Thesis Proposal Outline

This document provides a structured overview of your proposed research, modeled after NIH-style or institutional templates. Each section should be drafted with clarity, scientific rigor, and explicit rationale.

1. Background and Significance

• What biological or computational problem does your work address?
• Why is this an important and timely problem?
• How does your work build on, differ from, or fill gaps in existing literature?

2. Specific Aims

• What are the 2–3 central aims that drive your project?
  • Aim 1: [e.g., Identify functional variants using integrated regulatory annotations]
  • Aim 2: [e.g., Prioritize druggable pathways using expression and graph-based methods]

3. Preliminary Data

• What early analyses, simulations, or observations support your proposal?
• Include any pilot studies, existing cohorts, or code prototypes.

4. Research Strategy

Approach

• What methods will you use to address each aim?
• What datasets, tools, and benchmarks will you rely on?

Pitfalls and Alternatives

• What are the known risks in your design or analysis pipeline?
• What contingency plans or backup methods will you use?

5. References

• Include key primary literature, methods papers, and datasets you rely on.
• Format can follow journal or proposal-specific citation norms.