Thesis Research and PhD Mentorship
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. Our program is highly interdisciplinary and it is expected that while some students will gain a balanced training in experimental, computational, and statistical areas, others may master a specific field (in genomic or computational biology) but, at the same time, develop competence in the other areas. In other words, a student with a strong background in one area (genomics or computational biology) should develop skills that will facilitate productive interactions with investigators in other fields.
Thesis Committee
After passing the Preliminary Exam, students assemble a “Thesis Advisory Committee”. This committee, which is selected by the student in consultation with the thesis supervisor and approved by the Chair, includes the student's supervisor and at least four other faculty members (one to serve as “Chair”) experienced in the research area(s) involved. The Thesis Committee, like the Prelim Committee, will have a balance among biologists, computer scientists, and statisticians. Each student is expected to meet with this advisory committee at least once a year. Following each meeting, the committee chair submits a written report on the student's progress to the Program Chair. In addition, students are encouraged to communicate informally, as often as necessary, with members of their dissertation committee so that this committee is informed about results, changes in strategy, or problems that arise. All GCB students are advised to include faculty from other institutions to serve on their committee (in person or via teleconference). While our goal is for students to complete their study in about five years, we recognize that some will require additional time.
Permission to Write and Defend the Thesis
The Graduate Group requires a dissertation to represent a definitive contribution to scientific knowledge and to show that a student possesses the ability to perform independent research. The main information contained in the dissertation should be of a caliber sufficient for publication in a reputable, refereed scientific journal.
Before beginning the process of writing and defending his/her thesis, the student must convince the thesis committee that thesis research is substantially finished and that the thesis is ready to be written. If the committee agrees that the experimental work is sufficiently complete and defensible, the "Permission to Write" form must be signed by the committee chair and thesis advisor and returned to the Graduate Group Office. The committee should also agree on a time line that includes an approximate date for the defense. This is necessary to ensure that a time convenient for all committee members can be arranged and that an appropriate room can be scheduled.
The written document must conform to the dissertation rules of the University (see the Dissertation Manual issued by the Office of Graduate Studies). The mentor must be satisfied with the written document before it is distributed to the committee. A draft of the thesis must be presented to each committee member and the GCB office no later than two weeks prior to the scheduled defense. Failure to do this may result in cancellation of the scheduled thesis defense.
The Thesis Presentation and Defense
The thesis presentation will take the form of a public lecture. The lecture should be scheduled well in advance so that a time convenient to the entire committee can be found and notices can be sent to the faculty and student membership. The Graduate Group Office needs to know the defense date, title of the thesis and place and time of the defense at least three weeks in advance. The Graduate Group Office will then send a public notice to the University community advertising the thesis defense. The Graduate Group Office is responsible for the forms which are required after the thesis defense.
Every effort should be made to have the full four-member thesis committee present at the thesis defense. If a thesis committee member cannot be present at the defense, he/she may provide to the committee chair approval of and/or comments concerning the thesis prior to the defense. If that is not possible, the student is responsible for finding a substitute committee member, with the approval of their program chair. Following general questioning during the public phase of the presentation the thesis defense will commence. The defense is open only to the thesis committee and mentor. The decision on approval of the thesis will be made solely by a majority vote of the committee. The student should anticipate that the committee may require changes to the thesis that could include additional writing, editing and re-evaluation of data. Such changes must then be approved by the committee before the thesis is deposited. For this reason, it is imperative that thesis defenses be scheduled no later than two weeks before the deadline for depositing theses.
Before a student makes the appointment to deposit the thesis, the student must provide the Graduate Group Office with a copy of the abstract page, an original signed copy of the title page, and a mailing or email address where the student can be reached after graduation. The Graduate Group Office will then provide the student with a signed 153 form, which must accompany the dissertation to the Graduate Division of Arts and Sciences (GAS).
Graduation Procedures
The Graduate Division of Arts and Sciences sets three graduation dates each year in May, August, and December. A formal commencement ceremony is held in May. The Graduate Group Office will distribute a calendar for each degree period, giving the deadlines for signing up for graduation, and for defending and depositing the thesis. If a student is not able to graduate after they have signed up, they must re-apply for the next degree period. The graduate Group Office will guide students through the thesis submission and graduation scheduling.
Recertification Procedure
University rules govern the time a graduate student may take to complete requirements for the Ph.D. In GCB, after initial certification that the student has passed all course work and required preliminary exam(s), the student will have five years to complete: 1. the thesis, 2. the thesis defense, and 3. submission of approved thesis. Students who have not completed all three requirements within 5 years of first registering for dissertation tuition, will cease to be Ph.D. candidates unless they pass a Recertification Exam.