Develop Embeddings and Downstream Applications for Genomic Data
Mentors
Aarti Venkat, Robert Grossman
About Us
The Center for Translational Data Science is pioneering translational data science to advance biology, medicine, healthcare, and the environment. We’re a dedicated team of researchers and engineers drawing from different backgrounds and ideas to push the boundaries of data-intensive science. We work closely with researchers at the University of Chicago, along with other research groups and consortia. We develop and operate large-scale open-source data clouds and data commons for the scientific research community, including the Bionimbus Protected Data Cloud, OCC Open Science Data Cloud, and the NCI Genomic Data Commons. These computational platforms support thousands of users across the world with varying technical skills, backgrounds, and research objectives.
Externship Background
The Center for Translational Data Science (CTDS) is a leader in the development of data commons and data meshes to accelerate research and discovery from large biological datasets. It also develops large language models and generative AI models over this data. One of the data commons built by CTDS is the Veterans Precision Oncology Data Commons (VPODC), to support research on veteran oncologic data. We recently published on prostate cancer patient stratification by molecular signatures in the VPODC, using targeted sequencing and clinical data (Hernandez et al, 2023; PMID 38050021). This internship will focus on developing representations for somatic mutations and showing their downstream application for hierarchical clustering as described in the Hernandez et al paper. This experience will be valuable for learning more about embedding and showing applications on genomic data.
Externship Objectives
- Understand objectives from Hernandez et al paper
- Develop ways to embed somatic mutations and clinical data
- Apply hierarchical clustering on embeddings and analyze trends
The extern will receive specific training from mentors with structured weekly in-person time commitment in the CTDS office. Remote work will also be considered
Qualifications:
Doctoral/Postdoctoral