Mentorship

Research mentor

The student will select a primary research mentor no later than the end of their second semester in the program. The mentor will supervise the student's research, from developing a research project to carrying it out during the dissertation phase. Mentors' duties may also include advising on any additional courses needed to reach research goals. The dissertation research will be conducted by the student with input from their mentor, who is expected to regularly offer guidance on research procedures, give feedback, and read drafts, in addition to overseeing the dissertation defense. The student's progress will be monitored by a PhD. Advisory Committee.

PhD Advisory Committee

In consultation with their mentor, and subject to approval by the Director of Graduate Studies, each student will select a Ph.D. Advisory Committee and chairperson to guide them through their research no later than the end of their second year in the program. The committee will be composed of no less than four faculty, including the research mentor. The research mentor may not serve as chairperson. The chairperson and at least one other committee member must be tenured or tenure-track faculty in the Computational Biology program who hold a Ph.D. and/or M.D. degree and have a proven record of graduate-level training, funding and research. The committee must also include at least one faculty member who is not affiliated with the Computational Biology program.

In summary, the committee includes at least four faculty members:

  • Three with primary appointments in Computational Biology, including your mentor
  • One committee chair (Computational Biology faculty, not the student's mentor)
  • One external member from another UVA department

Committee meetings

Following successful completion of the qualifying exam, students will meet with their Ph.D. Advisory committee no less than once per year to monitor progress and recommend any additional or remedial actions.

Program expectations

Course requirements

Students complete at least 27 credits of coursework plus 45 credits of research. Students will take required courses in the first two years, and electives can be taken at any time during the degree. Students must maintain a cumulative GPA of 3.0 or higher to remain in good academic standing. Students are required to take a qualifying examination to advance to candidacy.

Time to degree

Students are expected to complete the program in 4-6 years. Students must make satisfactory progress toward their degree as determined by their advisory committee and the program faculty. Students who do not make satisfactory progress may be dismissed from the program.

Academic standing

Students must maintain a cumulative GPA of 3.0 or higher to remain in good academic standing. Students who fall below this threshold will be placed on academic probation. Students on academic probation must raise their GPA to 3.0 or higher within one academic year or they may be dismissed from the program.

Leave of absence

Students may request a leave of absence for medical, personal, or other reasons. Requests for leave must be approved by the Director of Graduate Studies and the Graduate School. Students on approved leave will have their financial support suspended but may return to the program with the same support level upon return. Leaves of absence are limited to 1 year total duration during the PhD. Absences that extend beyond 1 year are grounds for dismissal from the program.

Qualifying examination

Overview

Students are required to take a qualifying examination no later than the beginning of their third year in the program. The qualifying exam consists of a written research proposal in NIH F31 format and an oral defense. Students must pass to advance to candidacy.

Timeline

  • Proposal submission: At least two weeks before oral defense
  • Defense deadline: Before beginning of third year
  • Extensions: Submit requests to DGS with justification

Why writing matters

Good technical writing is an extremely important part of scientific research. Whether you pursue teaching, academic or industrial research, or government policy, your career will require writing technical documents, proposals, and reports. Writing is the most common form of scientific communication, and your success will depend not only on the creativity of your research, but also on your ability to communicate your ideas and results effectively.

The qualifying exam provides an opportunity to develop your scientific writing with guidance from an experienced faculty committee. Beyond preparing you for future grant applications, strong writing skills enable you to communicate better with other researchers and with the public who funds scientific research. We view this exam as a chance to help you grow and mature as a scientist, taking an important step toward your success as an independent investigator.

Examination committee

The qualifying exam committee is overseen by the student's PhD Advisory Committee.

Written proposal components

The proposal should follow the NIH F31 proposal format. This is a brief Project Summary, followed by a Specific Aims page, and then a 6 page Research Plan.

1. Project Summary/Abstract

Length: Maximum 30 lines
Content:

  • Brief project background
  • Specific aims and hypotheses
  • Significance and relevance to public health
  • Innovation and unique features
  • Methodology overview
  • Expected results and impact

Tips: Write this last; use plain language; avoid first person. This is on a dedicated page or title page.

2. Specific Aims

Length: Exactly 1 page
Content:

  • Long-term goals and objectives
  • 2-4 specific aims (one sentence each)
  • Brief paragraph under each aim if needed
  • Concluding impact statement that describes the big picture relevance

Key principles:

  • Most important page
  • Aims should be related but independent
  • Include preliminary data and citations where appropriate
  • Avoid open-ended or "fishing expedition" aims

3. Research Plan

Total Length: 6 pages maximum (F31 limit), split between Significance and Approach sub-sections. F31 applications do not include an Innovation section

3.1 Significance (.75-1.25 pages)

Content:

  • Background with focused literature review
  • Critical knowledge gap or barrier to progress
  • Rationale for proposed research
  • Potential contribution to field and public health

Focus on: What gap does your work fill? Why is this important?

3.2 Approach (remaining pages)

Many F31 applications begin the Approach section with Preliminary Data (recommended: 1-2 pages):

  • Present relevant experiments you've completed
  • Include pertinent work from your lab
  • Focus on demonstrating feasibility and your technical competence
  • Important: Do not delay your proposal to accumulate more preliminary results. The committee prioritizes your ability to think logically and present clear, insightful experiments over the quantity of preliminary data.
  • You can also choose to include preliminary data throughout each aim, instead of all together at the beginning of the approach

Content for each aim:

  • Experimental design and methods
  • Data analysis plans
  • Expected results and interpretation
  • Potential difficulties and alternative approaches
  • Timeline/work plan

Best practices:

  • Number sections to match Specific Aims numbers
  • Include relevant citations when possible

4. Literature Cited

Complete citations with all authors and titles. No page limit.

Guidelines:

  • You should have read all papers you cite
  • Target approximately 30-50 citations (not strict, but a helpful guide)
  • Include current and relevant literature
  • Ensure proper formatting for all citations

5. Appendix (Optional)

Use minimally or not at all. Only include if you have large supplemental figures or tables that are absolutely necessary but would disrupt the main narrative. The appendix should not be used to circumvent page limits. All primary content must appear in the main sections.

Formatting Requirements

  • Font: Arial 11pt or equivalent
  • Margins: Minimum 0.5 inch
  • Spacing: Single-spaced
  • Use clear subheadings throughout
  • Number sections consistently

Oral component

This oral defense of your proposal takes the form of a committee meeting. You should schedule a 2-hour slot, and prepare a 1-hour presentation of your proposal. The flow of your presentation should follow the logic of your written proposal; start with background/significance, describe the most relevant literature and the gap your project fills. Then, move into your approach and go through each specific aim individually.

You will not be able to go into as much detail in your presentation as you can in the written document. You should be prepared to answer very detailed questions about anything related to your proposal, and you should be familiar with the papers you cite.

Evaluation criteria

Committees assess:

  • Mastery of computational biology fundamentals
  • Research design and scientific reasoning
  • Technical writing proficiency
  • Understanding of literature and methods
  • Oral presentation and defense skills
  • Depth of knowledge and ability to answer questions
  • Readiness for independent thesis research

Important notes

  • The qualifying exam committee typically continues as your Thesis Advisory Committee
  • Revision and resubmission may be required
  • Focus on clear thinking and presentation over accumulating extensive preliminary data
  • This format prepares you for actual NIH F31 fellowship applications

For questions, consult your mentor or the Director of Graduate Studies.

Dissertation defense

Overview

Students are expected to conduct original research under the supervision of their research mentor. The research will result in a doctoral dissertation. Students are expected to present their research in a public defense of their dissertation. The dissertation committee must approve both the written dissertation and the oral defense to award the doctoral degree.

Timeline

  • Dissertation submission: At least two weeks before oral defense
  • Defense deadline: Students must follow BIMS time-to-degree policies.

Examination committee

The dissertation defense committee is overseen by the student's PhD Advisory Committee.