Jonathan Gootenberg

  • Program Years: 2014-2017
  • Academic Institution: Harvard University
  • Field of Study: Computational Biology
  • Academic Advisor: Feng Zhang
  • Practicum(s):
  • Degree(s):
    B.S. Biological Engineering, and B.S. Mathematics, Massachusetts Institute of Technology, 2013

Current Status

  • Status: McGovern Fellow
  • Research Area: Computational Biology and Bioengineering


Gootenberg, J.S.*, Omar O. Abudayyeh, O.O.*, Lee, J.W., Essletzbichler, P., Dy, A.J., 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.C., Collins, J.J., and Zhang, F. Nucleic acid detection with CRISPR-Cas13a/C2c2: attomolar sensitivity and single nucleotide specificity. Science (In Press)

Joung J., Konermann S., Abudayyeh O.O., Gootenberg J.S., Sanjana N.E., Wright J.B., Engreitz J.M., Fulco C.P., Lander E.S., Zhang F. Genome-scale CRISPR-Cas9 LincRNA activation screen identifies novel vemurafenib resistance mediators. Nature (In revision)

Yamada, M., Watanabe, Y., Gootenberg, J. S., Hirano, H., Ran, F. A., Nakane, T., Ishitani, R., Zhang, F., Nishimasu, H. and Nureki, O. (2017). Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems. Mol Cell 65(6): 1109-1121 e1103.

Myhrvold, C., Baym, M., Hanikel, N., Ong, L. L., Gootenberg, J. S. and Yin, P. (2017). Barcode extension for analysis and reconstruction of structures. Nat Commun 8: 14698.

Shmakov, S., Smargon, A., Scott, D., Cox, D., Pyzocha, N., Yan, W., Abudayyeh, O. O., Gootenberg, J. S., Makarova, K. S., Wolf, Y. I., Severinov, K., Zhang, F. and Koonin, E. V. (2017). Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol 15(3): 169-182.

Smargon, A. A., Cox, D. B., Pyzocha, N. K., Zheng, K., Slaymaker, I. M., Gootenberg, J. S., Abudayyeh, O. A., Essletzbichler, P., Shmakov, S., Makarova, K. S., Koonin, E. V. and Zhang, F. (2017). Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28. Mol Cell 65(4): 618-630 e617.

Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I., Kneppers, J., DeGennaro, E. M., Winblad, N., Choudhury, S. R., Abudayyeh, O. O., Gootenberg, J. S., Wu, W. Y., Scott, D. A., Severinov, K., van der Oost, J. and Zhang, F. (2017). Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol 35(1): 31-34.

Joung, J., Konermann, S., Gootenberg, J. S., Abudayyeh, O. O., Platt, R. J., Brigham, M. D., Sanjana, N. E. and Zhang, F. (2017). Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc 12(4): 828-863.

Hirano, H., Gootenberg, J. S., Horii, T., Abudayyeh, O. O., Kimura, M., Hsu, P. D., Nakane, T., Ishitani, R., Hatada, I., Zhang, F., Nishimasu, H. and Nureki, O. (2016). Structure and Engineering of Francisella novicida Cas9. Cell 164(5): 950-961.

Abudayyeh, O. O., Gootenberg, J. S.*, Konermann, S., Joung, J., Slaymaker, I. M., Cox, D. B., Shmakov, S., Makarova, K. S., Semenova, E., Minakhin, L., Severinov, K., Regev, A., Lander, E. S., Koonin, E. V. and Zhang, F. (2016). C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353(6299): aaf5573.

Zetsche, B.*, Gootenberg, J. S.*, Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., Koonin, E. V. and Zhang, F. (2015). Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163(3): 759-771.

Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., Semenova, E., Minakhin, L., Joung, J., Konermann, S., Severinov, K., Zhang, F. and Koonin, E. V. (2015). Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Mol Cell 60(3): 385-397.

Dahlman, J. E., Abudayyeh, O. O., Joung, J., Gootenberg, J. S., Zhang, F. and Konermann, S. (2015). Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nat Biotechnol 33(11): 1159-1161.

Bryson, B. D., Del Rosario, A. M., Gootenberg, J. S., Yaffe, M. B. and White, F. M. (2015). Engineered bromodomains to explore the acetylproteome. Proteomics 15(9): 1470-1475.

Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., Nureki, O. and Zhang, F. (2015). Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517(7536): 583-588.

Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., Koonin, E. V., Sharp, P. A. and Zhang, F. (2015). In vivo genome editing using Staphylococcus aureus Cas9. Nature 520(7546): 186-191.

Ran, F. A., Hsu, P. D., Lin, C. Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y. and Zhang, F. (2013). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154(6): 1380-1389.


Lockheed Martin UROP Scholar, MIT, 2011
John Reed UROP Scholar, MIT, 2012
Tau Beta Pi, MIT, 2012-2013
Finalist, John and Fannie Hertz Fellowship, 2013, 2014
Award for outstanding service to the biological engineering community at MIT, 2013