Project Grant 2310356

The Trustees of the University of Pennsylvania received a $526,084 Project Grant from the National Science Foundation Division of Integrative Organismal Systems. The grant is part of the Biological Sciences program (CFDA 47.074) to promote progress in the biological sciences.

Under the award, the University will conduct collaborative research to predict plant phenotypes from molecular profiles using topological data analysis and deep learning. Researchers will use X-ray computed tomography to measure leaf morphology and RNA sequencing to measure gene expression in Arabidopsis plants. They will apply the Euler characteristic transform and Mapper algorithm to extract total information embedded in leaf shape and gene expression patterns. An encoder-decoder neural network will then align molecular and phenotypic data structures to map gene expression profiles to leaf shape features. All project outcomes will be made publicly available through long-term data repositories. The research aims to address a grand challenge in biology by enabling prediction of an organism's characteristics from its genomic information.