Intercollegiate Program in Bioinformatics

The Bioinformatics Program offers unique interdisciplinary training for graduate students in the science, engineering, medicine, and ethics of twenty-first-century cell biology jointly through the College of Engineering and the Graduate School of Arts & Sciences. Bioinformatics is the integration of mathematics and computation into the biological sciences. Through coursework, collaborative training projects, and dissertation research, you will learn to apply analytic and computational methods and information technologies to current problems in biology, biomedical engineering, and chemistry. You’ll receive instruction in communications and ethics as appropriate to the social impact and implications of genomics and biotechnology.

The program offers both MS and PhD degrees and is designed to combine advanced computational methods with the latest techniques in molecular biology. Students participate in individual courses with closely coordinated wet labs that include biological modeling and information sciences; industrial rotations; internships and grand rounds. Because we are educating future leaders, the program will also include training designed to sensitize students to the social impact of technology, including ethical and legal implications of emerging technologies. Research areas are numerous and include biological information management, gene mining, drug design and targeting, protein and nucleic acid structure, and cellular regulatory networks.

Faculty

A distinguished faculty of more than 40 members is drawn from 18 departments in five schools and colleges at Boston University, as well as a group of outstanding adjunct faculty from industrial and nonprofit organizations. Areas of research include genomics, biological networks, statistical methods in bioinformatics, evolutionary genomics, metabolomics, and structural biology and bioinformatics.

Students in the program have access to state-of-the-art computational facilities, including:

• Two computational clusters.
• An Illumina HiSeq 2000 and an Illumina Genome Analyzer IIx.
• The Illumina Sequencing Core Facility (ISCF), which offers Next Generation Sequencing at Boston University School of Medicine.
• The Massachusetts Green High Performance Computing Center (MGHPCC): a research computing data center that is being designed and built in Holyoke, MA, by a collaboration comprising Boston University, MIT, Harvard, Northeastern, and the University of Massachusetts, as well as the Commonwealth of Massachusetts.
• The Molecular Genetics Core Facility, which provides DNA Isolation services from different sources, sample storage, preparation of lymphoblastic cell lines, high-throughput DNA sequencing, and high-throughput genotyping.

Innovative Features and Activities

The Bioinformatics program offers several innovative features to help enhance graduate education. These include:

• The annual International Workshop in Bioinformatics and Systems Biology, which is a joint undertaking of computational biology graduate programs in Boston, Kyoto/Tokyo, and Berlin.
• The Challenge Project offers teams of first-year students the opportunity to do original research on large-scale problems with direction, but minimal supervision, by faculty.
• The Wet-Lab Experience introduces new trainees to state-of-the-art experimental methods in the summer before they officially enter the program.
• The Student-Organized Symposium is an annual opportunity for students to identify an important or emerging area of science and invite leading researchers to present their latest results.

Master of Science (MS) in Bioinformatics

The emphasis of the MS program is preparation for mid-level industrial positions in bioinformatics, and the MS constitutes a “Pre-professional MS.” Credits earned in the MS program may be applicable to the PhD program, but the MS program is not intended to be a stepping-stone toward a PhD (MS candidates wishing to enter the PhD program must apply for admission to that program via the normal application process).

The master’s degree requires 32 credits of coursework, with at least 20 chosen from the program’s core. Students must also demonstrate a working knowledge of computational methods available to the modern bioinformatician by completing an internship as part of the degree requirements. Upon completion of the internship, the student is required to submit a written report on the internship experience. This report serves in lieu of an MS thesis. A brief written report from the intern’s supervisor is also required. Internship credit is obtained by registering for BF 541 Bioinformatics Internship, or BF 501/502 Bioinformatics Master’s Project. The required credit hours may vary.

MS Required Core Courses (20+ cr total)

• CAS BI 552* Molecular Biology I (4 cr)
• ENG BE 562** Computational Biology: Genomes, Networks, Evolution (4 cr)
• ENG BE 768 Biological Database Systems (4 cr)
• ENG BF 778 Physical Chemistry for Systems Biology (4 cr)
• ENG BF 821 Bioinformatics Graduate Seminar (2 cr each; 4 cr total)
• ENG BF 541 Bioinformatics Internship (variable cr)

*Students may take BI 553 Molecular Biology II if approved by their advisor.
**Students with no prior experience or exposure to bioinformatics application should take BF 527 Bioinformatics Applications before taking BE 562.

Fulfillment of core course equivalents will be determined based on documented previous academic and/or work experience. The student and his or her advisor 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 advisor will recommend other courses to fulfill the 20 core credit hours. Advanced elective courses should be taken in place of any waived course requirements.

The remaining credits needed to complete the requirements for the MS will consist of electives and/or additional research projects.

Suggested Curriculum

First Year

Fall Semester

• BI 552 Molecular Biology I (4 cr)
• BE 562 Computational Biology: Genomes, Networks, Evolution (4 cr)

Spring Semester

• BF 778 Physical Chemistry for Systems Biology (4 cr)
• BE 768 Biological Database Systems (4 cr)
• BF 821 Bioinformatics Graduate Student Seminar (2 cr each semester)

Summer

Students may begin the internship.

Second Year

Fall Semester

• BF 821 Bioinformatics Graduate Student Seminar (2 cr)
• BE 562 Computational Biology: Genomes, Networks, Evolution (4 cr) if not taken in first year

Elective

• BE 777 Computational Genomics (4 cr)

Spring Semester

• BF 541 Bioinformatics Internship or BF 501/502 Bioinformatics Master’s Project

Background enhancement: Typically, students enrolling in the Bioinformatics MS program have strength in either the computational area or in biochemistry/molecular biology, but not both. In consultation with their academic advisor, they may decide to take or audit some introductory courses to strengthen areas where their background has deficiencies. Examples of such courses (which do not carry graduate credit) are CS 113 Introduction to Computer Science and C++, CH 172 Life Science Chemistry II (organic chemistry), CH 273 Principles of Biochemistry, BI 203 Cell Biology, and BI 206 Genetics.

Internship Guidelines

Internships provide the bridge between classroom/laboratory study and “real-world” employment. Each student must complete an internship with a minimum of 400 hours of on-the-job experience (e.g., 10 weeks of full-time work in the summer). The format is very flexible, and part-time internships running concurrently with classes or employment are acceptable. Students whose regular, full-time job includes a strong bioinformatics component over at least a six-month period can request that this be considered an internship. Students must consult with their academic advisor to assess the suitability of a proposed internship. For this purpose, “bioinformatics” means extensive use of computational tools to analyze, display, and/or archive biological information (usually at the molecular level). The project supervisor must be familiar with the tools employed, and if possible, the position should involve regular interaction with “wet-bench” scientists. While most internships will take place in industrial settings, suitable projects can be completed in nonprofit or academic research laboratories. In every case the student must obtain final approval from the Program Director before commencing an internship. For full-time students the internship should begin no later than the third semester after beginning the MS program.

MS Academic Advising

The Associate Director of Graduate Studies serves as the MS student’s primary academic advisor. Students should consult with the director to tailor their coursework to meet specific curricular needs in the transition into an interdisciplinary program. The director will also be available to advise students with regard to internship placements that will satisfy degree requirements.

Doctorate in Philosophy (PhD)

The post-bachelor’s PhD requires a total of 64 course credits, consisting of a combination of lecture, laboratory, and research. The precise course of study will be determined in consultation with faculty advisors, and will reflect the student’s background and interest. 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.

The post-master’s PhD requires 38 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.

Dissertation

The PhD requires original research and presentation in a form suitable for publication in an archival journal. Two dissertation advisors, one predominantly an experimental researcher and the other predominantly a computational researcher, guide progress toward the degree. The two dissertation advisors and the Qualifying Exam Committee normally constitute the Dissertation Committee. The Dissertation Committee reviews the student’s progress annually and is responsible for judging both the dissertation prospectus and the completed dissertation.

PhD Required Core Courses (36 cr total)

• ENG BE 562 Computational Biology: Genomes, Networks, Evolution (4 cr)
• ENG BE 768 Biological Database Analysis (4 cr)
• ENG BE 777 Computational Genomics (4 cr)
• ENG BF 690 Bioinformatics Challenge Project (2 cr each; 4 cr 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 rotation; 3 cr total)
• ENG BF 820 Research Opportunities in Bioinformatics (1 cr)
• ENG BF 821 Bioinformatics Graduate Seminar (2 cr each; 4 cr total)

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.

Electives

For the post-bachelor’s PhD: 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 (BF 900 and/or BF 901). A minimum of 2 research credits is required.

For the post-master’s PhD: In addition to the core courses listed above, at least 2 credits of research (BF 900/901) are required. (Note: 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 BF 901 for research credit.)

Breadth Electives

• ENG BE 560 Biomolecular Architecture
• ENG BE 565 Molecular Biotechnology
• ENG BE 566 DNA Structure and Function
• ENG BF 527 Applications in Bioinformatics
• ENG BF 571 Dynamics in Evolution of Biological Networks
• CAS BI/CH 527/528 Biochemistry Laboratory I & II
• CAS BI 504 Evolution
• CAS BI 549 Molecular Phylogenetics and Evolution
• CAS BI 553 Molecular Biology II
• CAS BI 556 Membrane Biochemistry
• CAS BI 572 Advanced Genetics
• GRS BI 610 Cellular Aspects of Development and Differentiation
• GRS BI 735 Advanced Cell Biology
• GRS BI 755 Cellular and Systems Neuroscience
• CAS BB 522 Molecular Biology Laboratory
• CAS CH 525 Physical Biochemistry
• GRS CH 751 Advanced Topics in Physical Chemistry
• GRS CH 752 Advanced Topics in Chemical Physics
• CAS CS 542 Machine Learning
• CAS CS 549 Pattern Matching and Detection with Application 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 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
• CAS MA 684 Applied Multiple Regression and Multivariable Methods
• 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
• ENG EC 533 Advanced Discrete Mathematics
• ENG EC 534 Discrete Stochastic Models
• ENG EC 730 Information-Theoretical Design of Algorithms
• ENG EC 761 Information Theory and Coding
• SPH BS 703 Biostatistics
• SPH BS 830 Design and Analysis of Microarray Experiments
• SPH BS 850 Advanced Statistical Methodology for the Computational Biosciences
• SPH BS 855 Bayesian Modeling for Biomedical Research and Public Health
• SPH BS 858 Statistical Genetics I
• SPH BS 859 Applied Genetic Analysis
• SPH BS 860 Statistical Genetics II
• GMS PA 600 Introduction to Pathology & Pathophysiology of Disease

Curriculum and Requirements

The Bioinformatics Program offers the PhD (postbachelor’s and post-master’s) and MS degrees. The reader is referred to individual listings for descriptions of the courses listed above.

PhD Advisors

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 Examinations

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. 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.

Language Requirement

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.

Financial Aid

PhD graduate students may obtain financial aid in the form of competitive teaching fellowships or research assistantships available from grants or contracts held by faculty members. Annual (12 month) stipends are approximately $30,000. National Science Foundation Traineeship funding is also available to U.S. citizens and permanent residents.

Admission

Prospective students should have a strong undergraduate background in the hard sciences, engineering, or the biological sciences. PhD applicants are required to submit scores from the Graduate Record Examinations (use code 3087). General Graduate Record Examinations Subject Test scores are also accepted; normally, the subject test should be taken in biology, chemistry, or biochemistry, and molecular biology. Graduate Record Examinations is not required for admission to the MS program. Applicants whose native language is not English are also required to submit results of the Test of English as a Foreign Language (TOEFL). Applicants must submit the Graduate School of Arts & Sciences application. Applications may be obtained from, and all materials sent to: Boston University, Graduate School of Arts & Sciences, 705 Commonwealth Avenue, Boston, MA 02215. Applications are also available online at the Bioinformatics Graduate Program website.

The application deadline for fall admission is December 1, and for spring admission the deadline is October 1.