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GENE 25SI: The Art and Science of Beer

Colloquium-style lecture series. Topics include: basics of beer brewing, the science behind the brew, history of beer brewing, government regulation, regional traditions and techniques, American micro-brewing. Includes hands-on brewing experience.
Terms: Spr | Units: 1 | Grading: Satisfactory/No Credit
Instructors: Sherlock, G. (PI)

GENE 109Q: Genomics: A Technical and Cultural Revolution (BIOMEDIN 109Q)

Preference to sophomores. Concepts of genomics, high-throughput methods of data collection, and computational approaches to analysis of data. The social, ethical, and economic implications of genomic science. Students may focus on computational or social aspects of genomics.
Terms: Win | Units: 3 | UG Reqs: Writing2 | Grading: Letter or Credit/No Credit
Instructors: Altman, R. (PI)

GENE 199: Undergraduate Research

Students undertake investigations sponsored by individual faculty members. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr, Sum | Units: 1-18 | Repeatable for credit | Grading: Letter or Credit/No Credit
Instructors: Altman, R. (PI); Attardi, L. (PI); Baker, J. (PI);... more instructors for GENE 199 »
Instructors: Altman, R. (PI); Attardi, L. (PI); Baker, J. (PI); Barsh, G. (PI); Boothroyd, J. (PI); Brown, P. (PI); Brunet, A. (PI); Bustamante, C. (PI); Calos, M. (PI); Cherry, J. (PI); Cohen, S. (PI); Davis, R. (PI); Fire, A. (PI); Ford, J. (PI); Francke, U. (PI); Fuller, M. (PI); Herzenberg, L. (PI); Kay, M. (PI); Kim, S. (PI); Lipsick, J. (PI); McAdams, H. (PI); Myers, R. (PI); Ormond, K. (PI); Pollack, J. (PI); Pringle, J. (PI); Quake, S. (PI); Sage, J. (PI); Scott, M. (PI); Sherlock, G. (PI); Sidow, A. (PI); Snyder, M. (PI); Stearns, T. (PI); Tan, M. (PI); Tang, H. (PI); Villeneuve, A. (PI); Vollrath, D. (PI)

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.
Terms: Aut | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: Hudgins, L. (PI); Ormond, K. (PI)

GENE 203: Advanced Genetics (BIO 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.
Terms: Aut | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)

GENE 206: Epigenetics (BIO 156, BIO 256, PATH 206)

For graduate students in the Biosciences and upper level Biology undergraduates. 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 1920s 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: BIO41 and BIO42 , or GENE 203, or consent of instructor.
Terms: Spr, alternate years, not given next year | Units: 2 | Grading: Letter or Credit/No Credit
Instructors: Gozani, O. (PI); Lipsick, J. (PI)

GENE 210: Genomics and Personalized Medicine

Principles of genetics underlying associations between genetic variants and disease susceptibility and drug response. Topics include: genetic and environmental risk factors for complex genetic disorders; design and interpretation of genome-wide association studies; pharmacogenetics; full genome sequencing for disease gene discovery; population structure and genetic ancestry; use of personal genetic information in clinical medicine; ethical, legal, and social issues with personal genetic testing. Hands-on workshop making use of personal or publicly available genetic data. Prerequisite: GENE 202 or 203.
Terms: Sum | Units: 2 | Grading: Medical Satisfactory/No Credit

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.
Terms: Win | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: Cherry, J. (PI); Sherlock, G. (PI)

GENE 212: Introduction to Biomedical Informatics Research Methodology (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: BIOMEDIN 210, 211, 214, 217 or consent of instructor.
Terms: Spr | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

GENE 214: Representations and Algorithms for Computational Molecular Biology (BIOE 214, BIOMEDIN 214, CS 274)

Topics: introduction to bioinformatics and computational biology, algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, Gibbs Sampling, 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, microarray analysis, machine learning (clustering and classification), and natural language text processing. Prerequisites: programming ski... more description for GENE 214 »
Topics: introduction to bioinformatics and computational biology, algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, Gibbs Sampling, 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, microarray analysis, machine learning (clustering and classification), and natural language text processing. Prerequisites: programming skills; consent of instructor for 3 units.
Terms: Aut | Units: 3-4 | Grading: Medical Option (Med-Ltr-CR/NC)
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