Research Proposal

The research proposal begins with your making a Thesis Research Prospectus presentation in the first semester (fall) of your second year.

This 30-40 minute presentation includes your giving (1) an overview of the lab’s research program, (2) the objective of your thesis research within that context, and (3) the specific aims of the work you plan to complete directed toward that objective.

This first presentation counts towards the requirements in BCH 504–Doctoral Student Seminar.

Proposal Committee

The presentation is evaluated by your Proposal Committee specifically for its suitability as a starting point for a Research Proposal.

Your research mentor will not participate in the review and evaluation of your Research Proposal presentation, your written research proposal or the proposal’s oral defense. The Dissertation Committee without the mentor is referred to as the Proposal Committee.

In addition, for the purposes of the Research Proposal (BCH 565), each Proposal Committee is chaired by one of the members of the Graduate Affairs Committee, and this chair is a full member of the Proposal Committee.

This chair serves as the committee’s administrative head, ensuring that:

  • you and committee adhere to the proposal timetable;
  • both you and faculty are responsive to this timetable and to the academic objectives of this process;
  • your discussions of the written drafts and the oral defense are objective and consistent with the department’s academic goals.

This member chairs the Research Proposal Presentation evaluation meeting and the oral defense. A copy of the Doctoral Student Seminar critique prepared by the Proposal Committee members is given to you and to the research mentor. Copies of the oral defense summary also prepared by the Proposal Committee members are given to you, your mentor and to the director of graduate affairs, and accompany the grade submitted for BCH 565.

The Proposal Committee meets with you following the Research Proposal Presentation to present and discuss each member’s evaluation. The written critique prepared by the Proposal Committee members includes the criteria described under Doctoral Student Seminar, but is typically extended to evaluate whether an adequate discussion was presented of possible future experiments and/or further hypotheses that could be derived from reviewing the lab’s research and supporting paper(s) presented.

If this evaluation is positive, you may continue with the proposal process. This approval may be contingent on modification of the specific aims of the proposed research. Such changes should be made and approved within one week of the research presentation.

If the committee concludes that (1) the thesis research prospectus presentation, (2) the discussion of possible future experiments, (3) and/or the hypotheses to be tested are not adequate, you will be given an opportunity to repeat your presentation.

You are required to submit a written proposal to your Proposal Committee within 5 weeks of your research presentation, allowing for one week for approval of any changes in the specific aims.

Proposal format

The written proposal format our department follows is the NIH’s pre- and postdoctoral fellowship (NRSA Forms 416) and consists of the following sections:

Specific Aims: 1 page

This should be a logical extension of published research from your mentor’s lab and others and should contain a brief but explicit statement of the hypothesis being tested.

Background and Significance: 4 pages

This section should briefly describe the background, critically evaluate the most pertinent existing knowledge and specifically identify the problem that the proposal is intended to address. It should draw from the material described in the research presentation.

Research Design and Methods: 5 pages

This section should briefly describe how the specific aims can be accomplished. It need not contain exquisite detail, but you must be sufficiently conversant with the design and procedures to discuss their proper application and limitations during the oral defense and to describe probable results and their interpretations.

You should also be able to discuss the work proposed in the context of your field in general; for example, if you propose to work on transcription initiation, you should be able to discuss transcription in general, including mechanisms of regulation, the role of chromatin, and processing of the nascent mRNA.

References: No limit

Figures and Tables are incorporated in the text (as in NRSA applications) and are therefore included in the 10-page limit.

Page limitations refer to single-spaced pages and are maxima; they are not meant to imply that each proposal must reach the maximum limits.

Proposal evaluation

Within one week of receiving the written proposal, each member of the Proposal Committee returns his/her copy of the document to you along with a written evaluation. The evaluation should point out major problems to be addressed and corrections to be made. Two weeks after receiving the Proposal Committee’s evaluation, you must return a revised version to the committee. You are encouraged to meet individually with Proposal Committee members to discuss the revised version before the oral exam.

Oral exam

The oral exam typically begins with a brief (15- to 20-minute) summary by you of the background, hypothesis, specific aims and research plan presented in the written proposal, with the major focus on the experimental design adopted to address the proposal’s aims.

The four Proposal Committee members then question you about this plan, including its rationale and choice of experiments and experimental design, exploring possible shortcomings of the experimental protocols and possible alternative, negative or false positive results.

They also evaluate your knowledge of the general area of the proposal; for example, if on bacterial replication, how does this compare to eukaryotic replication?

The objective of the oral exam is not simply to have you recite orally what has been presented in writing but to examine your overall grasp of the research area in which the lab works and about which your proposal is written.

Monitoring your progress toward thesis completion

Doctoral students are required to meet with their Thesis Committee in the fall of each year. The proposal defense in your first semester in biochemistry represents the first such meeting. At these research progress presentations, you review the objectives of your thesis research, outline the objectives set for the preceding 12-month period, and summarize the results of the research conducted to address these objectives. You also present an outline of the objectives for the subsequent year.

The committee suggests how objectives and/or research plan might be altered, if necessary, and offers alternative interpretations of the results presented. The outcome of this meeting is an evaluation by the committee of your progress toward completion of a competitive doctoral thesis.

Biochemistry Research Day

 In the spring of each year, doctoral students are required to present their research at the Biochemistry Research Day. Students in their first year in biochemistry (in their fourth semester in the school) are required to present their work in poster form. In subsequent years, doctoral students make oral presentations to the department’s faculty, students and staff in attendance at the Research Day