Professional Education

  • Doctor of Philosophy, University of California San Diego (2024)
  • Doctor of Philosophy, University of California San Diego, Biomedical Sciences (2024)
  • Masters of Arts, Occidental College, Biophysics (2017)

Stanford Advisors

Lab Affiliations

All Publications

  • Bento: a toolkit for subcellular analysis of spatial transcriptomics data. Genome biology Mah, C. K., Ahmed, N., Lopez, N. A., Lam, D. C., Pong, A., Monell, A., Kern, C., Han, Y., Prasad, G., Cesnik, A. J., Lundberg, E., Zhu, Q., Carter, H., Yeo, G. W. 2024; 25 (1): 82


    The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. We demonstrate MERFISH, seqFISH+, Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.

    View details for DOI 10.1186/s13059-024-03217-7

    View details for PubMedID 38566187