- Didactic Curriculum: In consultation with their Academic Advisor and/or Program Director, students must take an appropriate selection of Gateway Courses. For example, an incoming student with a Computer Science background would be expected to take 8100 and 8101, but not 8111 and 8112. All students must complete the Core Courses prior to taking the Qualifying Examination. Many additional Elective Courses are available, but are not explicitly required.
- BINF 8100 Biological Basis of Bioinformatics
- BINF 8101 Energy and Interaction in Biological Modeling
- BINF 8111L Bioinformatics Programming I
- BINF 8112 Bioinformatics Programming II
- BINF 8200 Statistics for Bioinformatics
- BINF 8201Molecular Sequence Analysis
- BINF 8202 Computational Structural Biology
- Research Rotations: Each Ph.D. student must complete two Research Rotations, each worth two credits towards their degree, within the first year. Each Research Rotation provides a semester of faculty supervised research experience to supplement regular course offerings. A different faculty member must supervise each Research Rotation. At the end of each rotation, the student must prepare and deliver a formal presentation of the findings for the faculty and their peers.
- Select an Advisor: After two semesters of Research Rotation, students must make an advisor selection. This is done by the beginning of the third semester.
- Qualifying Exam: Prior to defining a research topic, stuents are required to pass a Qualifying Examination to demonstrate proficiency in bioinformatics and computational biology, as well as competence in fundamentals common to the field. The Qualifying Examination must be attempted for the first time before the student's 5th semester of residence. Each student will name a Qualifying Exam Commitee. The student will provide their qualifying exam committee with the written reports describing their rotation research.
- Written Portion: The Qualifying Exam Committee will prepare a written exam for the student. This exam will consist of questions that require the student to synthesize knowledge from the core courses, the literature relevant to their research in the program to date, and other elective coursework they may have completed. The students will have 24 hours to complete the written examination and may use relevant library materials, if properly cited.
- Oral Portion: After passing the written sections, students must pass an oral exam over the same and related topics
The passing grade for both the written and oral sections is 75%. Students who do not pass both sections of the Qualifying Examination will be dismissed from the program.
- Dissertation Committee: After passing the Qualifying Examination, the student must set up a Dissertation Committee of at least four graduate faculty members, which must include at least three BCB Ph.D. faculty members and one member appointed by the Graduate School.
- Dissertation Proposal and Ph.D. Candidacy: Each student must present and defend a Ph.D. Dissertation Research Proposal after passing the Qualifying Examination and within ten semesters of entering the Program. The proposal must address a significant, original and substantive piece of research. The proposal must include sufficient preliminary data and a timeline such that the Dissertation Committee can assess its feasibility.
- Dissertation: Each student must complete a well-designed original research contribution, as agreed upon by the student and Dissertation Committee at the Dissertation Proposal. The Ph.D. Dissertation is a written document describing the research and its results, and their context in the sub-discipline. The Dissertation Defense is a public presentation of the findings of the research, with any novel methods that may have been developed to support the conclusions.