Contact

  • Academic
    browne@stanford.edu
    University - Student Department: ICME Operations Position: Graduate

Additional Info

  • Mail Code: 4042

All Publications

  • Improved reconstruction of single-cell developmental potential with CytoTRACE 2. Nature methods Kang, M., Gulati, G. S., Brown, E. L., Qi, Z., Avagyan, S., Armenteros, J. J., Gleyzer, R., Zhang, W., Steen, C. B., D'Silva, J. P., Schwab, J., Clarke, M. F., Chaudhuri, A. A., Newman, A. M. 2025

    Abstract

    While single-cell RNA sequencing has advanced our understanding of cell fate, identifying molecular hallmarks of potency-a cell's ability to differentiate into other cell types-remains a challenge. Here we introduce CytoTRACE 2, an interpretable deep learning framework for predicting absolute developmental potential from single-cell RNA sequencing data. Across diverse platforms and tissues, CytoTRACE 2 outperformed previous methods in predicting developmental hierarchies, enabling detailed mapping of single-cell differentiation landscapes and expanding insights into cell potency.

    View details for DOI 10.1038/s41592-025-02857-2

    View details for PubMedID 41145665

    View details for PubMedCentralID 6390367

  • Charting spatially resolved cell states with CytoSPACE. Nature reviews. Cancer Brown, E. L. 2024

    View details for DOI 10.1038/s41568-024-00713-7

    View details for PubMedID 38858510

  • High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE. Nature biotechnology Vahid, M. R., Brown, E. L., Steen, C. B., Zhang, W., Jeon, H. S., Kang, M., Gentles, A. J., Newman, A. M. 2023

    Abstract

    Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution.

    View details for DOI 10.1038/s41587-023-01697-9

    View details for PubMedID 36879008

    View details for PubMedCentralID 6132072