Guidelines for Ph.D. Program

Qualifying ExamBose Lab

The Oral Comprehensive Exam (OCE) consists of the oral defense of a written research proposal developed by the student. As a first step the student will develop two pre-proposals, each on a different research topic. One of these will be developed into a complete proposal to be defended by the student before their examination committee.

Timetable. Students are expected to take the OCE during the fall semester of their third year of graduate study. The first step in the process is the submission of the pre-proposals, which are due by September 1.  Special permission from the Graduate Affairs Committee is required in advance if a student is unable to submit the pre-proposals by this deadline.  Permission must include an explanation for the delay and a proposed timeline for submitting the pre-proposals.  The Graduate Affairs Committee will evaluate special circumstances, such as medical leaves or department transfers, on a case-by-case basis.  The OCE can be taken earlier if so desired and it can be arranged. 

Committee Membership. The Director of the Microbiology Graduate Program must approve the examination committee.  The examination committee will consist of at least four members and the student's major advisor.  The chair of the committee must be a member of the Department and cannot be the student's major advisor.  At least three members of the committee must have primary appointments within the Department and at least one member must be from outside the Department. 

Pre-Proposal. To begin the process students will write two pre-proposals, neither of which can be related to research topics ongoing in the lab they have joined. If there is some question the student should consult their committee chair. The pre-proposals and the final proposal are to be based upon original ideas of the student and are to be written independently.  Consultations with other students or faculty who are not committee members are encouraged. Each pre-proposal should be limited to three pages, including figures and tables, but not including references. Each page should be single-spaced, with a left/right/top/bottom margin of 3/4", and a font size of 11 (Arial). The emphasis of the pre-proposals is to provide sufficient background to frame the hypothesis. This outline should include the specific aims and a brief outline of the experimental strategy. Be sure not to propose too many aims so that each aim can be explored in depth. Two or three specific aims are standard.

The exam committee will determine:

  1. If the pre-proposal differs sufficiently from the research ongoing in the laboratory the student has joined.
  2. If the pre-proposal can be developed into a full proposal. An important part of this decision is whether a significant research problem has been identified.

The Committee will meet within 14 days after submission without the student present and make one of the following decisions:

  1. Both pre-proposals are suitable. The student may choose one to develop into a full proposal.
  2. One pre-proposal is more suitable than the other. The student must base the full proposal on the one recommended by the committee.
  3. Neither pre-proposal is suitable. The committee can either request more detail on one pre-proposal or request a third pre-proposal on a separate topic. The committee's request must be honored within 10 days of the request.

If neither pre-proposal is suitable, the chair of the committee will summarize the suggestions of the committee and prepare a written statement for the student.    When the committee re-reviews a revised or new pre-proposal, the committee can either accept the pre-proposal or allow another 14 days to continue to revise the pre-proposal. If the student is unable to prepare an acceptable pre-proposal, the student will be dismissed from the Ph.D. program.

Proposal. The student will expand the pre-proposal selected by the committee into a full length proposal. The full proposal is due within 45 days of notification that a pre-proposal is acceptable. The proposal should follow the NIH guidelines of an R21 application, except that it can be expanded to 12 pages, excluding the cited references. An excellent resource for grant-writing tips can be found here. The proposed research should be capable of being completed by a team of three graduate students in three years. Be sure to consider the expected results as well as alternative results for each experiment. Consider the follow-up experiments for each possible result. Consider alternative approaches in case the first approach fails.

Recommended lengths for each section

  • Specific aims: 1 page
  • Background and significance: 3-4 pages
  • Experimental design: 6-9 pages

When the written proposal is prepared, a copy is distributed to each member of the committee. The committee will discuss the proposal (either in a meeting or via e-mail/teleconference/video conference) to decide whether the proposal is suitable for the examination.

The committee will make one of the following decisions within 14 days after submission:

  1. The proposal is suitable. The student may schedule the exam.
  2. The proposal requires revision. The committee may offer specific suggestions for the resubmission of the proposal. The chair of the committee will summarize the suggestions of the committee and prepare a written statement to guide the student. Students have 21 days from the date of receipt of the suggestions to re-submit the proposal to the committee. The committee will re-convene to evaluate the proposal. If further revisions are necessary, the student will have one more attempt to submit a satisfactory proposal. Failure to submit a satisfactory proposal may result in dismissal from the Ph.D. program.
  3. The proposal is unsuitable. If the proposal is rejected, the student may be dismissed from the Ph.D. program.

Examination. When the committee agrees that the proposal is suitable for examination, the student will schedule the examination. At this point, (i.e. about 2 weeks before the examination), the Departmental Graduate Studies Director needs to be supplied with (i) the scheduled date of the exam, and (ii) a list of the faculty serving on the examination committee. This time frame is required by the Graduate Studies Office to complete the required paperwork.

The examination will begin with a 15-minute presentation by the student that introduces the biological problem, briefly outlines the specific aims and summarizes the approaches to answer the aims. This presentation is followed by a question and answer period. The questions from the committee are to be based on the proposal and any background material, techniques, and concepts that are relevant to the proposal. If the exam continues past three hours, the student has the right to terminate the questioning without negative consequence on the committee's decision. After the examination, the student will be excused from the room while the committee deliberates.

The committee has the following options:

  1. Pass the student.
  2. Decide that the student will be re-examined on the same proposal within 14 days. The student must pass the re-examination in order to remain in the Ph.D. program.
  3. Fail the student. In this case, the student is dismissed from the Ph.D. program.

Dismissal from the Ph.D. Program. If at any stage, the committee decides that a student shall be dismissed from the Ph.D. program, the student may be allowed to continue to work toward a Master's degree if mutually agreed upon by the student and the committee.

The student is encouraged to meet with the Chair of the examining committee for procedural advice at any time during preparation of the pre-proposals or full proposal.


Research Committee Membership. The research committee will consist of at least five members. The chair of the committee must be a member of the Department and cannot be the student's major advisor. A majority of the committee must have primary appointments within the Department and at least one member must be from outside the Department. The committee must be approved by the Director of the Microbiology Graduate Program. The research committee must meet a minimum of three times, unless waived by the Director of the Microbiology Graduate Program.

Format for Committee Meetings. Prior to the first meeting (to be held in spring of the third year in the graduate program) the student will prepare a one-page report describing the background information for the project. In addition, the student will prepare a summary of their progress.  This document will be distributed to the committee one week prior to the scheduled meeting.  After the meeting, the chair of the research committee will add a summary of the committee's recommendations to the report and distribute the report to the student, the student's mentor, and the department file. In preparation for each subsequent meeting, students will add a progress report to the previous report. After each meeting, the chair will add the committee's recommendations.

Dissertation Committee Membership. The dissertation committee should consist of the research committee and will meet only when the committee approves the student's intent to defend. The chair of the dissertation committee is the student's mentor. The dissertation committee must pass the student prior to the scheduling of the public defense. Note that the Graduate School requires a minimum of 3 weeks (21 days) notice to schedule a public defense.

Last modified: Oct 07, 2015