Intercollegiate Program
in Bioinformatics

Director

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

Associate Directors

Jerome Brody, Professor of Medicine, Director of Pulmonary Center

Geoffrey Cooper, Professor and Chairman of Biology

Thomas Tullius, Professor and Chairman of Chemistry

The Graduate Program

The Bioinformatics Program is offered jointly by the College of Engineering and the Graduate School of Arts and 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; and requires a semester of teaching. 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 General Graduate Record Examination (use code 3087). Subject Graduate Record Examinations 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 and Sciences application. Applications may be obtained from, and all materials sent to: Boston University, Graduate School of Arts and Sciences, 705 Commonwealth Avenue, Boston, MA 02215. Applications are also available on-line at the Bioinformatics Graduate Progam website at Bioinformatics Graduate Program.

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

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.

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 sixteen 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 and an oral presentation.

Required Core Courses (31 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 778 Computational Genomics and Cell 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)

LAW JD 933 Biotechnology in Law and Ethics (3 cr)

Breadth Electives

ENG BE 535 Cell Mechanics

ENG BE 537 Biomedical and Biochemical Microsystems

ENG BE 560 Biomolecular Architecture

ENG BE 563 Cellular and Molecular System Analysis

ENG BE 565 Molecular Biotechnology

ENG BE 566 DNA Structure and Function

ENG BE 760 Structural Bioinformatics

ENG BF 752 Directed Study in Bioinformatics

CAS BI/CH527/528 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

GRS 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 and Chemical Physics

CAS MA 555 Numerical Analysis I

CAS MA 565 Mathematical Models in the Life Sciences

CAS MA 614 Statistical Methods

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

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. Thesis The PhD requires original research and 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, guide progress toward the degree. The two thesis advisors and the Qualifying Exam Committee normally constitute the Thesis Committee. The Thesis Committee reviews the student’s progress annually and is responsible for judging both the thesis prospectus and the completed thesis.

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.

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.

Michael Baram Professor and Director, Center for Law and Technology at the School of Law; Professor, School of Public Health. Legal aspects of health, safety, and environmental risks: e.g., corporate risk management; workplace and industrial process safety; product stewardship; toxic tort liability; biomonitoring; insurability of hazardous activities; hazardous waste management; sustainable development; biotech agriculture.

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 and Sciences. Algorithm and program development for DNA, RNA, and protein sequences.

Jerome Brody Professor of Medicine, Director of Pulmonary Center. Clinical and basic studies of lung cancer.

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

John L. Celenza Assistant Professor, Biology. Plant development; molecular biology; genetics.

Michael Christman Professor and Chair, Genetics and Genomics, School of Medicine. Human genetic variation and genomic instability.

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

Geoffrey M. Cooper Professor and Chairman, 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.

Micah Dembo Professor, Biomedical Engineering. Statistical mechanics in biological systems; cellular information processing and signal transduction; thermodynamics and mechanics of cell adhesion; biophysics of cell deformation, active motility.

James Deshler Assistant Professor, Biology. Cell polarity; biochemistry; developmental biology; and cell signaling and gene regulation.

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).

Timothy Gardner Assistant Professor, Biomedical Engineering. Genetic network inference, analysis and control via scalable methods, optimization of microbial metabolic networks for bioremediation and energy production, analysis and control of bacterial stress response to overcome antibiotic tolerance, inference of drug mechanism of action.

Hwai-Chen Guo Associate Professor, Biophysics/School of Medicine. Macromolecular Crystallography and Biological Functions.

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

Carlos B. Hirschberg Professor and Chairman, Molecular and Cell Biology, Goldman School of Dental Medicine. Novel regulation of posttranslational modifications in mammals and yeast.

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

Mark Kon Professor, Department of 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.

Nancy Kopell Professor, Mathematics. Dynamics of networks of neurons; synchronization of networks of neurons; central Pattern Generators; pattern formation; geometric methods for systems of many time scales.

Lev Levitin Distinguished Professor, Electrical and 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.

Matthew Nugent Associate Professor, Biochemistry and Opthalmology/School of Medicine. Growth Factor Transport through the extracellular matrix and interaction with the cell surface.

Phillips W. Robbins Professor, Molecular and Cell Biology, Goldman School of Dental Medicine. Glycoprotein processing and secretion.

John Samuelson Professor, Department of Molecular and 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 of 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.

Chris SchneiderAssistant Professor, Biology. Ecology and evolution of reptiles and amphibians; molecular systematics and population genetics; tropical biology.

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.

Michael Sorensen Assistant Professor, Biology. Genetic structure of natural populations; studies examining the systematic relationships among avian species, genera, families, and orders.

Avrum Spira Instructor in Medicine, Department of 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 Chairman, 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.

Zhiping Weng Associate Professor, Biomedical Engineering. Empirical free energy function for molecular docking and design; rational design of ligands specific to given receptors requires repeated evaluations of the free energy of candidate complexes.

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

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

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.

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.

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.

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 thesis dissertation. Variable cr.

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10 September 2007
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