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index.Rmd
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---
title: "Michael S. Cuoco"
image: "headshot.jpg"
links:
- label: CV `r fontawesome::fa("file-pdf", fill = "black")`
url: "cv.pdf"
- label: Email `r fontawesome::fa("paper-plane", fill = "black")`
url: "mailto:[email protected]"
- label: Twitter `r fontawesome::fa("twitter", fill = "black")`
url: "https://twitter.com/cuoco_michael"
- label: GitHub `r fontawesome::fa("github", fill = "black")`
url: "https://github.com/mikecuoco"
- label: Google Scholar `r fontawesome::fa("graduation-cap", fill = "black")`
url: "https://scholar.google.com/citations?user=8aKD8FoAAAAJ&hl=en"
# - label: LinkedIn `r fontawesome::fa("linkedin", fill = "black")`
# url: "https://www.linkedin.com/in/michaelcuoco/"
output:
postcards::solana
---
## 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 `r emo::ji("mountain")`, swim `r emo::ji("swimmer")`, and play tennis `r emo::ji("racquet")` 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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/10.1038/s41588-018-0287-5).
See a complete and up-to-date list on [my CV](./cv.pdf)!