Connor Duffy
Stanford Genetics Ph.D. candidate.; MIT Computer Science and Molecular Biology '17
Research Interests
About
Publications
ecDNA hubs drive cooperative intermolecular oncogene expression
Nature / Nov 24, 2021
Hung, K. L., Yost, K. E., Xie, L., Shi, Q., Helmsauer, K., Luebeck, J., Schöpflin, R., Lange, J. T., Chamorro González, R., Weiser, N. E., Chen, C., Valieva, M. E., Wong, I. T.-L., Wu, S., Dehkordi, S. R., Duffy, C. V., Kraft, K., Tang, J., Belk, J. A., … Chang, H. Y. (2021). ecDNA hubs drive cooperative intermolecular oncogene expression. Nature, 600(7890), 731–736. https://doi.org/10.1038/s41586-021-04116-8
Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence
Cancer Cell / Jul 01, 2022
Belk, J. A., Yao, W., Ly, N., Freitas, K. A., Chen, Y.-T., Shi, Q., Valencia, A. M., Shifrut, E., Kale, N., Yost, K. E., Duffy, C. V., Daniel, B., Hwee, M. A., Miao, Z., Ashworth, A., Mackall, C. L., Marson, A., Carnevale, J., Vardhana, S. A., & Satpathy, A. T. (2022). Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence. Cancer Cell, 40(7), 768-786.e7. https://doi.org/10.1016/j.ccell.2022.06.001
Covalently-crosslinked mucin biopolymer hydrogels for sustained drug delivery
Acta Biomaterialia / Jul 01, 2015
Duffy, C. V., David, L., & Crouzier, T. (2015). Covalently-crosslinked mucin biopolymer hydrogels for sustained drug delivery. Acta Biomaterialia, 20, 51–59. https://doi.org/10.1016/j.actbio.2015.03.024
Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection
Apr 23, 2021
Biering, S. B., Sarnik, S. A., Wang, E., Zengel, J. R., Sathyan, V., Nguyenla, X., Van Dis, E., Catamura, C., Yamashiro, L. H., Begeman, A., Stark, J. C., Shon, D. J., Fox, D. M., Puschnik, A. S., Bertozzi, C. R., Carette, J. E., Stanley, S. A., Harris, E., Konermann, S., & Hsu, P. D. (2021). Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection. https://doi.org/10.1101/2021.04.22.440848
Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism
Dec 12, 2021
Ezran, C., Liu, S., Chang, S., Ming, J., Botvinnik, O., Penland, L., Tarashansky, A., de Morree, A., Travaglini, K. J., Hasegawa, K., Sin, H., Sit, R., Okamoto, J., Sinha, R., Zhang, Y., Karanewsky, C. J., Pendleton, J. L., Morri, M., … Krasnow, M. A. (2021). Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism. https://doi.org/10.1101/2021.12.12.469460
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting
Cell Systems / Dec 01, 2023
Wei, J., Lotfy, P., Faizi, K., Baungaard, S., Gibson, E., Wang, E., Slabodkin, H., Kinnaman, E., Chandrasekaran, S., Kitano, H., Durrant, M. G., Duffy, C. V., Pawluk, A., Hsu, P. D., & Konermann, S. (2023). Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting. Cell Systems, 14(12), 1087-1102.e13. https://doi.org/10.1016/j.cels.2023.11.006
Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets
Nov 19, 2021
Zhao, J., Wang, G., Ming, J., Lin, Z., Wang, Y., Wu, A. R., & Yang, C. (2021). Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets. https://doi.org/10.1101/2021.11.16.468892
An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome
Dec 14, 2021
Liu, S., Ezran, C., Wang, M. F. Z., Li, Z., Awayan, K., Long, J. Z., De Vlaminck, I., Wang, S., Epelbaum, J., Kuo, C., Terrien, J., Krasnow, M. A., & Ferrell, J. E. (2021). An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. https://doi.org/10.1101/2021.12.13.472243
Mouse lemur transcriptomic atlas elucidates primate genes, physiology, disease, and evolution
Aug 07, 2022
Ezran, C., Liu, S., Ming, J., Guethlein, L. A., Wang, M. F. Z., Dehghannasiri, R., Olivieri, J., Frank, H. K., Tarashansky, A., Koh, W., Jing, Q., Botvinnik, O., Antony, J., Chang, S., Pisco, A. O., Karkanias, J., Yang, C., Ferrell, J. E., … Krasnow, M. A. (2022). Mouse lemur transcriptomic atlas elucidates primate genes, physiology, disease, and evolution. https://doi.org/10.1101/2022.08.06.503035
Education
Stanford University
Ph.D., Genetics / January, 2025 (anticipated)
Massachusetts Institute of Technology
S.B., Computer Science and Molecular Biology / February, 2017
Experience
Flatiron Health
Data Insights Engineer / October, 2018 — October, 2019
oncology data and software
Reverie Labs
Co-Founder / September, 2017 — September, 2018
computation-driven drug discovery; acq. Ginkgo Bioworks (NYSE: DNA)
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