Project Mentor
Dr. Dongyuan Song
Department of Genetics and Genome Sciences
Undergraduate Research Opportunity Description
| Project Description | This summer research project focuses on improving and evaluating spAlign, a computational method for aligning multi-slice spatial transcriptomics data. The student will work on comparing spAlign with existing alignment methods using both simulated and real biological datasets, and create a more user-friendly package with newly added functionalities. Through this project, the student will gain hands-on experience in spatial omics data analysis, algorithm benchmarking, and reproducible computational research. The work will contribute directly to improving how spatial transcriptomics data are integrated across tissue sections. |
| Project Direction | spAlign will be further extended to support additional data modalities, such as brain Common Coordinate Framework (CCF) references and histological images. Ultimately, the spAlign package is intended to serve as a general-purpose registration tool for spatial data analysis, including the alignment of multiple mouse brain sections. |
| Mentorship and Supervision | The student will work directly with Dr. Song. We will have a weekly one-on-one meeting, and the student will also attend our regular group meeting. I will meet with the student in the lab space to answer questions/provide instructions. The student will present the project to the lab at the end of the summer. |
| Student Qualifications | Courses in basic computer science + machine learning and/or statistics. Students should have experience in programming with Python and R, as they will be working on package development. Knowledge of "omics" data is not required but preferred. |
| Summer Schedule Options | Research Dates: May 18 to July 24, 2026 Schedule: To be arranged within the schedule parameters of M-F, 9am-5pm, but it is flexible. Remote work is also possible under appropriate supervision. We do expect the student to come to the office at least four days per week and attend the group meeting in person |
| Project Continuation | Fall 2026, Spring 2027 |
| Academic Year Time Commitment | 9 hours/week |
| Possible Thesis Project | Yes |
Application
Submit an online application for this research opportunity at https://quest.uconn.edu/prog/HRPSU26-35. The application deadline is Monday, February 16, 2026.
This application requires a resume or CV, an unofficial transcript, GPA minimum of 3.5, and references.