Intercollegiate Program
in Bioinformatics

Chair

Charles DeLisi, Arthur G.B. Metcalf Professor of Science and Engineering

Directors

Scott Mohr, Associate Professor, Director of Graduate Studies

Gary Benson, Associate Professor, Director of IGERT Program

The Graduate Program

The Bioinformatics Program is offered jointly by 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, students will learn to apply analytic and computational methods and information technologies to current problems in biology, biomedical engineering, and chemistry. Students will 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. Its curriculum is designed to provide interdisciplinary training that combines advanced computational methods with the latest techniques in molecular biology. The graduate curriculum entails 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.

Students in the program 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.

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 at www.bu.edu/bioinformatics.

The application deadline for fall admission is December 15, and for spring admission the deadline is October 1.

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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 below.

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 postbachelor’s PhD.

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 and a written report. A committee of three members of the Bioinformatics faculty, including the student’s advisor, evaluates the report.

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 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/ Biochemistry Laboratory I & II
CH 527/528
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

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 The written preliminary examination is offered at the end of the first year. Students are required to pass three sections of the exam—computational, biophysical, and molecular—and demonstrate a level of mastery in each section. The oral examination must be completed by the end of the student’s third year. The oral examination consists of a defense of a research proposal developed by the student. The Oral Qualifying Examination Committee should consist of the two advisors (computational and experimental) of the student, plus three additional scientists. At least two of these latter scientists should be faculty members of the Bioinformatics Program. The final committee members can either be a faculty member from Boston University or a scientist in the field from other institutions where appropriate. This oral qualifying exam committee will also later serve as the Dissertation Committee.

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.

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.

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 $20,250. National Science Foundation Traineeship funding is also available to U.S. citizens and permanent residents.

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Research Interests of the Faculty

Karen Allen Associate Professor, Physiology, School of Medicine. Mechanism of phosphate transfer reactions, evolution of substrate specificity in enzyme superfamilies, deciphering moonlighting functions of enzymes via examination of protein-protein interactions on the molecular level.

Solomon Amar Professor and Associate Dean for Research, BU Henry M. Goldman School of Dental Medicine; Professor of Periodontology & Oral Biology; Research Associate Professor of Biochemistry. High-throughput genomic and proteomic tools to reconstruct networks for translational studies involving host-parasite interactions in systemic diseases (CVD, obesity) validated by molecular biological methods.

Calin Belta Assistant Professor, Manufacturing Engineering. Verification and control of hybrid systems, robot motion planning and control, gene and metabolic networks.

Gary Benson Associate Professor, Biology and Computer Science, College of Arts & Sciences. Algorithm and program development for DNA, RNA, and protein sequences.

Cynthia Bradham Assistant Professor of Biology. Developmental biology; cell signaling and gene regulation; systems biology.

Charles R. Cantor Professor, Biomedical Engineering and Pharmacology. Human genome analysis; molecular genetics; new biophysical tools and methodologies; genetic engineering.

James J. Collins Professor, Biomedical Engineering. Dynamical systems in physiology; posture and locomotion.

Geoffrey M. Cooper Professor and Chair, Biology. Cellular growth control; cancer; and signal transduction.

Charles DeLisi Professor, Biomedical Engineering. Analysis of DNA function; protein structure; optimization algorithms; neural net applications to molecular biology; drug and vaccine design; membrane biophysics.

Lindsay Farrer Professor of Medicine, Neurology and Public Health; Chief, Genetics Program; Director, Genetic Epidemiology Center. Genetic epidemiology; gene mapping and linkage; neurogenetics.

John Finnerty Assistant Professor, Biology. Evolution of development; developmental genetics; phylogenetics; evolutionary genomics; invertebrate zoology.

Maxim Frank-Kamenetskii Professor, Biomedical Engineering. DNA structures; DNA topology; DNA functioning, PNA (peptide nucleic acid).

Hwai-Chen Guo Associate Professor, Biophysics, School of Medicine. Macromolecular crystallography and biological functions.

Mayetri Gupta Assistant Professor, Biostatistics. Statistical methodology for genomics and sequence analysis; missing data problems and Monte Carlo methods; Bayesian model and variable selection for high dimensional data.

Ulla Hansen Professor, Biology. Molecular biology; transcriptional control; chromatin; cell growth.

Simon Kasif Professor, Biomedical Engineering. Computational bioinformatics; whole genome; comparison and gene prediction; analysis of gene expression and evolution; proteomics.

Eric Kolaczyk Associate Professor, Mathematics & Statistics. Statistical methods and theory for temporal, spatial, and network indexed processes; wavelets and multi-scale methods.

Mark Kon Professor, Mathematics. Statistical phenomenon in which an intelligent system learns to combine a priori information with current data to form a model of an input-output function to be learned.

Lev Levitin Distinguished Professor, Electrical & Computer Engineering. Information theory; physics of communication and computing; quantum theory of measurements; complex and organized systems; reliable computing.

Edward L. Loechler Professor, Biology. Molecular biology; mutagenesis and carcinogenesis, mechanisms of anticancer drugs.

Kim McCall Assistant Professor, Biology. Drosophila developmental biology; apoptosis; oogenesis.

Scott C. Mohr Associate Professor, Chemistry. Fast kinetics (T-junp and stopped-flow); spectroscopic methods (circular dichroism, fluorescence, UV-Vis, and FTIR); X-ray; crystallography; high-field NMR.

Richard Myers Professor, Neurology, School of Medicine. Neurogenetics.

John Samuelson Professor, Molecular & Cell Biology, Goldman School of Dental Medicine. Use of molecular biological methods to study the biochemistry, cell biology, and evolution of Entamoeba histolytica and Giardia lamblia, simple eukaryotes that cause dysentery and diarrhea.

Scott E. Schaus Assistant Professor, Chemistry. The understanding of how we can apply organic chemistry, genomics, genetics, gene regulation, and proteomics in the development of compounds that alter specific cellular pathways.

Paola Sebastiani Associate Professor, Biostatistics, School of Public Health. Analysis of gene markers and of gene expression data in comparative and temporal experiments.

Daniel Segrè Assistant Professor, Biology. Computational systems biology; functional genomics; and evolution of biochemical networks.

Cassandra L. Smith Professor, Biomedical Engineering, Biology, Pharmacology, and Center for Advanced Biotechnology. Mapping and sequencing of large and small genomes; biology of whole chromosomes; RNA and DNA fingerprinting of closely related genomes; sensitive detection methods, with and without the use of molecular amplification; methods for the sequence specific capture and purification of nucleic acids; the genetic basis of sensory perception and behavior.

Temple Smith Professor, Biomedical Engineering, Pharmacology, and Director of Biomolecular Engineering Research Center. Syntactic and semantic structure of the genetic information in biomolecular sequences, structures, and their evolution.

Avrum Spira Instructor in Medicine, Pulmonary Medicine. Application of high-throughput genomic tools to translational studies of lung cancer and other smoking-related pulmonary diseases.

H. Eugene Stanley Professor, Physics. Theoretical condensed-matter physics; polymer physics; and statistical mechanics.

John E. Straub Associate Professor, Chemistry. Theoretical chemistry and biophysics.

Dean R. Tolan Associate Professor, Biology. Human genetics; molecular genetics; biochemistry; and developmental biology of aldolases.

Thomas Tullius Professor and Chair, Chemistry. Structure of DNA and DNA-protein complexes; DNA flexibility; and structural features of complexes of DNA with RNA polymerase or homeodomains.

Sandor Vajda Professor, Biomedical Engineering. Scientific computing; computational chemistry; combinatorial optimization; molecular biology; protein and peptide structure determination; protein engineering; drug and vaccine design.

David J. Waxman Professor, Biology. Molecular endocrinology and cell signaling; cancer gene therapy and pharmacology; liver genes and transcriptional control.

Adrian Whitty Associate Professor, Department of Chemistry. Biochemistry and bioorganic chemistry; protein-protein and protein-ligand interactions; molecular mechanisms of growth factor receptor activation and signaling; inhibitors and activators of protein-protein interactions.

Yu (Brandon) Xia Assistant Professor, Chemistry. Research is focused on computational systems biology. Computational techniques are applied to study the structure, function, and evolution of complex bio-molecular systems, such as proteins and protein networks.

Courses

ENG BF 501, 502 Master’s Project

Prereq: consent of instuctor. Required for MS students in bioinformatics. Participation in a research project under the direction of two faculty advisors. Variable cr.

ENG BF 527 Applications in Bioinformatics

Prereq: CAS BI/CH 421 or CAS BI 203 and BI 206 and consent of instructor; CAS MA 121, MA 123 or MA 127 or equivalent. The material will be presented in a case-based format, using real-world examples to investigate the most widely used bioinformatic applications, e.g., BLAST, Clustal, GRAIL, INSIGHT II, or RASMOL. We will address a broad range of biological questions currently addressed via genomic data, including sequence alignment, pattern recognition and identification, extrapolation of sequence to structure, and intermolecular interactions. 4 cr.

ENG BF 541, 542 Internship in Bioinformatics

Prereq: consent of instructor. This course allows MS and PhD students in bioinformatics to take part in an industrial internship which involves utilizing the tools and applications in the field. Students will be required to present a report on their training to a program committee. Students who receive a stipend by a company should register for zero credit hours. Variable cr.

ENG BF 778 Physical Chemistry for Systems Biology

This course introduces students to quantitative modeling in bioinformatics and systems biology. We begin with basic principles of statistical thermodynamics, chemical kinetics, with selected applications in biomolecular systems. Next we describe molecular driving forces in biology, and computation with biomolecular structures. Finally we discuss quantitative models of biomolecular networks, and design principles of biological circuits. 4 cr.

ENG BF 821 Bioinformatics Graduate Seminar

This course is a graduate seminar covering current topics in bioinformatics. This is achieved through the critical reading, presentation, and discussion of recent literature. Additionally, the course is intended to give students the opportunity to practice and improve their scientific presentation abilities. As such, peer feedback on presentations is an integral aspect of the course. Students will present twice during the semester so that they may improve upon their presentation skills based on peer comments. 2 cr.

ENG BF 810 PhD Laboratory Rotation System

This course is for PhD students to take part in a laboratory rotation system. Students will become familiar with research activity in bioinformatics labs. These rotations will help students identify the laboratory in which they will perform their dissertation research. Post-bachelor PhD students must complete one 9-week rotation in their first semester of matriculation and two in their second semester. PhD standing required. 1 cr per rotation.

ENG BF 820 Research Opportunities in Bioinformatics

Required for entering bioinformatics PhD students. The course will consist of a series of presentations by Bioinformatics faculty that focuses on research projects being investigated in their laboratories. Emphasis is placed on the description of collaborative projects involving experimental and computational approaches to bioinformatics research problems. 1 cr.

ENG BF 900 Pre-Candidacy Research

Prereq: consent of instructor. For PhD students prior to candidacy. Participation in a research project under the direction of two faculty advisors. Requires the development of a brief document outlining the proposed research leading to a PhD prospectus (for the PhD students). Variable cr.

ENG BF 901, 902 Post-Candidacy Thesis Research

Prereq: consent of instructor. For PhD students post-candidacy. Participation in a research project under the direction of two faculty advisors. Requires the development of dissertation. Variable cr.

Published by Trustees of Boston University
One Silber Way
Boston, MA 02215

1 October 2009
Boston University
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