Intercollegiate Program in Bioinformatics

Administration

  • Interim Chair Thomas Tullius, Professor
  • Directors Scott Mohr, Professor, Director of Graduate Studies
  • Gary Benson, Associate Professor, Director of IGERT Program

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.

Through the program, you’ll have access to state-of-the-art computational facilities, including SGI/CRAY Origin 2000 with 192 processors, SGI POWER CHALLENGE array with 38 processors, and 2 ImmersaDesks. The experimental facilities include pulse-field apparati, high-speed sequencers, a MALDI mass spectrometer, and various NMR spectrometers.

Master of Science (MS) in Bioinformatics

The master’s degree requires thirty-two credits of coursework, with at least twenty chosen from the program’s core. Students must also demonstrate a working knowledge of the array of computational methods available to the modern molecular biologist. This usually consists of the completion of a carefully circumscribed research project or internship and a written report. A committee of three members of the Bioinformatics faculty, including the student’s advisor, evaluates the report.

Admission

Prospective students should have a strong undergraduate background in the hard sciences, engineering, or the biological sciences. Applicants are required to submit scores from the Graduate Record Examination Test (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. 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 Progam website.

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

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 thirty-two 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.

Required Core Courses (32 cr total):

  • ENG BE 561 DNA and Protein Sequence Analysis (4 cr)
  • ENG BE 768 Biological Database Analysis (4 cr)
  • ENG BE 777 Computational Genomics (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)
  • CAS BI 552 Molecular Biology I (4 cr)

Breadth Electives

  • ENG BE 535 Cell Mechanics
  • ENG BE 537 Biomedical and Biochemical Microsystems
  • ENG BE 560 Biomolecular Architecture
  • ENG BE 562 Computational Biology: Genomes, Networks, Evolution
  • ENG BE 565 Molecular Biotechnology
  • ENG BE 566 DNA Structure and Function
  • ENG BE 760 Structural Bioinformatics
  • ENG BE 764 Biophysics of Large Molecules
  • ENG BF 527 Applications in Bioinformatics
  • ENG BF 571 Dynamics in Evolution of Biological Networks
  • ENG BF 752 Directed Study in Bioinformatics
  • 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 723 Physical Chemistry of Biological Macromolecules
  • 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 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 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

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.

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.

Admission and 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 $28,200. National Science Foundation Traineeship funding is also available to U.S. citizens and permanent residents.