-
Amy Sitapati, M.D.
Project Title: Improving Health Outcomes via Population Health in Biomedical Informatics
Project Description: Together define the domain in health prevention and then use UCSD tools to devise an evaluation of population health impact using quality metrics.
Special Considerations for Mentee: Preferred either lived or learned experience in health basic knowledge.
Minimum Requirements for Mentee: Background in excel and data, basic science background, additional programming is optional.
-
Hannah Carter, PhD.
Project Title: Cancer data analysis for precision medicine
Project Description: The project will focus on analyzing tumor genomic data to either identify biomarkers of outcome or drug response, or investigate mechanisms of response or resistance.
Special Considerations for Mentee: Preferred experience with computational data analysis and writing code.
Minimum Requirements for Mentee: Familiarity with python or R, ideally some experience with genomics/transcriptomics.
-
Sandip Patel, M.D.
Project Title: Never smoking NSCLC germline risk
Project Description: Never smoking NSCLC germline risk will be assessing cohort from Taiwan from risk factors around development of NSCLC.
Special Considerations for Mentee: N/A.
Minimum Requirements for Mentee: Interest in germline genomic risk.
-
Sally Baxter, M.D.
Project Title: Ophthalmology Informatics
Project Description: The UCSD Division of Ophthalmology Informatics and Data Science is engaged in several research areas, including advancing data standards in ophthalmology and conducting secondary analyses of large databases (e.g. the NIH All of Us Research Program, the NIH Bridge2AI AI-READI dataset, the UC Health Data Warehouse, and local UCSD institutional research datasets) to evaluate risk factors, treatment outcomes, and predictive models for a variety of vision-threatening eye diseases. We also have some prospective patient-facing research studies that are actively enrolling participants, such as a study of flexible electronic medication adherence sensors to help measure and improve eye medication adherence. We welcome summer interns to engage/participate in these projects based on their interests/goals.
Special Considerations for Mentee: Spanish speaking skills are beneficial for our prospective studies. Programming skills (R, Python) are helpful for our data analytic studies.
Minimum Requirements for Mentee: Prior statistical programming experience.
-
Pengtao Xie, PhD
Project Title: Multi-modal foundation model for proteins
Project Description: In this project, we will develop a large pretrained model on multi-modal protein data.
Special Considerations for Mentee: N/A.
Minimum Requirements for Mentee: Knowledge of Python and PyTorch.
-
Cinnamon Bloss, PhD
Project Title: Stakeholder Perspectives on Social Media Surveillance in Schools
Project Description: A growing number of U.S. middle and high schools are implementing commercially available social media surveillance (SMS) of students in an effort to address youth mental health and school safety. Although SMS technology is increasingly being purchased by schools, there has been no systematic assessment of the ethical, legal, and social implications, including how it affects the students whom it purportedly aims to help. This project will document the ways in which SMS is currently being used by school administrators across the U.S., assess the perspectives of students and parents, and develop and disseminate student-centered policy recommendations.
Special Considerations for Mentee: N/A.
Minimum Requirements for Mentee: N/A.
-
Kathleen (Kit) Curtius, PhD
Project Title: Analyzing copy number variants in peripheral blood and tissue as early biomarkers for colorectal cancer progression in inflammatory bowel disease
Project Description: Copy number alterations (CNAs) are common in inflammatory bowel disease and can risk-stratify patients during lifelong surveillance for early colorectal cancers. This project will quantify CNAs in tissue and blood whole genome sequencing data for patients from UCSD IBD Biobank as part of a case-control study.
Special Considerations for Mentee: N/A.
Minimum Requirements for Mentee: Bioinformatics experience and knowledge of R, Python, C++, or any programming languages. Experience with analyzing next generation sequencing data.
-
Amit Majithia, M.D.
Project Title: aiDose: a foundation model for diabetes management
Project Description: we are using LLMs with 10 years worth of physician notes on treatment of diabetes in hospitalized patient to perform retrevial augmented generation powered clinical decision support tool for diabetes management
Special Considerations for Mentee: N/A.
Minimum Requirements for Mentee: Familiarity with python and data structures/ databases would be useful. Transformer training is a plus but not required