Graduate School of Arts and Sciences Bulletin of Yale University
 
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Computational Biology and Bioinformatics

Bass 432A, 432.8189
M.S., Ph.D.

Directors of Graduate Studies
Mark Gerstein (Bass 432A, 432.6105. mark.gerstein@yale.edu)
Perry Miller (300 George St, Suite 501, 737.2903, perry.miller@yale.edu)

Professors
Joseph Chang (Statistics), Ronald Coifman (Mathematics), Lynn Cooley (Genetics; Cell Biology), Donald Engelman (Molecular Biophysics & Biochemistry), William Jorgensen (Chemistry), Douglas Kankel (Molecular, Cellular & Developmental Biology), Kenneth Kidd (Genetics), Perry Miller (Anesthesiology; Molecular, Cellular & Developmental Biology), Willard Miranker (Computer Science), Anna Pyle (Molecular Biophysics & Biochemistry), Martin Schultz (Computer Science), Gordon Shepherd (Neurobiology), Avi Silberschatz (Computer Science), Michael Snyder (Molecular, Cellular & Developmental Biology), Dieter Söll (Molecular Biophysics & Biochemistry; Chemistry), Günter Wagner (Ecology & Evolutionary Biology), Sherman Weissman (Genetics; Medicine), Steven Zucker (Computer Science; Biomedical Engineering)

Associate Professors
James Aspnes (Computer Science), Mark Gerstein (Molecular Biophysics & Biochemistry; Computer Science), Elias Lolis (Pharmacology), Michael Stern (Genetics), Heping Zhang (Epidemiology & Public Health; Statistics), Hongyu Zhao (Epidemiology & Public Health; Genetics)

Assistant Professors
Andrew Miranker (Molecular Biophysics & Biochemistry), Valerie Reinke (Genetics), David Tuck (Pathology), Kevin White (Genetics)

Fields of Study
Computational biology and bioinformatics (CB&B) is a rapidly developing multidisciplinary field. The systematic acquisition of data made possible by genomics and proteomics technologies has created a tremendous gap between available data and their biological interpretation. Given the rate of data generation, it is well recognized that this gap will not be closed with direct individual experimentation. Computational and theoretical approaches to understanding biological systems provide an essential vehicle to help close this gap. These activities include computational modeling of biological processes, computational management of large-scale projects, database development and data-mining, algorithm development and high-performance computing, as well as statistical and mathematical analyses.

To enter the Ph.D. program, students apply to an interest-based track within the interdepartmental program in the Biological and Biomedical Sciences.

Special Admissions Requirements
Applicants are expected (1) to have a strong foundation in the basic sciences, such as biology, chemistry, and mathematics, and (2) to have training in computing/informatics, including significant computer programming experience. The Graduate Record Examination (GRE) General Test is required, and the GRE Subject Test in cell and molecular biology, biology, biochemistry, chemistry, computer science, or other relevant discipline is recommended. Applicants for whom English is not their native language are required to submit results from the Test of English as a Foreign Language (TOEFL).

Special Requirements for the Ph.D. Degree
With the help of a faculty advisory committee, each student plans a program that includes courses, seminars, laboratory rotations, and independent reading. Students are expected to gain competence in three core areas: (1) computational biology and bioinformatics, (2) biological sciences, and (3) informatics (including computer science, statistics, and applied mathematics). The courses taken to satisfy the core areas of competency may vary considerably. A typical program will include nine courses. Completion of the core curriculum will typically take three to four terms, depending in part on the prior training of the student. Students will typically take two to three courses each term and three research rotations during the first year. After the first year, students will start working in the laboratory of their Ph.D. thesis supervisor. Students must pass a qualifying examination normally given at the end of the second year or the beginning of the third year. There is no language requirement. Students will serve as teaching assistants in two term courses.

Master's Degree
M.S. (en route to the Ph.D.). To qualify for the awarding of the M.S. degree a student must (1) complete two years (four terms) of study in the Ph.D. program, (2) complete the required course work for the Ph.D. program with an average grade of High Pass, (3) successfully complete three research rotations, and (4) meet the Graduate School's Honors requirement.

Courses
Students normally take at least three of the following four core courses.

MB&B 752bu, Genomics and Bioinformatics.

MCDB 750a, Core Topics in Biomedical Informatics.

STAT 645b, Statistical Methods in Genetics and Bioinformatics.

CHEM 526au, Computational Chemistry and Biochemistry.

Additional courses focused on the biological sciences and on areas of informatics are selected by the student in consultation with CB&B faculty.

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