Syllabus

Assignments, lecture notes, and external links will be provided on the assignment (materials) page or as provided by the indvidual lecturers. In general, each individual lecturer will provide background on a topic* and will assign a short feasible programming project that will be done in rotating pairs (although individual instructors may ask you to program separately). Each programming project will be written up separately by each student (no more than 2-3 concise, double-spaced, and well-organized pages, not including figures). The overall focus is on gaining sufficient experience in practical problem-solving and communicating research plans to pass the preliminary exams.

January 23 - Course overview (Dr. Pollock)
January 25,30 - Genomic analysis of repeat structure (Dr. Gu)
February 1, 6, 20 - Regulatory elements (Mr. Kim)
February 8, 13, 15 - Protein function, structure, and prediction (Dr. Osguthorpe)
February 20 - ChIP assays (Mr. Kim)
February 22, 27, March 1 - Microarrays and/or motif finding (Dr. Kechris). EM reading here [1, 2].
March 6, 8, 13 - Combinatorial and graph algorithms to solve problems in genomics (Dr. Goldberg)
March 15 - Student Presentations
March 20, 22- No class (Spring break)
March 27, 29 - Biomedical language processing; Compensatory mutations in proteins (Mr. Caporaso)
April 3, 5 - Making a stink: modeling the neural organization of smell (Mr. McTavish)
April 10, 12, 17 - Molecular Evolution and Evolutionary Genomics (Dr. Pollock) April 20 - Student presentations
April 24 - Overview of the Research Topics part of the course (Dr. Pollock)
April 26 - Review Criteria (TBA) (NOT OD-05-002)
Late April/early May - Sequence alignment, modeling RNA structure, evolution of the genetic code (Dr. Knight)
May 1 - Mock study section (Dr. Osguthorpe)
May 3 - Introduction to Reviewing Manuscripts (Dr. Kechris)
May 8 - The Educational Objectives (Dr. Pollock)
May 10 - Student presentations
May 14 through end of May - Prepare for prelims

*Any notes are linked to the day of presentation. Assignment descriptions and due dates are on the "materials" page.

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