Michael Cuoco

I am a PhD candidate in Bioinformatics and Systems Biology at UC San Diego, where I am developing computational genomics methods to study the activity of LINE-1 retrotransposons in the mammalian brain.

My interests span genetics, cellular and molecular biology, machine learning, and bioinformatics algorithms. I am passionate about scientific rigor, reproducbility, and discovery.

Education

University of California, San Diego | La Jolla, California
Ph.D. in Bioinformatics and Systems Biology | 2020 - present
Advised by Rusty Gage and Eran Mukamel

Trinity College | Hartford, Connecticut
B.S. in Molecular and Cellular Biology | 2012 - 2016

Experience

Research Associate | 2016 – 2020
Regev Lab, Broad Institute Cambridge, Massachusetts
Mentors: Aviv Regev, Benjamin Izar, Pratiksha Thakore, Yaara Oren

Undergraduate Researcher | 2014 – 2016
Meyerson Lab, Dana-Farber Cancer Institute Boston, Massachusetts
Mentors: Matthew Meyerson and Alison Taylor

Undergraduate Researcher | 2013
Trinity College Hartford, Connecticut
HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program (SEA-PHAGES).

Select Publications

Otto, J. E., Ursu, O., Wu, A. P., Winter, E. B., Cuoco, M. S., Ma, S., Qian, K., Michel, B. C., Buenrostro, J. D., Berger, B., Regev, A., Kadoch, C., “Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.” Molecular cell 83 (8 Apr. 2023). doi: 10.1016/j.molcel.2023.03.013.

He, M. X., Cuoco, M. S., Crowdis, J., Bosma-Moody, A., Zhang, Z., Bi, K., Kanodia, A., Su, M.-J., Ku, S.-Y., Garcia, M. M., Sweet, A. R., Rodman, C., DelloStritto, L., Silver, R., Steinharter, J., Shah, P., Izar, B., Walk, N. C., Burke, K. P., Bakouny, Z., Tewari, A. K., Liu, D., Camp, S. Y., Vokes, N. I., Salari, K., Park, J., Vigneau, S., Fong, L., Russo, J. W., Yuan, X., Balk, S. P., Beltran, H., Rozenblatt-Rosen, O., Regev, A., Rotem, A., Taplin, M.-E., Allen, E. M. V., “Transcriptional mediators of treatment resistance in lethal prostate cancer.” Nature medicine 27 (3 Mar. 2021). doi: 10.1038/s41591-021-01244-6.

Oren, Y., Tsabar, M., Cuoco, M. S., Amir-Zilberstein, L., Cabanos, H. F., H ̈utter, J.-C., Hu, B., Thakore, P. I., Tabaka, M., Fulco, C. P., Colgan, W., Cuevas, B. M., Hurvitz, S. A., Slamon, D. J., Deik, A., Pierce, K. A., Clish, C., Hata, A. N., Zaganjor, E., Lahav, G., Politi, K., Brugge, J. S., Regev, A., “Cycling cancer persister cells arise from lineages with distinct programs.” Nature 596 (7873 Aug. 13, 2021). doi: 10.1038/s41586- 021-03796-6.

Nayar, U., Cohen, O., Kapstad, C., Cuoco, M. S., Waks, A. G., Wander, S. A., Painter, C., Freeman, S., Persky, N. S., Marini, L., Helvie, K., Oliver, N., Rozenblatt-Rosen, O., Ma, C. X., Regev, A., Winer, E. P., Lin, N. U., Wagle, N., “Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor-directed therapies.” Nature genetics 51 (2 Dec. 12, 2018). doi: 10.1038/s41588-018-0287-5.

Michael Cuoco

I am a PhD candidate in Bioinformatics and Systems Biology at UC San Diego, where I am developing computational genomics methods to study the activity of LINE-1 retrotransposons in the mammalian brain.

My interests span genetics, cellular and molecular biology, machine learning, and bioinformatics algorithms. I am passionate about scientific rigor, reproducbility, and discovery.

Education

University of California, San Diego | La Jolla, California
Ph.D. in Bioinformatics and Systems Biology | 2020 - present
Advised by Rusty Gage and Eran Mukamel

Trinity College | Hartford, Connecticut
B.S. in Molecular and Cellular Biology | 2012 - 2016

Experience

Research Associate | 2016 – 2020
Regev Lab, Broad Institute Cambridge, Massachusetts
Mentors: Aviv Regev, Benjamin Izar, Pratiksha Thakore, Yaara Oren

Undergraduate Researcher | 2014 – 2016
Meyerson Lab, Dana-Farber Cancer Institute Boston, Massachusetts
Mentors: Matthew Meyerson and Alison Taylor

Undergraduate Researcher | 2013
Trinity College Hartford, Connecticut
HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program (SEA-PHAGES).

Select Publications

Otto, J. E., Ursu, O., Wu, A. P., Winter, E. B., Cuoco, M. S., Ma, S., Qian, K., Michel, B. C., Buenrostro, J. D., Berger, B., Regev, A., Kadoch, C., “Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.” Molecular cell 83 (8 Apr. 2023). doi: 10.1016/j.molcel.2023.03.013.

He, M. X., Cuoco, M. S., Crowdis, J., Bosma-Moody, A., Zhang, Z., Bi, K., Kanodia, A., Su, M.-J., Ku, S.-Y., Garcia, M. M., Sweet, A. R., Rodman, C., DelloStritto, L., Silver, R., Steinharter, J., Shah, P., Izar, B., Walk, N. C., Burke, K. P., Bakouny, Z., Tewari, A. K., Liu, D., Camp, S. Y., Vokes, N. I., Salari, K., Park, J., Vigneau, S., Fong, L., Russo, J. W., Yuan, X., Balk, S. P., Beltran, H., Rozenblatt-Rosen, O., Regev, A., Rotem, A., Taplin, M.-E., Allen, E. M. V., “Transcriptional mediators of treatment resistance in lethal prostate cancer.” Nature medicine 27 (3 Mar. 2021). doi: 10.1038/s41591-021-01244-6.

Oren, Y., Tsabar, M., Cuoco, M. S., Amir-Zilberstein, L., Cabanos, H. F., H ̈utter, J.-C., Hu, B., Thakore, P. I., Tabaka, M., Fulco, C. P., Colgan, W., Cuevas, B. M., Hurvitz, S. A., Slamon, D. J., Deik, A., Pierce, K. A., Clish, C., Hata, A. N., Zaganjor, E., Lahav, G., Politi, K., Brugge, J. S., Regev, A., “Cycling cancer persister cells arise from lineages with distinct programs.” Nature 596 (7873 Aug. 13, 2021). doi: 10.1038/s41586- 021-03796-6.

Nayar, U., Cohen, O., Kapstad, C., Cuoco, M. S., Waks, A. G., Wander, S. A., Painter, C., Freeman, S., Persky, N. S., Marini, L., Helvie, K., Oliver, N., Rozenblatt-Rosen, O., Ma, C. X., Regev, A., Winer, E. P., Lin, N. U., Wagle, N., “Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor-directed therapies.” Nature genetics 51 (2 Dec. 12, 2018). doi: 10.1038/s41588-018-0287-5.