Qualifying Exam, Admission to Candidacy and the Dissertation

As early as the fourth semester and no later than the sixth semester, the student undertakes a series of activities that lead to admission to candidacy for the PhD degree, with the major milestones being the selection of a Qualifying Exam Committee, passing of the Qualifying Exam and selection of a Dissertation Committee.

As part of the Qualifying Exam, the student presents a dissertation prospectus, which must be approved by the Qualifying Exam Committee. The Qualifying Exam must be successfully completed before the beginning of the seventh semester. Following admission to candidacy, the student selects a Dissertation Committee, which may have the same members as the Qualifying Exam Committee. The adviser must be a member of the Dissertation Committee. The Dissertation Committee’s role is to guide the student towards the PhD degree and to approve the thesis.

Qualifying Exam Process

The basic purpose of the Qualifying Exam is to assure that the student is well prepared to pursue significant dissertation research. The possible outcomes of the Qualifying Exam include Pass with Distinction, Pass, Conditional Pass, and Fail. At the end of the second QE meeting, the QE Committee may put in writing a specific set of conditions and a time-frame in which these conditions must be fulfilled, in order for the student to pass the Qualifying Exam.

Committee Selection:

In the fourth or fifth semester, the student should select a Qualifying Exam (QE) Committee.

  • The QE Committee may have 3 or 4 members. The adviser may be a member of the QE Committee, but does not need to be.
  • The Committee may contain members outside of Yale if necessary.
  • The composition of the QE Committee must be approved by the adviser and the CBB Director of Graduate Studies (DGS).
  • The adviser designates a Chair of the QE Committee. This may be the adviser, but does not need to be.

The student then notifies the CBB Graduate Registrar of the members and chair of the QE Committee.

Committee Meetings:

The QE process requires two meetings of the QE Committee, a Pre-Qualifying Exam meeting and the actual Qualifying Exam. The QE may be completed before all required CBB program coursework has been taken and before the two Teaching Fellowships.

Pre-Qualifying Exam Meeting

For the pre-qualifying exam meeting, the student prepares a 2-3 page double-spaced preliminary research proposal and distributes it to Committee members before the meeting. The student meets with the Qualifying Exam Committee to present and discuss that proposal. There will typically be 45 minutes for the proposal followed by 15 minutes of questions, although this can vary depending upon your Committee.

The Committee then decides whether the student is ready to prepare for the QE exam itself. If so, the Committee identifies 3 or 4 topic areas on which the student will be questioned during the oral qualifying exam.

  • These topics are typically chosen to represent a mix of biological and computational areas.
  • The QE Committee completes an evaluation form at the end of this meeting, identifying any concerns and recommendations for the student, and listing the topics on which the student will be questioned at the actual Qualifying Exam.

Qualifying Exam Meeting

For the second QE meeting (typically 2-3 months later), the student prepares a 15-20 page double-spaced dissertation prospectus in the form of a research proposal, which should contain:

  1. a specific question or questions that will be addressed,
  2. a brief literature review indicating the present state of the field of intended research,
  3. an overview of preliminary work that the student has performed to date, and
  4. a research plan outlining work to be undertaken in the future.

Committee members may provide further guidance on the exact structure of the prospectus. The prospectus should ideally be distributed to the committee two weeks before the second QE meeting. During the QE, the student presents and discusses the prospectus (usually in the form of a brief PowerPoint presentation) for approximately 1 to 1.5 hrs, then is questioned on it and on the several topic areas previously identified by the Committee.

  • The QE Committee completes an evaluation form at the end of this meeting, listing any concerns and recommendations for the student.
  • Participation of the adviser in the Qualifying Exam is desirable but not required.

Admission to Candidacy:

The Chair of the QE Committee informs the CBB DGS and Registrar of the results of the QE. After the student passes the QE, the CBB program recommends to the Graduate School that the student be admitted to candidacy for the PhD. Unlike many other programs and departments within BBS, CBB does not have a separate process for admission to candidacy.

  • A copy of the prospectus should be sent by the student to the CBB Registrar.
  • The Registrar will then send a copy of the prospectus along with the relevant forms to the Graduate School.
  • The student must have fulfilled the Graduate School’s requirement of two Honors grades in classes taken at Yale.
  • The student need not have completed all coursework, fulfilled all TA requirements, nor, if relevant, passed the Speak Test in order to be admitted to candidacy.

Dissertation Committee and Procedures

A general checklist from the Graduate School can be found here.

1. After the student has passed the Qualifying Exam and been admitted to candidacy, the QE Committee transitions to the Dissertation Committee. Subject to the approval of the adviser and the CBB DGS, the membership of the Dissertation Committee may be changed from the QE Committee. The adviser must be a member of the Dissertation Committee. The Dissertation Committee is typically 3 to 4 faculty members, the majority of which must have Graduate School appointments. The Dissertation Committee and CBB DGS are responsible for ensuring that student’s PhD research is within the broad field of computational biology and bioinformatics, and that it does not veer off significantly into experimental biology or non-biological computation. This is usually demonstrated by a first-author or joint first-author paper in a respected journal in computational biology or bioinformatics.

2. If there are unusual circumstances, such as an adviser moving to another school, the CBB DGS will work with the student to determine the best course of action for making progress with the student’s research.

3. Students must meet with their Dissertation Committee at least yearly to discuss their progress. This meeting should be a joint Committee meeting, at which a formal evaluation form is completed by the committee. Such meetings may be held for the purpose of discussing the Dissertation Progress Report (discussed below), or they may be held at other times in the year.

4. After the student has been admitted to candidacy, he or she must prepare a Dissertation Progress Report (DPR) each year in the spring. This report maps the achievements of the past year and the goals for the upcoming year. This report should be emailed to each member of the Dissertation Committee, and each member should informally sign off on the DPR by email to the student, with copies to the adviser and the DGS. The student is also required to submit the DPR through the Graduate School’s online DPR submission process, by the required deadline. The adviser and the DGS must formally approve the DPR through the online system as well.

5. In the final year, the student writes the dissertation, distributes it to the Dissertation Committee, and then defends the dissertation in a presentation which any interested individual may attend. All of the Committee members are expected to attend the dissertation defense and to give comments on the dissertation. Committee comments must be addressed in the final version before it is submitted to the Graduate School. The Dissertation defense should be scheduled sufficiently in advance of Graduate School deadlines that there is time to make any necessary changes.

6. There are two deadlines for submission of the dissertation to the Graduate School: October 1 for a December degree and March 15 for a May degree. These deadlines may change slightly each year, so students are advised to check the academic calendar for the exact date. The Graduate School does not make exceptions to these deadlines.

7. The Graduate School requires that each dissertation be read and evaluated by at least three people. The number and necessary qualifications of the readers are specified by the Graduate School.

8. Students should obtain a dissertation submission packet from the Graduate School. This contains several forms that the student needs to complete and submit along with four copies of the dissertation, including one copy which goes to the Graduate School and three copies which will be delivered to the Readers (all electronically). The CBB Registrar will deliver the 3 copies to the Readers. The Readers then review the dissertation and fill out a Reader evaluation form for the Graduate School.

9. After all Reader evaluation forms have been returned to the Graduate School and any requested changes to the dissertation have been made, the CBB Director of Graduate Studies will sign a form recommending award of the PhD degree. Then the Graduate School Degree Committee and finally the Yale Corporation will vote to approve conferral of the degree.