Michael S. Cuoco

Bio

I am a PhD Candidate in the Bioinformatics and Systems Biology Graduate Program at UC San Diego and a National Science Foundation Graduate Research Fellow. Before grad school, I spent ~5 years working in the wet lab to study the genetic and transcriptional basis of cancer drug resistance. Following my interest in somatic mutations outside of cancer, I have pivoted to neuroscience and bioinformatics where I am now working on computational methods to study the activity of retrotransposons in the mammalian brain.

I enjoy working in collaborative, interdisciplinary research groups to conceive and pursue research questions. I am also very passionate about taking reproducible, rigorous, and data-driven approaches to scientific discovery.

In my free time, I like to hike ⛰, swim 🏊, and play tennis 🏸 all over San Diego County!

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

Graduate Student Researcher | 2021 – present
Gage Lab, Salk Institute | Mukamel Lab, UC San Diego
La Jolla, California

Research Associate | 2016 – 2020
Regev Lab, Broad Institute of MIT and Harvard
Cambridge, Massachusetts

Undergraduate Researcher | 2014 – 2016
Meyerson Lab, Dana-Farber Cancer Institute
Boston, Massachusetts

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

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.

Li, J., Pinto-Duarte, A., Zander, M., Cuoco, M. S., Lai, C.-Y., Osteen, J., Fang, L., Luo, C., Lucero, J. D., Gomez-Castanon, R., Nery, J. R., Silva-Garcia, I., Pang, Y., Sejnowski, T. J., Powell, S. B., Ecker, J. R., Mukamel, E. A., Behrens, M. M., “Dnmt3a knockout in excitatory neurons impairs postnatal synapse mat- uration and increases the repressive histone modification H3K27me3.” eLife 11 (May 24, 2022). doi: 10.7554/eLife.66909.

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.

See a complete and up-to-date list on my CV!

Michael S. Cuoco

Bio

I am a PhD Candidate in the Bioinformatics and Systems Biology Graduate Program at UC San Diego and a National Science Foundation Graduate Research Fellow. Before grad school, I spent ~5 years working in the wet lab to study the genetic and transcriptional basis of cancer drug resistance. Following my interest in somatic mutations outside of cancer, I have pivoted to neuroscience and bioinformatics where I am now working on computational methods to study the activity of retrotransposons in the mammalian brain.

I enjoy working in collaborative, interdisciplinary research groups to conceive and pursue research questions. I am also very passionate about taking reproducible, rigorous, and data-driven approaches to scientific discovery.

In my free time, I like to hike ⛰, swim 🏊, and play tennis 🏸 all over San Diego County!

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

Graduate Student Researcher | 2021 – present
Gage Lab, Salk Institute | Mukamel Lab, UC San Diego
La Jolla, California

Research Associate | 2016 – 2020
Regev Lab, Broad Institute of MIT and Harvard
Cambridge, Massachusetts

Undergraduate Researcher | 2014 – 2016
Meyerson Lab, Dana-Farber Cancer Institute
Boston, Massachusetts

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

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.

Li, J., Pinto-Duarte, A., Zander, M., Cuoco, M. S., Lai, C.-Y., Osteen, J., Fang, L., Luo, C., Lucero, J. D., Gomez-Castanon, R., Nery, J. R., Silva-Garcia, I., Pang, Y., Sejnowski, T. J., Powell, S. B., Ecker, J. R., Mukamel, E. A., Behrens, M. M., “Dnmt3a knockout in excitatory neurons impairs postnatal synapse mat- uration and increases the repressive histone modification H3K27me3.” eLife 11 (May 24, 2022). doi: 10.7554/eLife.66909.

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.

See a complete and up-to-date list on my CV!