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GENE 104Q: Law and the Biosciences

Preference to sophomores. Focus is on human genetics; also assisted reproduction and neuroscience. Topics include forensic use of DNA, genetic testing, genetic discrimination, eugenics, cloning, pre-implantation genetic diagnosis, neuroscientific methods of lie detection, and genetic or neuroscience enhancement. Student presentations on research paper conclusions.
Last offered: Spring 2014 | Units: 3 | UG Reqs: WAY-ER, Writing 2

GENE 200: Genetics and Developmental Biology Training Camp (DBIO 200)

Open to first year Department of Genetics and Developmental Biology students, to others with consent of instructors. Introduction to basic manipulations, both experimental and conceptual, in genetics and developmental biology.
Terms: Aut | Units: 1

GENE 202: Human Genetics

Utilizes lectures and small group activities to develop a working knowlege of human genetics as applicable to clinical medicine. Basic principles of inheritance, risk assessment, and population genetics are illustrated using examples drawn from diverse areas of medical genetics practice including prenatal, pediatric, adult and cancer genetics. Practical aspects of molecular and cytogenetic diagnostic methods are emphasized. Existing and emerging treatment strategies for single gene disorders are also covered. Prerequisites: basic genetics.
Terms: Aut | Units: 4
Instructors: ; Bernstein, J. (PI)

GENE 205: Advanced Genetics

For PhD students in any of the Biosciences Departments and Programs at Stanford University. Emphasis on developing the ability to solve problems using genetic ideas and methods, to understand the nature and reliability of genetic inference, and to apply genetic reasoning to biological research. Weekly paper discussions based on original research papers that define or illustrate the ideas and techniques covered in the lecture.
Terms: Win | Units: 3

GENE 209: Current Topics in Human, Population, and Statistical Genomics

Intensive seminar/workshop. Topics, drawn from current and past literature, may include: assessing and population genetic analysis of genomic variation; genome-to-phenome mapping; reconstructing demographic history from genome sequence data; domestication genomics; host-pathogen genome evolution; detecting signatures of selection; experimental design in human genetics; linkage and association mapping; ethical and social issues in human, plant, and animal genetics research. Emphasis on analysis and logic or experimental and observational genomics research. Faculty-led discussion with evaluation of response papers, problem sets, and intensive course project. May be repeated for credit.
Terms: Spr | Units: 2 | Repeatable for credit

GENE 210: Genomics and Personalized Medicine (DBIO 220)

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, Gene 205 or BIOS 200.
Terms: Spr | Units: 3
Instructors: ; Gitler, A. (PI); Kim, S. (PI)

GENE 211: Genomics

The goal of this course is to explore how different experimental strategies are applied to a variety of biological questions. By experimental strategy, we refer to both the general method and the logic with which the method is applied. An underlying theme of the course is that each strategy we discuss can be applied to problems that cut across different disciplines, for example immunology, cancer biology, or embryology. Genome evolution, organization, and function; technical, computational, and experimental approaches; hands-on experience with representative computational tools used in genome science; and a work knowledge of the scripting language Python.
Terms: Win | Units: 3

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. Because the team projects start in the first week of class, attendance that week is strongly recommended. Prerequisites: BIOMEDIN 210 or 211 or 214 or 217 or consent of instructor.
Terms: Spr | Units: 3
Instructors: ; Altman, R. (PI)

GENE 213: Neurogenetics Core

For first-year Neurosciences graduate students; open to other graduate students as space permits with preference given to Neurosciences students. Intensive introduction to genetics. Classical and modern genetics with an emphasis on their application to neurosciences research. Topics include: model organisms, genetic screens, genome editing, genetically-encoded tools, GWAS, next-generation sequencing, epigenetics, genetic interactions, human genetics, and neurological disease genetics. Interactive class with student-led discussions, presentations, and group work, including next-generation sequencing workshops and data analysis tutorials. Limited enrollment.
Terms: Spr | Units: 1
Instructors: ; Gitler, A. (PI)

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 skills; consent of instructor for 3 units.
Terms: Aut | Units: 3-4

GENE 215: Frontiers in Biological Research (BIOC 215, DBIO 215)

Literature discussion in conjunction with the Frontiers in Biological Research seminar series in which 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 directions, commonly used techniques to study problems in biology, and comparison between the genetic and biochemical approaches in biological research.
Terms: Aut, Win, Spr | Units: 1 | Repeatable 3 times (up to 3 units total)

GENE 217: Translational Bioinformatics

(Same as BIOMEDIN 217, CS 275) Analytic, storage, and interpretive methods to optimize the transformation of genetic, genomic, and biological data into diagnostics and therapeutics for medicine. Topics: access and utility of publicly available data sources; types of genome-scale measurements in molecular biology and genomic medicine; analysis of microarray data; analysis of polymorphisms, proteomics, and protein interactions; linking genome-scale data to clinical data and phenotypes; and new questions in biomedicine using bioinformatics. Case studies. Prerequisites: programming ability at the level of CS 106A and familiarity with statistics and biology.
Terms: Win | Units: 4

GENE 218: Computational Analysis of Biological Information: Introduction to Python for Biologists (MI 218, PATH 218)

Computational tools for processing, interpretation, communication, and archiving of biological information. Emphasis is on sequence and digital microscopy/image analysis. Intended for biological and clinical trainees without substantial programming experience.
Terms: Sum | Units: 2
Instructors: ; Fire, A. (PI)

GENE 221: Current Issues in Aging

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, 205 or BIOS 200.
Terms: Spr | Units: 2

GENE 232: Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 132, BIO 232, BIOPHYS 232)

Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, microendoscopy, and optical trapping. Limited enrollment. Recommended: basic physics, Biology core or equivalent, and consent of instructor.
Terms: Spr | Units: 4

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.
Last offered: Spring 2014 | Units: 2

GENE 241: Biological Macromolecules (BIOC 241, BIOPHYS 241, SBIO 241)

The physical and chemical basis of macromolecular function. Topics include: forces that stabilize macromolecular structure and their complexes; thermodynamics and statistical mechanics of macromolecular folding, binding, and allostery; diffusional processes; kinetics of enzymatic processes; the relationship of these principles to practical application in experimental design and interpretation. The class emphasizes interactive learning, and is divided equally among lectures, in-class group problem solving, and discussion of current and classical literature. Enrollment limited to 50. Prerequisites: Background in biochemistry and physical chemistry recommended but material available for those with deficiency in these areas; undergraduates with consent of instructor only.
Terms: Spr | Units: 3-5

GENE 243: Intellectual Propery: Scientific Evidence in Patent Litigation

(Same as LAW 343) Open to clinical MD and graduate students. Explores the role of scientific experts in patent infringement litigation. In other areas of the law where scientific experts are used -- medical malpractice, environmental law, criminal law -- the science itself is often in dispute. In patent cases, however, the parties generally agree on the science. This affects the relationship between the lawyer and the expert and the substantive content of their interactions. Patent experts need to be able to explain science to the judge and jury. But they also must help the litigators choose which legal issues to press and which to concede, and to be aware of how the complications of the science might help, hurt, obscure or reveal how the law should be applied to the facts. The class examines judicial decisions and trial documents involving scientific evidence in patent litigation, followed by work in teams on final projects: simulations of expert testimony in a patent case. Simulations are performed at the end of the quarter before panels of practicing patent lawyers. Prerequisite: graduate students must have completed their required coursework and have TGR status.
Terms: Spr | Units: 3
Instructors: ; Morris, R. (PI)

GENE 245: Statistical and Machine Learning Methods for Genomics (BIO 268, BIOMEDIN 245, CS 373, STATS 345)

Introduction to statistical and computational methods for genomics. Sample topics include: expectation maximization, hidden Markov model, Markov chain Monte Carlo, ensemble learning, probabilistic graphical models, kernel methods and other modern machine learning paradigms. Rationales and techniques illustrated with existing implementations used in population genetics, disease association, and functional regulatory genomics studies. Instruction includes lectures and discussion of readings from primary literature. Homework and projects require implementing some of the algorithms and using existing toolkits for analysis of genomic datasets.
Terms: Spr | Units: 3

GENE 271: Human Molecular Genetics

For genetic counseling students, graduate students in genetics, medical students, residents, and postdoctoral fellows interested in the practice of medical genetics and genomics. Gene structure and function; the impact of mutation and polymorphism as they relate to developmental pathways and human disease; mitochondrial genetics; approaches to the study of complex genetic conditions; GWAS and genome sequencing technologies; variant curation; gene therapy, stem cell biology, and pharmacogenetics. Undergraduates require consent of instructor and a basic genetics course.
Terms: Aut | Units: 4
Instructors: ; Hanson-Kahn, A. (PI)

GENE 272: Introduction to Medical Genetics

For genetic counseling students, graduate students in human genetics, medical students, residents, and fellows; undergraduates with consent of instructor. Principles of medical genetics practice, including taking a family history, modes of inheritance and risk assessment, and mathematical principles of medical genetics (Bayes theorem, population genetics). An additional problem set is required for 3 units.
Terms: Aut | Units: 2-3

GENE 273: Introduction to Clinical Genetics Testing

For genetic counseling students, medical students, residents, and fellows. Uses a combination of case based assignments, laboratory observation and didactic lectures to introduce the laboratory concepts of cytogenetics, molecular genetics and biochemical genetics, and to illustrate common genetic conditions that are commonly diagnosed through genetic testing, introducing students to skills in case preparation, management and presentation.
Terms: Aut | Units: 1

GENE 274A: A Case Based Approach to Clinical Genetics

For genetic counseling students, graduate students in genetics, medical students, residents and fellows. Case-based scenarios and guest expert lectures. Students learn skills in case preparation, management, and presentation, as well as content around common genetic disorders.
Terms: Win | Units: 2

GENE 274B: A Case Based Approach to Clinical Genetics

For genetic counseling students, graduate students in genetics, medical students, residents, and fellows. Case-based scenarios and guest expert lectures. Students learn skills in case preparation, management, and presentation, as well as content around common genetic disorders. This course is a continuation of GENE 274A, but may be taken individually with instructor permission.
Terms: Spr | Units: 2

GENE 275: Role Play and Genetic Counseling Observations

Students role play aspects of genetic counseling sessions and learn through clinical observations. Observation includes genetic counseling sessions in prenatal, pediatric, and cancer settings.
Terms: Aut | Units: 2

GENE 276: Genetic Counseling Clinical Rotations

For genetic counseling students only. Supervised clinical experiences. May be repeated for credit. Prerequisite: GENE 275.
Terms: Aut, Win, Spr, Sum | Units: 4-7 | Repeatable for credit

GENE 278: Prenatal Genetic Counseling

Internet-based course for genetic counseling students, graduate students in genetics, medical students, residents, and fellows; genetic counseling students should take this course in conjunction with their initial prenatal genetics rotation. Topics include prenatal genetic screening and diagnosis in the first and second trimesters, ultrasound, teratology, and genetic carrier screening.
Terms: Aut, Win, Spr, Sum | Units: 1
Instructors: ; Ormond, K. (PI)

GENE 279: Pediatric and Adult Genetic Counseling

Internet based course for genetic counseling students, graduate students in genetics, medical students, residents, and fellows; genetic counseling students should take this course in conjunction with their initial general genetics rotation. Topics include: common genetic conditions, assessment of child development and medical history in the context of a genetic workup, the pediatric genetics medical examination, dysmorphology, introduction to laboratory genetic testing, development of a differential diagnosis, and resources for case management and family support.
Terms: Aut, Win, Spr, Sum | Units: 1

GENE 280: Metabolic Genetic Counseling

Internet based course for genetic counseling students, graduate students in genetics, medical students, residents, and fellows genetic counseling students should take this course in conjunction with their metabolic genetics rotation. Topics include: overview of metabolic diseases; common pathways; diagnosis, management, and treatment of metabolic disorders; and newborn screening.
Terms: Aut, Win, Spr, Sum | Units: 1

GENE 281: Cancer Genetic Counseling

Internet based course for genetic counseling students, graduate students in genetics, medical students, residents, and fellows; genetic counseling students should take this course in conjunction with their initial cancer genetics rotation. Topics include: cancer biology and cytogenetics; diagnosis and management of common cancer genetic syndromes¿ predictive testing; psychology of cancer genetic counseling; and topics recommended by ASCO guidelines.
Terms: Aut, Win, Spr, Sum | Units: 1
Instructors: ; Ormond, K. (PI)

GENE 282A: Genetic Counseling Research Seminar

For genetic counseling students only. Facilitated discussions on identifying a topic and mentor for genetic counseling departmental research projects.
Terms: Win | Units: 1
Instructors: ; Ormond, K. (PI)

GENE 282B: Genetic Counseling Research Seminar

For genetic counseling students only. Lectures and facilitated discussions on research methodology for genetic counseling departmental research projects. Prerequisite: GENE 282A.
Terms: Spr | Units: 1
Instructors: ; Ormond, K. (PI)

GENE 283: Genetic Counseling Research

Genetic counseling students conduct clinical research projects as required by the department for graduation. May be repeated for credit. Pre- or corequisite: GENE 282.
Terms: Aut, Win, Spr, Sum | Units: 1-8 | Repeatable for credit

GENE 284: Medical Genetics Seminar

Presentation of research and cases. Students enrolling for 2 units also attend and report on external seminars. May be repeated for credit.
Terms: Aut, Win, Spr | Units: 1-2 | Repeatable for credit
Instructors: ; Hanson-Kahn, A. (PI)

GENE 285A: Genetic Counseling Seminar

Year-long seminar primarily for genetic counseling students. Autumn: basics of medical communication; crosscultural and disability sensitive communication about genetics, and principles of providing genetic counseling. Undergraduates may enroll in Autumn Quarter with consent of instructor.
Terms: Aut | Units: 2-3
Instructors: ; Ormond, K. (PI)

GENE 285B: Genetics Counseling Seminar

Year-long seminar primarily for genetic counseling students. Winter: the impact of chronic illness and genetic disease in a developmental manner.
Terms: Win | Units: 2
Instructors: ; Ormond, K. (PI)

GENE 285C: Genetic Counseling Seminar

Year-long seminar primarily for genetic counseling students. Spring: applying therapeutic counseling approaches to the practice of genetic counseling.
Terms: Spr | Units: 2
Instructors: ; Ormond, K. (PI)

GENE 286: Advanced Genetic Counseling Seminar

For genetic counseling students only. Psychosocial issues associated with genetic counseling cases are discussed through presentation of cases that students have seen throughout their training. Professional development topics will be included. Must be taken for 3 quarters. Prerequisites: GENE 285 A,B,C and 276.
Terms: Aut, Win, Spr | Units: 2 | Repeatable 3 times (up to 6 units total)

GENE 286C: Advanced Genetic Counseling Seminar

Continuation of 286A/B. For genetic counseling students only. Psychosocial issues associated with genetic counseling cases are discussed through presentation of cases that students have seen throughout their training. Professional development topics including: the expanding roles of genetic counselors; billing, reimbursement, and licensing; the role of genetic counseling in the changing healthcare system; the incorporation of genetics into all areas of medicine and public health; and implications of direct-to-consumer genetic testing. Prerequisites: GENE 285 A,B,C and 276.
| Units: 2

GENE 287: CARDIOVASCULAR GENETICS

Internet-based course for genetic counseling students, graduate students in genetics, medical students, residents, and fellow; genetic counseling students should take this course in conjunction with their cardiovascular genetics rotation. Topics include: Basic cardiology principles, including relevant anatomy and physiology; diagnosis, management and genetic testing as it relates to common inherited cardiovascular conditions in both the pediatric and adult setting; predictive genetic testing issues specific to inherited cardiovascular conditions; psychologic issues related to sudden death conditions. This course is designed for genetic counseling students, medical students, residents, post-doctoral fellows and nurses interested in inherited cardiovascular conditions.
Terms: Aut, Win, Spr, Sum | Units: 1
Instructors: ; Ormond, K. (PI)

GENE 224: Principles of Pharmacogenomics (BIOMEDIN 224)

Introduction to the relevant pharmacology, genomics, experimental methods for high-throughput measurements (sequencing, expression, genotyping), analysis methods for GWAS, chemoinformatics, and natural language processing. Review of key gene classes (cytochromes, transporters, GPCRs), key drugs for which genetics is critical (warfarin, clopidogrel, statins, NSAIDs, neuropsychiatric drugs and cancer drugs). Also reviews resources for pharmacogenomics (PharmGKB, Drugbank, CMAP, and others) as well as issues in doing clinical implementation of pharmacogenomics testing. Reading of key papers, including student presentations of this work. Problem sets; final project selected with approval of instructor. Prerequisites: two of BIO 41, BIO 42, BIO 43, BIO 44X, BIO 44Y or consent of instructor.
| Units: 3

GENE 244: Introduction to Statistical Genetics (STATS 344)

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.
| Units: 3
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