antigens,” Proceedings of the 42nd Middle Atlantic Regional Meeting, Chemical Society of Washington, College Park, MD, March 2011.
  3. Kwong, G., von Maltzahn, G., Abudayyeh, O., Mo, S., Murugappan, G., Papayannopoulos, I., and Bhatia, S., “Diagnostic peptide-nanoparticle probes for multiplexed profiling of tumor protease activity,” Proceedings of the 2010 Biomedical Engineering Society Annual Meeting, Austin, TX: October 6-9, 2010.
  4. Hogan, N. C., Talei-Franzesi, G., Abudayyeh, O., Constantine-Paton, M., and Hunter, I., “A chip-based platform for long-term neuronal culture, stimulation, and imaging,” Proceedings of the 2009 Society for Neuroscience Annual Conference, Chicago, IL: October 17-21, 2009.
  5. Abudayyeh, O., Brinas, R., Sanford, M., Young, H., and Barchi, J., “Gold Nanoparticles Bearing Tumor Associated Carbohydrate Antigens as a Cancer Vaccine Construct: Determination of their Antigen Coverage and Investigation of Cellular Uptake,” NIH Poster Day. Bethesda, MD, August 6th, 2009.
  6. Jellies, J., Eskander, C., Abudayyeh, O., and Jellies, J., “Revising a View of Chemical Circuits: Multiple Diverse Synaptic Phenotypes Generated by a Single Identified Motor Neuron,” Proceedings of the 38th Annual Meeting of the Michigan Chapter of the Society for Neuroscience: Cognitive Neuroscience of Aging, Detroit, MI, May 31st, 2008.

 

 

 

 

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