Project Guidelines
GitHub Classroom Assignment Link
Note
Following are the expectations for the independent project assignment.
The independent project, which should utilize computational or bioinformatic approaches covered in the class, can be based on what you are familiar with or something you are interested in learning more about. Regular exchanges with the instructors about your project ideas are highly recommended. These exchanges will help refine your initial broad areas of biomedical questions or interests into a specific problem, ensuring your project aligns with the course objectives.
Some potential project ideas:
- Reanalyze old genomic data (RNA-seq, ChIP-seq) in the context of a new genome build, integration of multiple data sources, and a novel combination of analyses and genomic data. The goal is to reveal new insights missed from prior studies—careful planning and selection of data would be needed.
- Gene-centric analysis: disease-causing genes or sequence variants; identify potential tissues and cell types affected; identify potential mechanisms of disease action; propose validation experiments; propose potential interventions. This would be a more direct analysis but needs more research/reading and employing numerous databases and online resources.
- Hypothesis-driven data mining: searching genes in disease process X; network and tissue analysis of genes with shared phenotypes from OMIM (physical features, genetic disorders, diseases); evolution of key features in species (i.e., what might have led to tail loss in humans); goal is to establish next set of experimentally testable hypotheses.
- Building diagnostic assays for diseases/pathologies: collation of relevant and necessary genetic/epigenetic information. Proposing how the assays will work. Scoring and reporting of diagnosis.
The independent projects will be presented in the last two sessions of the class. Each presentation should be about 15-20 minutes. The presentation of the project should cover four sections:
- Rationale/Motivation/Significance
- Approaches/Data sources
- Results/Interpretations
- Conclusion/Future directions
| Date | Presentations |
|---|---|
| August 1 | Anne Fu, Ryan Leap, Charlotte Marasigan |
| August 6 | Stephanie Nguyen, Nikhitha Raghavaraju |