PhD in Bioinformatics
The post-bachelor’s PhD requires a total of 64 course credits, consisting of the 40 required credits listed below, or their equivalents, and additional elective lecture, laboratory, and research credits. The precise course of study will be determined in consultation with faculty advisors and will reflect the student’s background and interests. Although participants in the program will not necessarily take the same set of core courses, all students must demonstrate mastery of core subject matter in biophysical chemistry, biology, and computation/mathematics. In order to be admitted to PhD candidacy, students must demonstrate mastery of the core subject matter (no lower than a B in each of the core courses) and successfully complete a qualifying examination.
The post-master’s PhD requires 40 credits of coursework, consisting of an appropriate combination of lecture, laboratory, and research, as recommended by the student’s thesis advisor. Other requirements are the same as for the post-bachelor’s PhD.
Required Core Courses (40 cr total)
- ENG BE 562 Computational Biology: Genomes, Networks, Evolution (4 cr)
- ENG BE 768 Biological Database Systems (4 cr)
- ENG BE 777 Computational Genomics I (4 cr)
- ENG BF 690 Bioinformatics Challenge Project (2 cr each; 4 total)
- ENG BF 751 Molecular Biology and Biochemistry: Molecules and Processes (4 cr)
- ENG BF 752 Legal and Ethical Issues of Science and Technology (4 cr)
- ENG BF 778 Physical Chemistry for Systems Biology (4 cr)
- ENG BF 810 Laboratory Rotation System (1 cr each; 3 total)
- ENG BF 820 Research Opportunities in Bioinformatics (1 cr)
- ENG BF 821 Bioinformatics Graduate Seminar (2 cr each; 4 total)
- GRS MA 681 Accelerated Introduction to Statistical Methods for Quantitative Research (4 cr)
Fulfillment of core course equivalents will be determined based on documented previous academic and/or work experience. The student and his or her advisors will petition the curriculum committee for such equivalencies. When either past work or an alternate course has been accepted as a core equivalent, the student’s advisors will recommend another course to fulfill the 36 core credit hours. Advanced elective courses should be taken in place of any waived course requirements.
For the post-bachelor’s PhD degree: In addition to the core courses listed above, students are required to complete at least one additional elective course (i.e., non-research). The remainder of the 64 credits may be satisfied by completing additional electives and/or research credits (ENG BF 900 and/or BF 901). A minimum of 2 research credits is required.
For the post-master’s PhD degree: In addition to the core courses listed above, at least 2 credits of research (ENG BF 900/901) are required. (Note: ENG BF 900 is taken as research credit for PhD students who have not yet passed the qualifying examination. After admission to PhD-candidate status, students enroll in ENG BF 901 for research credit.)
- CAS BB 522 Molecular Biology Laboratory
- CAS BI 502 Topics in the Theory of Biological Networks
- CAS BI 504 Advanced Evolutionary Analysis
- CAS BI 549 Molecular Phylogenetics and Evolution
- CAS BI 553 Molecular Biology II
- CAS BI 556 Membrane Biochemistry and Cell Signaling
- CAS BI 560 Systems Biology
- CAS BI 572 Advanced Genetics
- CAS BI/CH 527/528 Biochemistry Laboratory I & II
- CAS CH 525 Physical Biochemistry
- CAS CS 542 Machine Learning
- CAS CS 549 Pattern Matching and Detection with Applications in Biological Sequence Analysis
- CAS CS 565 Data Mining
- CAS MA 555 Numerical Analysis I
- CAS MA 565 Mathematical Models in the Life Sciences
- CAS MA 575 Linear Models
- CAS MA 576 Generalized Linear Models
- CAS MA 581 Probability
- CAS MA 582 Mathematical Statistics
- CAS MA 583 Introduction to Stochastic Processes
- CAS MA 584 Multivariate Statistical Analysis
- CAS MA 614 Statistical Methods II
- CAS MA 684 Applied Multiple Regression and Multivariable Methods
- ENG BE 560 Biomolecular Architecture
- ENG BE 565 Molecular Biotechnology
- ENG BE 566 DNA Structure and Function
- ENG BE 569 Next Generation Sequencing
- ENG BE 764 Biophysics of Large Molecules
- ENG BF 527 Applications in Bioinformatics
- ENG BF 571 Dynamics and Evolution of Biological Networks
- ENG EC 533 Advanced Discrete Mathematics
- ENG EC 534 Discrete Stochastic Methods
- ENG EC 730 Information-Theoretical Design of Algorithms
- GMS PA 600 Introduction to Pathology & Pathophysiology of Disease
- GRS BI 610 Developmental Biology
- GRS BI 735 Advanced Cell Biology
- GRS BI 755 Cellular and Systems Neuroscience
- GRS CH 751 Advanced Topics in Physical Chemistry
- GRS CH 752 Advanced Topics and Chemical Physics
- GRS MA 770 Mathematical and Statistical Methods of Bioinformatics
- GRS MA 881 Statistics Seminar I
- GRS MA 882 Statistics Seminar II
- GRS MB 721 Graduate-Level Biochemistry
- GRS MB 722 Advanced Biochemistry
- GRS PY 771 Systems Biology for Physical Scientists and Engineers
- SPH BS 704 Introduction to Biostatistics
- SPH BS 830 Design and Analysis of Microarray Experiments and Next Generation Sequencing
- SPH BS 855 Bayesian Modeling for Biomedical Research & Public Health
- SPH BS 858 Statistical Genetics I
- SPH BS 859 Applied Genetic Analysis
- SPH BS 860 Statistical Genetics II
Upon entry into the Bioinformatics Program, each student will be appointed an academic advisor from the Bioinformatics faculty. The advisor will act as the student’s primary academic advisor until the student selects a research advisor(s).
Qualifying (Oral) Examination
All Boston University graduate students must pass a qualifying exam in order to advance to the level of PhD candidacy. In the Bioinformatics Program, this exam takes the form of an oral qualifying exam. The goal of the exam is for the student to demonstrate his or her general proficiency in bioinformatics, as well as command of the area(s) in which he or she intends to conduct research. All parts of the qualifying examination must be passed before the dissertation or thesis prospectus will be accepted by the Graduate School of Arts & Sciences.
Each student in the Bioinformatics Program will select a Qualifying Committee (QC) of four faculty members in the program, typically by sometime during the first semester of their second year. It is strongly encouraged that the QC include both faculty members with biological/experimental expertise and faculty members with computational expertise. The Director of Graduate Studies (DGS) must approve the committee membership and will be an ex-officio member of the committee.
Students must schedule their qualifying exam by March 31 of their second year, and must take the exam by June 30. Students who fail to pass the exam on their first try are allowed a second attempt, to be scheduled and completed by the end of the first semester of their third year.
There is no foreign language requirement for the Bioinformatics degree. However, basic mastery of spoken and written English as determined by oral presentations, written reports, and publishable manuscripts is a requirement for the PhD.
The PhD requires original research and its presentation in a form suitable for publication in an archival journal. Two thesis advisors, one predominantly an experimental researcher and the other predominantly a computational researcher, will guide progress toward the degree. The two thesis advisors and the Qualifying Exam Committee will normally constitute the Thesis Committee. The Thesis Committee will review the student’s progress annually and will also be responsible for judging both the thesis prospectus and the completed thesis.
Important: Please refer to the Graduate School of Arts & Sciences’ Forms, Policies & Procedures website (under the header “Graduation Requirements (PhD)” for detailed information and required forms regarding the Qualifying (Oral) Examination and the required thesis. Note that the Bioinformatics Program uses the term “thesis,” instead of “dissertation” when referring to PhD requirements. All “dissertation” items appearing under the “Graduation Requirements (PhD)” header should be considered as referring to Bioinformatics PhD “thesis” information.