Dissertation Phase

The GCB program is designed to provide mentorship and develop skills that will produce independent research scientist in the field of genomics and computational biology. It is the responsibility of the advisor and the thesis committee to evaluate the scientific quality and importance of the student's work and to decide at which point the student will receive permission to write the thesis. It is expected that the body of work accomplished is relevant and important to the scientific community. This criterion can be met by having at least two first-author papers published or "in press" in peer-reviewed scientific journals.

BGS developed a set of expectations for thesis mentors, students, and thesis committee members in 2016.  It can be found here.

The University has issued an extensive set of guidelines for Advising and Mentoring PhD Students

Students or faculty with questions or concerns about expectations should contact the graduate group chair or the BGS director.


Thesis committee members can serve a variety of roles in the student’s project. At a minimum, they attend all thesis committee meetings and offer feedback, read and comment on the thesis manuscript, and attend the defense. Often, they serve as informal advisors on the thesis project, and meet with the student as needed between committee meetings. The Committee Chair is specifically responsible for running the committee meetings, completing the paperwork, and submitting it to the GCB office.

The student should work closely with his or her advisor(s) on the composition of the Thesis Committee. The committee must include the advisor/co-advisors, a Chair, and at least three other members, one of whom must be external to Penn/CHOP/Wistar. The chair must be of Associate Professor rank or higher, and must be a member of GCB. Students should aim for diversity of field of expertise and gender in their committee. Once the committee members are selected, they must be approved by the Graduate Group Chair.


GCB strongly encourages students to be co-mentored by faculty with complementary fields of expertise. This can take a variety of forms, depending on the student’s interests and the faculty members’ needs. Often, students will have a primary mentor, who hosts and supports the student, and a secondary mentor, either formally (e.g. co-authorship, registration on the university level), or informally. Occasionally mentors will split the financial support of the student. Co-mentoring arrangements should be discussed with the GCB office as soon as the secondary mentor is identified


PhD students should meet with their Thesis Committees at least once per year for Combined Degree students, meetings should take place every six months. The purpose of these meetings is to provide objective advice and fresh points of view to the student and Advisor. A lively discussion may be expected at these meetings, which is sure to benefit the student and his or her research.

Committee meetings are also important for ensuring that the student is:
i) on schedule to complete his or her Thesis in an appropriate time frame, including maintaining the appropriate balance of experiments, analysis, writing, and dissemination;
ii) thinking about and effectively pursuing post-graduation career plans; and
iii) at the appropriate time is given permission to write and defend the thesis.

Current students can find more details about thesis committee meetings here.


Permission to Write

When a suitable body of research has been completed, the Thesis Advisory Committee is convened. If the committee approves, Permission to Write is granted, and the dissertation writing is begun. After permission is granted, students have six months to complete and defend their thesis. If the student has not finished at the end of the six-month period, another thesis committee must be convened and permission must be reissued. 

Scheduling the Defense

The student should schedule the defense well in advance, confirm with all members of their Committee, and work with the Graduate Group Coordinator to reserve a suitable location. When the dissertation has been written, the student is to distribute a penultimate draft to the Thesis Committee, at least two weeks before the scheduled defense. Thus, before the final draft is submitted, each committee member can identify necessary revisions and suggest improvements.

Defense Process

After the student has had the opportunity to meet the criticisms and incorporate the suggestions of the committee in a final draft, a thesis defense is held. This defense includes a formal “public” seminar followed by a private session with the Thesis Committee. Following this private session, the Thesis Committee renders its recommendation on granting the degree. All thesis committee members must sign a certification form, which is then submitted to the GCB Chair for signature. Traditionally, the student’s mentor introduces the student at the beginning of the public defense, and hosts a party after the committee informs the student of its decision.

Dissertation Deposit

Students must schedule an appointment to deposit the dissertation with the Graduate Division office. The dissertation must be approved by the student's thesis committee before the deposit appointment takes place. Appointments can be scheduled by emailing the Graduate Division office at gas-degree@sas.upenn.edu. The Graduate Division and GCB coordinator will follow up with information about specific paperwork needed before this appointment. The Dissertation Manual, including templates, and online application for graduation can be found here. The final electronic version is submitted online the day before the deposit appointment, and final hardcopy, signed by the student’s advisor and the Graduate Group Chair, is given to the Graduate Division during the deposit appointment.

Current students should visit the resources page for more details on the above.