Intercollegiate Program in Bioinformatics

The following list reflects the 2006/2007 faculty.

Director

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

Associate Directors

Jerome Brody, Professor of Medicine; Director, Pulmonary Center

Geoffrey Cooper, Professor and Chairman of Biology

Thomas Tullius, Professor and Chairman of Chemistry

Karen N. Allen Assistant Professor, Physiology, School of Medicine. BS, Tufts University; PhD, Brandeis University

Michael Baram Professor and Director, Center for Law and Technology, School of Law; Professor, School of Public Health. LLB, Columbia University

Andy Baxevanis Deputy Scientific Director, Director, Computational Genomics Program, Nathonal Human Genome Research Institute, National Institutes of Health

Calin Belta Assistant Professor of Manufacturing Engineering, College of Engineering. BS, Universitatea Tehnica “GH.Asachi”, Iasi, Romania; MS, Universitatea Tehnica, Louisiana State University, University of Pennsylvania; PhD, University of Pennsylvania

Gary Benson Associate Professor of Biology and Computer Science, College of Arts and Sciences. BS, MS, PhD, University of Maryland

Robert Berwick Adjunct Professor of Bioinformatics, College of Engineering. AB, Harvard College; SM, PhD, Massachusetts Institute of Technology

Gyan Bhanot Adjunct Assistant Professor of Bioinformatics, College of Engineering. BSc, University of Baroda (India); MSc, Indian Institute of Technology, Bombay (India); MA, SUNY at Stony Brook; PhD, Cornell University

Christopher Bouton Adjunct Assistant Professor of Bioinformatics, College of Engineering. BA, Amherst College; PhD, Johns Hopkins University

Jerome Brody Professor of Medicine; Director, Pulmonary Center. MD, University of Illinois

Charles R. Cantor Professor of Biomedical Engineering; Professor of Biochemistry, School of Medicine. Director, Center for Advanced Biotechnology. AB, Columbia University; PhD, University of California, Berkeley

John L. Celenza Assistant Professor of Biology, College of Arts and Sciences (molecular genetics). BS, Adelphi University; MA, PhD, Columbia University

Michael F. Christman Chairman, Department of Genetics and Genomics; Professor of Genetics and Genomics, School of Medicine. PhD, University of California, Berkeley

James J. Collins Co-Director, Center for BioDynamics; Professor of Biomedical Engineering, College of Engineering. AB, College of the Holy Cross; PhD, University of Oxford (England)

Geoffrey M. Cooper Chairman, Department of Biology; Professor of Biology; College of Arts and Sciences. BS, Massachusetts Institute of Technology; PhD, University of Miami

Charles DeLisi Metcalf Professor of Science and Engineering. BA, City College of New York; PhD, New York University

Micah Dembo Professor of Biomedical Engineering, College of Engineering. BS, Allegheny College; PhD, Cornell University

James Deshler Assistant Professor of Biology, College of Arts and Sciences. BS, PhD, University of California, Los Angeles

Lindsay Farrer Professor of Medicine, Neurology and Public Health; Chief, Genetics Program; Director, Genetic Epidemiology Center. PhD, Indiana University School of Medicine

John Finnerty Assistant Professor of Biology. PhD, University of Chicago

Timothy Gardner Professor of Biomedical Engineering, College of Engineering. BS, Princeton University; PhD, Boston University

Joel H. Graber Adjunct Assistant Professor of Bioinformatics, College of Engineering. BS, Michigan Technological University; MS, PhD, Cornell University

Kamalakar Gulukota Adjunct Assistant Professor of Bioinformatics, College of Engineering. MB,BS, Jawaharlal Institute of Post-Graduate Medical Education and Research (India); MBA, Auburn University; PhD, University of Illinois at Urbana-Campaign

Hwai-Chen Guo Associate Professor of Biophysics, School of Medicine. BS, National Taiwan University (Taiwan); PhD, Cornell University

Ulla Hansen Professor of Biology, College of Arts and Sciences. AB, Oberlin College; PhD, Harvard University

Carlos B. Hirschberg Professor and Chairman, Department of Molecular and Cell Biology, Goldman School of Dental Medicine. PhD, University of Illinois

Enoch S. Huang Adjunct Assistant Professor of Bioinformatics, College of Engineering. AB, Princeton University; PhD, Stanford University

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Maxim Frank-Kamenetskii Professor of Biomedical Engineering. MSc, PhD, Moscow Physical-Technical Institute (Russia); ScD, USSR Academy of Sciences, Moscow (Russia)

Minoru Kanehisa Visiting Professor of Bioinformatics, College of Engineering. DSc, University of Tokyo (Japan)

Simon Kasif Professor of Biomedical Engineering. PhD, University of Maryland

Mark Kon Professor, Department of Mathematics. PhD, Massachusetts Institute of Technology

Eugene Koonin Adjunct Professor of Bioinformatics, College of Engineering. Biology Diploma (equiv. of MSc), PhD, Moscow State University (Russia)

Nancy Kopell Professor of Mathematics, College of Arts and Sciences. BA, Cornell University; MA, PhD, University of California, Berkeley

David Landsman Adjunct Professor of Bioinformatics, College of Engineering. BSc, PhD, University of Cape Town (South Africa)

Joseph Lehar Adjunct Assistant Professor of Bioinformatics, College of Engineering. BA, Brandeis University; PhD, Massachusetts Institute of Technology

Stan Letovsky Adjunct Professor of Bioinformatics, College of Engineering. BA, Cornell University; MSc/Phil, PhD, Yale University

Lev Levitin Distinguished Professor, Electrical and Computer Engineering

Edward L. Loechler Professor of Biology, College of Arts and Sciences (molecular biology). BS, Ohio State University; PhD, Brandeis University

Kim McCall Assistant Professor of Biology. PhD, Harvard University

Jill Mesirov Adjunct Professor of Bioinformatics, College of Engineering. AB, University of Pennsylvania; MA, PhD, Brandeis University

Scott C. Mohr Associate Professor of Chemistry, College of Arts and Sciences. BA, Williams College; AM, PhD, Harvard University

Richard Myers Professor of Neurology (Neurogenetics), School of Medicine. MEd, Georgia State University; MA, PhD, Georgia State University

Hasan Otu Adjunct Instructor of Bioinformatics, College of Engineering. BS, MS, Bogazici University, Istanbul (Turkey); PhD, University of Nebraska-Lincoln

Alan Perelson Adjunct Professor of Bioinformatics, College of Engineering. BS, Massachusetts Institute of Technology; PhD, University of California, Berkeley

Phillips W. Robbins Professor, Department of Molecular and Cell Biology, Goldman School of Dental Medicine. PhD, University of Illinois

Richard Roberts Distinguished Scientist and Research Scholar of Bioinformatics

John C. Samuelson Professor, Department of Molecular and Cell Biology, Goldman School of Dental Medicine. MD, PhD, Harvard University

Scott E. Schaus Assistant Professor of Chemistry, College of Arts and Sciences. BA, Boston University; PhD, Harvard University

Chris Schneider Assistant Professor of Biology. PhD, University of California, Berkeley

Paola Sebastiani Associate Professor of Biostatistics, School of Public Health. PhD, University of Rome (Italy)

Daniel Segre Assistant Professor, Department of Biology. PhD, Wiezmann Institute of Science (Israel)

Cassandra L. Smith Deputy Director, Center for Advanced Biotechnology; Professor of Biomedical Engineering, College of Engineering; Professor of Biology, College of Arts and Sciences; Professor, Department of Pharmacology and Experimental Therapeutics, School of Medicine. BA, MS, West Virginia University; PhD, Texas A & M University

Temple Smith Director, Biomolecular Engineering Research Center; Professor of Biomedical Engineering. BS, Purdue University; PhD, University of Colorado

Michael D. Sorenson Assistant Professor of Biology, College of Arts and Sciences (population biology). BA, Lutheran College; PhD, University of Minnesota

Avrum Spira Instructor in Medicine, Department of Pulmonary Medicine. MD, McGill University (Canada)

John Spouge Adjunct Professor of Bioinformatics, College of Engineering. BSc, MD, University of British Columbia (Canada); PhD, Oxford University (England)

H. Eugene Stanley Professor, Department of Physics. PhD, Harvard University

John E. Straub Associate Professor of Chemistry, College of Arts and Sciences. BS, University of Maryland; PhD, Columbia University

Dean R. Tolan Professor of Biology, College of Arts and Sciences. BA, University of Colorado; PhD, University of California, Davis

Thomas Tullius Chairman, Department of Chemistry; Professor of Chemistry, College of Arts and Sciences. BS, University of California at Los Angeles; PhD, Stanford University

Sandor Vajda Professor of Biomedical Engineering, College of Engineering. MSc, Gubkin Institute (Russia); MSc, Eötvös Lorand Tudományegyetem (Hungary); PhD, Hungarian Academy of Science

David J. Waxman Professor of Biology, College of Arts and Sciences. BA, Queens College, City University of New York; AM, PhD, Harvard University

Zhiping Weng Associate Professor, Biomedical Engineering. BS, University of Science and Technology of China, Hefei, Anhui, P. R. China; PhD, Boston University

Yu (Brandon) Xia Assistant Professor of Chemistry, College of Arts and Sciences. BS, Peking University; PhD, Stanford University

Itai Yanai Adjunct Assistant Professor of Bioinformatics, College of Engineering. BA, BS, PhD, Boston University

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The Graduate Program

The Bioinformatics Program is offered jointly by the College of Engineering and the Graduate School of Arts and 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 cell and molecular biology.

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. Accepted students will attend a pre-entrance training program in order to establish a common core of knowledge with emphasis on the integration of the biological and mathematical disciplines. The graduate curriculum entails individual courses that integrate mathematical modelling, wet labs and information sciences; industrial rotations, internships and grand rounds; and a semester of teaching. Research areas are numerous and include biological information management, gene mining, drug design and targeting, protein and nucleic acid structure, and cellular regulatory networks. 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.

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.

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.

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Master of Science (MS) in Bioinformatics

The master’s degree requires thirty-two credits of coursework, with at least 16 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 will usually consist 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, will evaluate the report and an oral presentation.

Doctor of Philosophy (PhD)

The postbachelor’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.

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Required Core Courses (31 cr total)

Breadth Electives

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 Examination 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 member can either be a faculty member from Boston University or a scientist in the field from another institution 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 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.

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Published by Trustees of Boston University
One Sherborn Street
Boston, MA 02215

31 October 2007
Boston University
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