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| Biosciences |
GENE 202. Human Genetics—Theoretical and experimental basis for the genetics of human health and disease. Molecular, chromosomal, biochemical, developmental, cancer, and medical genetics, emphasizing the last. Clinical case discussions. Prerequisites: biochemistry; basic genetics.
4 units, Aut (Ford, J; Myers, R)HOOL O
GENE 203. Advanced Genetics—(Same as BIOSCI 203, DBIO 203.) For graduate students in Bioscience programs; may be appropriate for graduate students in other programs. The genetic toolbox. Examples of analytic methods, genetic manipulation, genome analysis, and human genetics. Emphasis is on use of genetic tools in dissecting complex biological pathways, developmental processes, and regulatory systems. Faculty-led discussion sections with evaluation of papers. Students with minimal experience in genetics should prepare by working out problems in college level textbooks.
4 units, Aut (Stearns, T; Barsh, G; Sidow, A; Kim, S)
GENE 206. Epigenetics—(Same as PATH 206.) For graduate students; undergraduates by consent of instructor. Mechanisms by which phenotypes not determined by the DNA sequence are stably inherited in successive cell divisions. From the discovery of position-effect variegation in Drosophila in the 20s to present-day studies of covalent modifications of histones and DNA methylation. Topics include: position effect, gene silencing, heterochromatin, centromere identity, genomic imprinting, histone code, variant histones, and the role of epigenetics in cancer. Prerequisite: background in genetics and molecular biology.
2 units, Win (Lipsick, J)
GENE 211. Genomics—Genome evolution, organization, and function; technical, computational, and experimental approaches; hands-on experience with representative computational tools used in genome science; and a beginning working knowledge of PERL.
3 units, Win (Cherry, J; Myers, R; Sidow, A; Sherlock, G)
GENE 212. Introduction to Biomedical Informatics Research Methodology—(Same as BIOE 212, BIOMEDIN 212, CS 272.) Hands-on software building. Student teams conceive, design, specify, implement, evaluate, and report on a software project in the domain of biomedicine. Creating written proposals, peer review, providing status reports, and preparing final reports. Guest lectures from professional biomedical informatics systems builders on issues related to the process of project management. Software engineering basics. Prerequisites: 210, 211 or 214, or consent of instructor.
3 units, Aut (Altman, R; Cheng, B; Klein, T; Garten, Y)
GENE 214. Representations and Algorithms for Computational Molecular Biology—(Same as BIOE 214, BIOMEDIN 214, CS 274.) Topics: algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, computing with networks of genes, basic structural computations on proteins, protein structure prediction, protein threading techniques, homology modeling, molecular dynamics and energy minimization, statistical analysis of 3D biological data, integration of data sources, knowledge representation and controlled terminologies for molecular biology, graphical display of biological data, machine learning (clustering and classification), and natural language text processing. Prerequisites: programming skills; consent of instructor for 3 units.
3-4 units, Spr (Altman, R)
GENE 215. Frontiers in Biological Research—(Same as BIOC 215, DBIO 215.) Literature discussion in conjunction with the Frontiers in Biological Research seminar series hosted by Biochemistry, Developmental Biology, and Genetics in which distinguished investigators present current work. Students and faculty meet beforehand to discuss papers from the speaker’s primary research literature. Students meet with the speaker after the seminar to discuss their research and future direction, commonly used techniques to study problems in biology, and comparison between the genetic and biochemical approaches in biological research.
1 unit, Aut, Win (Harbury, P; Brunet, A; Villeneuve, A)
GENE 221. Current Issues in Aging—(Same as DBIO 221, NENS 221.) Current research literature on genetic mechanisms of aging in animals and human beings. Topics include: mitochondria mutations, insulin-like signaling, sirtuins, aging in flies and worms, stem cells, human progeria, and centenarian studies. Prerequisite: GENE 203.
1-2 units, Win (Kim, S; Brunet, A; Rando, T), Spr (Kim, S)
GENE 222. Method and Logic in Experimental Genetics—For graduate students only. How experimental strategies are applied to biological questions irrespective of discipline boundaries. Examples include purifying activities from complex mixtures, localizing molecules in space and time, discovering macromolecular interactions, inferences from sequence similarity, using structure to elucidate function, and applying genomics to biological problems. Weekly discussion of two representative papers selected by faculty and a student presentation of a third paper which illustrate principles of biochemistry and cell and molecular biology, and the historical context of important scientific advances.
3 units, Win (Baker, J; Brunet, A)
GENE 233. The Biology of Small Modulatory RNAs—(Same as MI 233, PATH 233.) Open to graduate and medical students. How recent discoveries of miRNA, RNA interference, and short interfering RNAs reveal potentially widespread gene regulatory mechanisms mediated by small modulatory RNAs during animal and plant development. Required paper proposing novel research.
2 units, Aut (Fire, A; Chen, C), alternate years, not given next year
GENE 235. C. Elegans Genetics—Genetic approaches to C. elegans, practice in designing experiments and demonstrations of its growth and anatomy. Probable topics include: growth and genetics, genome map and sequence, mutant screens that start with a desired phenotype, reverse genetics and RNAi screens, genetic duplications, uses of null phenotype non-null alleles, genetic interactions and pathway analysis, and embryogenesis and cell lineage. Focus of action, mosaic analysis, and interface with embryological and evolutionary approaches.
2 units, Win (Fire, A), not given next year
GENE 238. Current Concepts and Dilemmas in Genetic Testing— (Same as INDE 238.) Issues arising from the translational process from research to commercialization. Diagnostic inventions and applications, community implications, newborn screening, cancer genetics, and pharmacogenomics. Guest experts. For M.D., biomedical graduate, and genetic counseling students.
2 units, Spr (Tobin, S; Schrijver, I; Cowan, T; Magnus, D)
GENE 244. Introduction to Statistical Genetics—Statistical methods for analyzing human genetics studies of Mendelian disorders and common complex traits. Probable topics include: principles of population genetics; epidemiologic designs; familial aggregation; segregation analysis; linkage analysis; linkage-disequilibrium-based association mapping approaches; and genome-wide analysis based on high-throughput genotyping platforms. Prerequisite: STATS 116 or equivalent or consent of instructor.
3 units, Aut (Tang, H)
GENE 260. Supervised Study—Genetics graduate student lab research from first quarter to filing of candidacy. Prerequisite: consent of instructor.
1-18 units, Aut, Win, Spr, Sum (Staff)
GENE 299. Directed Reading in Genetics—Prerequisite: consent of instructor.
1-18 units, Aut, Win, Spr, Sum (Staff)
GENE 399. Graduate Research—Investigations sponsored by individual faculty members. Prerequisite: consent of instructor.
1-18 units, Aut, Win, Spr, Sum (Staff)
COGNATE COURSE
See respective department listings for course descriptions. See degree requirements above or the program’s student services office for applicability of this course to a major or minor program.
MED 255. The Responsible Conduct of Research
1 unit, Aut, Win, Spr, Sum (Karkasiz, K)
