PiN students are required to complete a Preliminary Qualifying Examination (PQE) on or before March 31 of their second year in order to demonstrate their ability to embark on original scientific investigation. The PQE comprises a written research proposal and a two-hour oral examination, and typically provides the foundation for the thesis project. Preliminary data are NOT required. While the main focus of the oral exam is the written proposal, students are also expected to demonstrate substantial knowledge in their field of research and related areas of neuroscience. Students are encouraged to discuss their specific aims and their proposal in depth with their thesis advisor. Their advisor may read and provide suggestions on drafts for the proposal, as long as the final document is the student’s own work. Students typically practice presenting and answering questions in lab meetings and in small groups with peers in the program. Students are expected to have completed (or have in progress) at least 4 credits of elective coursework at the time of the exam and a minimum GPA of 3.0.

PQE Guidelines for PiN Students

Goals of the Exam

The purpose of the PQE  is to assess your preparation and ability to embark on an original scientific investigation. Preliminary data are not required. The goals of the exam are to demonstrate that you are able to: (1) define a question in a particular area of research, (2) review the literature pertinent to that question with an emphasis on what makes the proposed experiments interesting and important, (3) formulate an experimental plan that would address and answer the question, and (4) interpret possible experimental outcomes in a manner that indicates awareness of the limitations of the methods used.

Forming your Committee

The Preliminary Exam Committee comprises three examiners, which you should select in consultation with your dissertation advisor. You must obtain the program director’s written approval before inviting the three proposed examiners to join your committee; this can be done by email, no form required. The committee chair and at least one other member of the committee must be affiliated with PiN. One committee member may be external to Harvard. The examiners may also serve subsequently on your Dissertation Advisory Committee. The committee chair serves as an examiner, oversees the administration of the exam, and ensures you receive an oral summary of the outcome and evaluation at the end of your exam. The chair is also responsible for returning the PQE report to the PiN administrator.

Submitting "Specific Aims"

Before writing your research proposal, you should receive approval from your exam committee (and dissertation advisor) of the specific aims and overall direction of the proposal. This can be done by submitting to the committee, generally by email, a one or two page description of 2-4 specific experimental aims. This written description should follow the typical “Specific Aims” format of most NIH grant proposals, with a short introduction and a description of each aim. Committee members will either approve the aims or suggest appropriate changes in the aims or scope. You may arrange a meeting with your dissertation advisor and one or more examiners to discuss suggested changes before writing your proposal.

Writing your Proposal

You must deliver your research proposal to your exam committee and the program administrator at least 7 days prior to your PQE. If the proposal is late or too long, the committee chair may request a postponement of the exam. Your thesis advisor is encouraged to discuss your proposed project with you in depth and to review and provide suggestions for your proposal.

Your proposal should not exceed 13 pages, including any figures and legends (optional) and excluding references, using Arial, Helvetica, Palatino Linotype, or Georgia typeface, a font size of 11 points or larger, and at least half inch margins. Figure legends may use a smaller type size. (Note that sections 1, 3, and 4 conform to the revised NIH guidelines for F31 applications. In an F31 application, section 2 would be shortened and folded into section 3.) The proposal should include the following sections (using the prescribed subheadings):

Specific Aims (1 page)

List succinctly the specific objectives of the proposed project. Two or three Specific Aims are suggested.

Background (6-7 pages)

Briefly sketch the background leading to the present application. Critically evaluate existing knowledge, and specifically identify the gaps that the project is designed to fill.

Significance (less than 1 page)

Explain the importance of the problem that the proposed project addresses. Identify the gaps that the project is intended to fill. Explain how the proposed project will improve scientific knowledge or technical capability in one or more broad fields.

Approach (4-5 pages)

Describe the overall strategy, methodology, and analyses to be used to accomplish the specific aims of the project. Describe how the data will be collected, analyzed, and interpreted. Discuss potential problems, alternative strategies, and benchmarks for success anticipated to achieve the aims. If the project is in the early stages of development, describe any strategy to establish feasibility, and address the management of any high -risk aspects of the proposed work. Preliminary data is optional. Any figures and legends should be included within this page limit.


There is no length limit, but you are expected to have read all the papers cited in this section.

Exam Outcomes

Students will be asked to leave the room during deliberations at the beginning and end of the exam. The exam committee will decide on one of two outcomes.


This outcome indicates the Exam Committee’s opinion that the student is fully ready to initiate work on the proposed projects. In the written report, the Exam Committee will comment on the student’s strengths and weaknesses noted during the exam. At the end of the exam, it should be discussed whether the Exam Committee will serve as the Dissertation Advisory Committee. This is often the case, but the student is free to change the composition of the Committee with the approval of the Program Director. The Exam Committee should recommend the time frame for the first DAC meeting, which should not be later than 9 months after the PQE. When giving a grade of “Pass” the Examining Committee may recommend work to correct minor deficiencies. This recommendation will be communicated to the advisor, who will supervise the student as appropriate. If the Committee feels that the problems are substantive enough to require re-review by the Committee, then the outcome of the exam should be “Special Committee Review” rather than “Pass”.

Special Committee Review

This means that the student’s status will be reviewed within 3 months. The review will be performed by a special committee consisting of the members of the original Preliminary Exam committee, plus the Program Director or Associate Director. This outcome indicates substantive problems in the student’s written proposal, oral presentation, laboratory work on the project prior to the PQE, or coursework. Any student whose grade point average falls below 3.0 at the time of the exam is automatically given a grade of “special committee review.” These problems may be the usual sorts of problems that ultimately successful students sometimes experience at this stage, and this outcome should not be viewed as a failure. Instead, it is a mechanism for helping to ensure that all students embarking on a Ph.D. thesis have a strong chance of succeeding in a reasonable amount of time.

If this is the outcome of the exam, the Program Director will send the student a letter describing the goals and expectations for the coming months. This letter will be written in consultation with the committee Chair and the student’s Advisor. The letter may set goals relating to any of the following issues: the written proposal, the oral presentation, research activities, coursework, and professional conduct. The letter may request that the student repeat the exam; however, in some cases, this may not be indicated. Copies of the letter should be sent to the entire Special Committee.

The Special Committee Review meeting should focus on the issues described in the letter. The meeting may represent a “repeat” of the PQE. Alternatively, the meeting may take a different format. The format and goals of the meeting should be tailored to the student’s circumstances, but they should made clear to all participants in the letter. After the Special Committee Review meeting, the Program Director will determine the student’s status in the program. This decision will be made in consultation with the student’s Advisor and the Associate Dean of Basic Graduate Studies, and it should be decided within 3 days of the meeting.