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		2008-09 Bulletin of the Duke University Graduate School

Genetics and Genomics, University Program in (UPGEN)

Professors Heitman and Marchuk, Co-Directors; Professor Noor, Director of Graduate Studies; Professors Andrews (medicine), Been, (biochemistry), Benfey (biology), Cullen (molecular genetics and microbiology), Dong (biology), Endow (cell biology), Garcia-Blanco (molecular genetics and microbiology), Goldstein (molecular genetics and microbiology), Greenleaf (biochemistry), Heitman (molecular genetics and microbiology), Hershfield (medicine), Hogan (cell biology), Hsieh (biochemistry), Jinks-Robertson (molecular genetics and microbiology), Jirtle (Radiation Oncology), Keene (molecular genetics and microbiology), Kiehart (biology), Kirby (pediatrics), Kornbluth (pharmacology and cancer biology), Kreuzer (biochemistry), Lew (pharmacology and cancer biology), Linney (molecular genetics and microbiology), Marchuk (molecular genetics and microbiology), McCusker (molecular genetics and microbiology), Means (pharmacology and cancer biology), Mitchell-Olds (biology), Modrich (biochemistry), Nevins (molecular genetics and microbiology), Nicklas (biology), Nijhout (biology), Perfect (medicine), Petes (molecular genetics and microbiology), Raetz (biochemistry), Rausher (biology), Shaw (chemistry), Steege (biochemistry), St. Geme (pediatrics), Sullenger (Surgery), Sun (biology), Thiele (pharmacology and cancer biology), Uyenoyama (biology), Vilgalys (biology), Wharton (molecular genetics and microbiology), Willard (molecular genetics and microbiology), Wray (biology), Young (ophthalmology); Associate Professors Alberts (biology), Amrein (molecular genetics and microbiology), Ashley-Koch (medicine), Bejsovec (bio), Capel (cell biology), Counter (pharmacology and cancer biology), Cox (medicine), Cunningham (biology), Ferreira (molecular genetics and microbiology), Klingensmith (cell biology), Lutzoni (biology), Markert (pediatrics), Pickup (molecular genetics and microbiology), Pei (biology), Rushe (biochemistry), Schachat (cell biology), Willis (biology), J. York (pharmacology and cancer biology), Zhuang (immunology); Assistant Professors Aballay (molecular genetics and microbiology), Alspaugh (medicine), Chi (molecular genetics and microbiology), Crawford (pediatrics), Dietrich (molecular genetics and microbiology), Gregory (medicine), Haase (biology), Kuehn (biochemistry), Lechler (cell biology), Liedtke (neurobiology), Luftig (molecular genetics and microbiology) MacAlpine (pharmacology and cancer biology), Magwene (biology), Matsunami (molecular genetics and microbiology), Ohler (biostatistics and bioinformatics), Poss (cell biology), Seed (pediatrics), Sherwood (biology), Soderling (cell biology), Sullivan (molecular genetics and microbiology), Tracey (cell biology), Valdevia (molecular genetics and microbiology), F. Wang (cell biology), Wechsler-Reya (pharmacology and cancer biology), West (neurobiology), Winn (medicine), S. York (medicine), You (biomedical engineering), Zhu (cell biology); Associate Research Professors: Cardenas-Carona (molecular genetics and microbiology) and Hauser (medicine); Assistant Research Professors Asano (molecular genetics and microbiology), Koh (surgery), and N. Sherwood (biology); Adjunct Professors Drake (National Institute of Environmental Health Science), Kunkel (National Institute of Environmental Health Science), and Resnick (National Institute of Environmental Health Science)

The Duke University Program in Genetics and Genomics (UPGG) is an umbrella graduate training program that spans several basic science and clinical departments and bridges the medical center and the college of arts and sciences. There are currently 103 faculty with three adjunct faculty, and 79 students in the program, which was founded in 1967 and has been continuously supported by a training grant from the NIH for the past 25 years. Over the past several decades, the program has served as an important forum for training and education in genetics, including model systems (bacteria, yeast, fungi, drosophila, zebrafish, mouse), population genetics, and human genetics. We hope to also forge a close link between the program and the emerging Institute of Genome Sciences and Policy (IGSP) at Duke.

The Duke UPGG is unique in that it is degree granting. Thus students can either receive their degree via the University Program in Genetics and Genomics, or via their host department that students affiliate with upon joining a laboratory for graduate training. The requirements for the two are different, since students who choose to earn their degree from the host department satisfy both UPGG and departmental requirements. In many cases, the requirements for the UPGG satisfy the departmental requirements.

The relationship between the University Program in Genetics and Genomics and the Department of Genetics is evolving as a consequence of the merger of the Departments of Genetics and Microbiology to form the Department of Molecular Genetics and Microbiology. In the past, the Department of Genetics administered a graduate program in concert with the University Program in Genetics and Genomics. Now the merged and expanded Department of Molecular Genetics and Microbiology has established a departmental graduate training program, the MGM department, that students from UPGG can choose to adopt if they join an MGM member laboratory. Alternatively, students have the option to seek their degree via the genetics program independent of a departmental affilitiation. These mechanisms ensure a great degree of flexibility in serving the needs of the member labs, 13 different departments, and ensure that students in the UPGG have both a common home and can pursue their own unique career paths within the umbrella of the program.

The curriculum requirements for the Duke University Program in Genetics and Genomics are flexible. Students are required to take two full semester courses, Genetic Approaches to the Solutions of Biological Problems (UPG 378) and Evolutionary Genetics (UPG 287), one additonal full semester course with an emphasis in genetics, and two minicourses selected from a variety of offerings. Courses for first year students are chosen in consultation with the Director of Graduate Studies and a first year advisory committee. Courses are available and encouraged for students past the first year of study, and decisions about additional coursework are made in consultation with the student's faculty advisor and committee to complement the requirements of the student's own research interests.

In addition to courses, students participate in other educational activities. These include an annual student organized retreat at the beach, and a biweekly student research seminar series that alternates with a biweekly student-faculty lunch. There is a fall genetics seminar series that is interspersed with four distinguished lecturer seminars, two in the spring and two in the fall. Students organize and invite the distinguished lecturer series with advice from the program co-director, Doug Marchuk, and students host the dinners with the distinguished lecturers. Students have the opportunity to develop teaching skills as an assistant for one semester. Finally, students complete a preliminary examination at the end of the second year of graduate student and form their thesis committee.

225. Critical Readings in Classical Human Statistical Genetics. In-depth readings of classical human statistical genetics papers that shaped the field including Morton's lod score analysis, Penrose's affected sibling pair studies, and the Elston-Stewart algorithm, among others. Student-led discussions of content. Instructors: Speer and Scott. 1 unit.

232. Human Genetics. 3 units. C-L: Molec Genetics & Microbiology 232

233. Genetic Epidemiology. This course will cover traditional genetic epidemiologic methods such as study design, linkage analysis and genetic association. Instructor: Ashley-Koch. 3 units.

247. Macromolecular Synthesis. 2 units. C-L: see Cell and Molecular Biology 247

258. Structural Biochemistry I. 2 units. C-L: see Biochemistry 258; also C-L: Cell and Molecular Biology 258, Cell Biology 258, Immunology 258, Structural Biology and Biophysics 258, Computational Biology and Bioinformatics 258

259. Structural Biochemistry II. 2 units. C-L: see Biochemistry 259; also C-L: Cell Biology 259, Immunology 259, Computational Biology and Bioinformatics 259, Structural Biology and Biophysics 259

268. Biochemical Genetics II: From RNA to Protein. 2 units. C-L: see Biochemistry 268; also C-L: Cell Biology 268, Immunology 268

285S. Ecological Genetics. Interaction of genetics and ecology and its importance in explaining the evolution, diversity, and distribution of plants and animals. Instructor: Staff. 3 units.

286. Evolutionary Mechanisms. 3 units.

287. Evolutionary Genetics. An introduction to the principles of evolutionary genetics, with discussion of the current literature. Levels of selection; neutral theory; variation in populations; speciation. Reconstructing evolutionary history; genomic evolution. Instructor: Noor. 3 units.

288. Mathematical Population Genetics. 3 units.

301. Advanced Topics in Genetics and Genomics. Course open only to first year UPGG graduate class. Weekly discussion of current literature in genetics (Fall semester) and genomics (Spring semester). Permission of instructor required. Instructor: Staff. 2 units.

306. Writing Grant Proposals. A course to prepare students in writing grant proposals. Instructor: Marchuk. 2 units.

316. Genetics Student Research. Presentations by genetics program students on their current research. Required course for all graduate students specializing in genetics. Credit grading only. Instructor: Haase. 1 unit.

317. Independent Research for the Master's Degree. This course is an independent research course specifically for students who have been given the option by the DGS and their mentor to receive a Master's Degree from the Program. Any student taking this course must have permission from the DGS and from the instructor. Successful completion of the course will be determined by the instructor, the student's mentor, and the DGS. Instructor: Staff. Variable credit.

346. The Mouse as a Model Organism. 2 units. C-L: see Cell Biology 346

350. Genetics Colloquium. Lectures, discussion sections, and seminars on selected topics of current interest in genetics. Required of all students specializing in genetics. Prerequisite: a course in genetics. Instructor: Staff. 1 unit.

378. Genetic Approaches to the Solution of Biological Problems. Use of genetic approaches to address research problems in cell and developmental biology. Genetic fundamentals build up to modern molecular genetic strategies including genetic screens, reverse genetics, genetic interactions, dominant negative mutants, and more. Several major genetic model organisms used to illustrate general principles. Consent of instructor required for undergraduates. Instructor: Lew. 4 units. C-L: Cell and Molecular Biology 378, Molec Genetics & Microbiology 378, Biology 378