Guidelines for Ph.D. Program

Comprehensive Exam

The Comprehensive Exam consists of the oral defense of a written research proposal developed by the student. As a first step, the student will develop a pre-proposal on any Microbiology or Immunology topic, including their planned or related research.

Timetable. Students are expected to finish the Comprehensive Exam no later than the 5 ^th semester of graduate study, excluding summer semesters. The first step in the process is the submission of the pre-proposal. For a student admitted in the Fall, this timeline requires pre-proposal submission in the summer (by July 31) following their second year and Comprehensive Exam completion during the Fall semester of their third year. Special permission from the Graduate Affairs Committee is required in advance if a student is unable to submit the pre-proposal by this deadline. Permission must include an explanation for the delay and a proposed timeline for submitting the pre-proposal. The Graduate Affairs Committee will evaluate special circumstances, such as medical leaves or department transfers, on a case-by-case basis. The Comprehensive Exam can be taken earlier if so desired if 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 five members. The chair of the committee must be a member of the Department and cannot be the student's mentor. 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 a pre-proposal. This 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 1/2", and a font size of 11 (Arial). The emphasis of the pre-proposal 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 student's mentor can offer advice on the content of the aims if requested by the student, but the ideas and proposal must be written by the student and consist of his/her ideas.

The exam committee will determine 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 calendar days after submission without the student present and make one of the following decisions:

1. Pre-proposal is suitable for development into a full proposal.
2. Pre-proposal is not suitable. The committee requests more detail on the pre-proposal or request a major rewrite of the pre-proposal. The chair of the committee will summarize the suggestions of the committee and prepare a written statement for the student. The student can follow up with the chair of the committee (or other committee members) to discuss the comments. The committee's request must be honored within 14 calendar days of the request.

When the committee re-reviews a revised or new pre-proposal, the committee can either accept the pre-proposal or allow another 14 calendar days to continue to revise the pre-proposal. If the student is unable to prepare an acceptable pre-proposal, the student may be dismissed from the Ph.D. program.

Proposal. The student will expand the pre-proposal by the committee into a full-length proposal. The full proposal is due within 45 calendar days of notification that a pre-proposal is acceptable. The proposal should follow the NIH Guidelines for an F31 Fellowship. A guideline for grant-writing can be found here: https://grants.nih.gov/grants/how-to-apply-application-guide/format-and-write/write-your-application.htm and here:  https://grants.nih.gov/grants/how-to-apply-application-guide.html. In addition, sample NIH applications are available here:  https://www.niaid.nih.gov/grants-contracts/calix-sample-f31-application-and-summary-statement. The proposed research should be capable of being completed by a graduate student in two years. Be sure to consider the expected results and alternative results for each experiment as well as 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
• Research strategy: 6 pages total
  -Background and significance
  -Experimental design 

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 calendar days after submission:

1. The proposal is suitable. The student may schedule the exam.
2. The proposal requires revision. The committee will 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. The student can follow up with the chair of the committee to discuss the comments. Students have 21 calendar 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, at the discretion of the committee. 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 will report the following results:

1. Satisfactory: The student passes, needing a simple majority vote.
2. Unsatisfactory:
   a. The student may be re-examined on the same proposal in no less than 90 days at the discretion of the committee. If necessary, a second re-examination is allowed. The student must pass the re-examination in order to remain in the Ph.D. program.
   b. Fail the student, the student is dismissed from the Ph.D program.

Dismissal from the Ph.D. Program. Per department dismissal policy, 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 department.

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

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 membership must be approved by the Graduate Affairs Committee.

Research CommitteeMeetings. The research committee must meet a minimum of three times, unless waived by the Director of the Microbiology Graduate Program. The first meeting of the committee should occur within 3 months of completion of the comprehensive examination (typically by March 31 in the third year in graduate studies). Thereafter, annual meetings of the committee will be held by March 31 of each year unless the committee members recommend more frequent meetings to evaluate progress.

Prior to the first meeting of the Research Committee 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

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) noticeto schedule a public defense.