Xin Maizie Zhou, assistant professor of biomedical engineering and computer science at Vanderbilt University, has received a National Science Foundation CAREER Award to advance AI-driven computational tools used to analyze 3D complex biological tissue systems using spatial transcriptomics.
Zhou and her team develop algorithms and mathematical models to address biological and neuroscience questions. They investigate multiple dimensions of these questions, spanning computational genomics, bioinformatics, computational neuroscience, and machine learning.
The more than $640,000 NSF award will be used for her project, “CAREER: Decoding Tissue Architecture Through Spatial Transcriptomics Integration and 3D Reconstruction.”
Spatial transcriptomics adds a crucial dimension to gene expression analysis: location. Instead of treating tissues as collections of isolated cells, it allows scientists to study how gene activity is organized in space, revealing how cells interact within their native environment. This has made it a powerful tool in cancer biology, neuroscience, developmental biology, and precision medicine.
Current lab technologies let scientists measure which genes are active in individual cells while also recording exactly where those cells are located within a tissue. The problem, Zhou said, is that these measurements are usually captured as thin, separate 2D slices — like individual pages of a book — even though tissues themselves are actually three-dimensional.
“Without a way to bind those “pages” back together, it’s hard to see the full picture of how a tissue is really built and organized,” she said.
Zhou’s project is developing AI-based computational tools that stitch those separate 2D slices back into an accurate 3D reconstruction of the tissue, supporting analyses of spatial organization, tissue topography, developmental trajectories, and cellular interactions in three dimensions.
“All of the resulting software will be released as free, open-source tools so labs anywhere can use it to study complex biological systems,” Zhou said.
The Faculty Early Career Development (CAREER) Program is NSF’s most prestigious award for junior faculty who demonstrate potential as teacher‑scholars and leaders in both research and education.