Summary of Research
Proteins are fascinating molecular machines responsible for most of life's essential functions. They convert our food into energy, allow our neurons to fire, and enable our immune system to fight disease. Yet, our understanding of exactly how proteins function remains limited by the tools we have to observe them in action. One of the biggest challenges facing the field of protein biology is being able to visualize and predict the interactions between proteins and other molecules, such as other proteins, DNA, or RNA, in their native cellular environments. In my graduate research, I aim to develop a method for single-molecule in situ protein sequencing and apply it to create the first complete spatial proteome of a cell.
Publications
Niu, Z., O'Farrell, A., Li, J., Reffsin, S., Jain, N., Dardani, I., Goyal, Y., & Raj, A. (2024). Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning. Submitted to Cell Systems, under revision. bioRxiv. doi:10.1101/2024.01.31.578123
Niu, Z., Bruyere, T., Manthey, D., Li, J., O'Farrell, A., & Raj, A. (2024). NimbusImage: a cloud-computing platform for image analysis. Submitted to Nature Methods, under revision.
O'Farrell, A., Niu, Z., Li, J., Van Eyndhoven, L., Sarma, K., Shin, S., & Raj, A. (2025). Innate Immune Memory is Stimulus Specific. Submitted to Cell, under review. bioRxiv. doi:10.1101/2025.01.22.634275
Li, J., Ravindran, P. T., O'Farrell, A., Busch, G. T., Boe, R. H., Niu, Z., Woo, S., Dunagin, M. C., Jain, N., Goyal, Y., Sarma, K., Herlyn, M., & Raj, A. (2024). AP-1 Mediates Cellular Adaptation and Memory Formation during Therapy Resistance. Submitted to Nature Communications, under revision. bioRxiv. doi:10.1101/2024.07.25.604999
Harmange, G., Hueros, R. A., Schaff, D. L., Emert, B., Saint-Antoine, M., Kim, L. C., Niu, Z., Nellore, S., Fane, M. E., Alicea, G. M., Weeraratna, A. T., Simon, M. C., Singh, A., & Shaffer, S. M. (2023). Disrupting cellular memory to overcome drug resistance. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-41811-8
Awards
Hertz Foundation Fellowship, 2024
PD Soros Fellowship for New Americans, 2024
Penn Arts and Sciences Dean's Scholar, 2024
Penn Physics and Astronomy William E. Stephens Memorial Prize, 2024
Barry M. Goldwater Scholarship, 2023
Roy and Diana Vagelos Science Challenge Award, 2022
Roy and Diana Vagelos Scholar, 2020