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GENE 104Q. Law and the Biosciences. 3 Units.

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.

GENE 199. Undergraduate Research. 1-18 Unit.

Students undertake investigations sponsored by individual faculty members. Prerequisite: consent of instructor.

GENE 200. Genetics and Developmental Biology Training Camp. 1 Unit.

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.
Same as: DBIO 200

GENE 202. Human Genetics. 4 Units.

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. Only available to MD and MOM students.

GENE 204. Essentials of Multidimensional Flow Cytometry. 1 Unit.

Keep pace with automated flow cytometry data analysis via hands-on training. Learn how to design multicolor flow cytometry experiments. Elements of quantitative flow cytometry. Course for all students, staff and faculty. Prerequisite is background in topic.

GENE 205. Advanced Genetics. 3 Units.

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.

GENE 207. Microfluidic Device Laboratory. 3-4 Units.

This course exposes students to the design, fabrication, and testing of microfluidic devices for biological applications through combination of lectures and hands-on lab sessions. In teams of two, students will produce a working prototype devices designed to address specific design challenges within the biological community using photolithography, soft lithography, and imaging techniques.
Same as: BIOE 301D

GENE 208. Gut Microbiota in Health and Disease. 2-3 Units.

Preference to graduate students. Focus is on the human gut microbiota. Students enrolling for 3 units receive instruction on computational approaches to analyze microbiome data and must complete a related project.
Same as: BIOE 221G, MI 221

GENE 209. Current Topics in Human, Population, and Statistical Genomics. 2 Units.

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.

GENE 210. Genomics and Personalized Medicine. 3 Units.

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.
Same as: DBIO 220

GENE 211. Genomics. 3 Units.

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.

GENE 212. Introduction to Biomedical Informatics Research Methodology. 3-5 Units.

Capstone Biomedical Informatics (BMI) experience. 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. Issues related to research reproducibility. 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. Preference to BMI graduate students. Consent of instructor required.
Same as: BIOE 212, BIOMEDIN 212, CS 272

GENE 214. Representations and Algorithms for Computational Molecular Biology. 3-4 Units.

Topics: introduction to bioinformatics and computational biology, algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, 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. Prerequisite: CS 106B; recommended: CS161; consent of instructor for 3 units.
Same as: BIOE 214, BIOMEDIN 214, CS 274

GENE 215. Frontiers in Biological Research. 1 Unit.

Students analyze cutting edge science, develop a logical framework for evaluating evidence and models, and enhance their ability to design original research through exposure to experimental tools and strategies. The class runs in parallel with the Frontiers in Biological Research seminar series. Students and faculty meet on the Tuesday preceding each seminar to discuss a landmark paper in the speaker's field of research. Following the Wednesday seminar, students meet briefly with the speaker for a free-range discussion which can include insights into the speakers' paths into science and how they pick scientific problems.
Same as: BIOC 215, DBIO 215

GENE 216. Practical Considerations and Industry Perspective on Academic-Industry Collaborations. 1 Unit.

Provides an overview, fundamentals and practical considerations for different aspects of academic-industry collaborations by inviting current industrial experts to share their views and to answer questions. The different aspects include collaboration models, proposal building, IP right sharing, funding opportunities, sabbatical and internship in industry, industry job searching, etc. This class also serves as a platform to connect with Bay Area biotech and pharmaceutical executives and experts.

GENE 217. Translational Bioinformatics. 4 Units.

(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.

GENE 218. Computational Analysis of Biological Information: Introduction to Python for Biologists. 2 Units.

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.
Same as: MI 218, PATH 218

GENE 221. Current Issues in Aging. 2 Units.

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.

GENE 224. Principles of Pharmacogenomics. 3 Units.

This course is an introduction to pharmacogenomics, including the relevant pharmacology, genomics, experimental methods (sequencing, expression, genotyping), data analysis methods and bioinformatics. The course reviews key gene classes (e.g., cytochromes, transporters) and key drugs (e.g., warfarin, clopidogrel, statins, cancer drugs) in the field. Resources for pharmacogenomics (e.g., PharmGKB, Drugbank, NCBI resources) are reviewed, as well as issues implementing pharmacogenomics testing in the clinical setting. Reading of key papers, including student presentations of this work; problem sets; final project selected with approval of instructor. Prerequisites: two of BIO 41, 42, 43, 44X, 44Y or consent of instructor.
Same as: BIOMEDIN 224

GENE 232. Advanced Imaging Lab in Biophysics. 4 Units.

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.
Same as: APPPHYS 232, BIO 132, BIO 232, BIOPHYS 232

GENE 233. The Biology of Small Modulatory RNAs. 2 Units.

Open to graduate and medical students. Explores recent progress and unsolved questions in the field of RNA intereference and microRNA biology. Students are required to read assigned primary literature before each class and actively participate in guided discussions on related technical and conceptual issues during class meetings. Assignments include critiques of assigned papers and developing a novel research proposal.
Same as: MI 233, PATH 233

GENE 234. Fundamentals of RNA Biology. 2 Units.

For graduate or medical students and (if space allows) to active participants from other segments of the Stanford Community (e.g., TGR students); undergraduates by instructor consent. Fundamental issues of RNA biology, with the goal of setting a foundation for students to explore the expanding world of RNA-based regulation. Each week a topic is covered by a faculty lecture and journal club presentations by students.
Same as: MI 234, PATH 234

GENE 235. C. Elegans Genetics. 2 Units.

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.

GENE 236. Deep Learning in Genomics and Biomedicine. 3 Units.

Recent breakthroughs in high-throughput genomic and biomedical data are transforming biological sciences into "big data" disciplines. In parallel, progress in deep neural networks are revolutionizing fields such as image recognition, natural language processing and, more broadly, AI. This course explores the exciting intersection between these two advances. The course will start with an introduction to deep learning and overview the relevant background in genomics and high-throughput biotechnology, focusing on the available data and their relevance. It will then cover the ongoing developments in deep learning (supervised, unsupervised and generative models) with the focus on the applications of these methods to biomedical data, which are beginning to produced dramatic results. In addition to predictive modeling, the course emphasizes how to visualize and extract interpretable, biological insights from such models. Recent papers from the literature will be presented and discussed. Students will be introduced to and work with popular deep learning software frameworks. Students will work in groups on a final class project using real world datasets. Prerequisites: College calculus, linear algebra, basic probability and statistics such as CS109, and basic machine learning such as CS229. No prior knowledge of genomics is necessary.
Same as: BIODS 237, BIOMEDIN 273B, CS 273B

GENE 243. Intellectual Propery: Scientific Evidence in Patent Litigation. 3 Units.

(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.

GENE 244. Introduction to Statistical Genetics. 3 Units.

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.
Same as: STATS 344

GENE 245. Statistical and Machine Learning Methods for Genomics. 3 Units.

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.
Same as: BIO 268, BIOMEDIN 245, CS 373, STATS 345

GENE 260. Supervised Study. 1-18 Unit.

Genetics graduate student lab research from first quarter to filing of candidacy. Prerequisite: consent of instructor.

GENE 267. Molecular Mechanisms of Neurodegenerative Disease. 4 Units.

The epidemic of neurodegenerative disorders such as Alzheimer's and Parkinson's disease occasioned by an aging human population. Genetic, molecular, and cellular mechanisms. Clinical aspects through case presentations.
Same as: BIO 267, NENS 267

GENE 271. Human Molecular Genetics. 4 Units.

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 interpretation; gene therapy, stem cell biology, and pharmacogenetics. Undergraduates require consent of instructor and a basic genetics course.
Same as: CHPR 271

GENE 272. Introduction to Medical Genetics. 2-3 Units.

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.
Same as: CHPR 272

GENE 273. Introduction to Clinical Genetics Testing. 1 Unit.

For genetic counseling students, medical students, residents, and fellows. Uses a combination of case based assignments, laboratory observation and didactic lectures to introduce techniques and technology used in cytogenetics, molecular genetics and biochemical genetic testing, and to introduce clinical features of common genetic conditions that are commonly diagnosed through genetic testing.

GENE 274A. A Case Based Approach to Clinical Genetics. 2 Units.

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.
Same as: CHPR 274A

GENE 274B. A Case Based Approach to Clinical Genetics. 2 Units.

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.
Same as: CHPR 274B

GENE 275. Role Play and Genetic Counseling Observations. 2 Units.

Students role play aspects of genetic counseling sessions and learn through clinical observations. Observation includes genetic counseling sessions in prenatal, pediatric, and specialty settings.

GENE 276. Genetic Counseling Clinical Rotations. 1-7 Unit.

For genetic counseling students only. Supervised clinical experiences. May be repeated for credit. Prerequisite: GENE 275.

GENE 278. Prenatal Genetic Counseling. 1 Unit.

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.
Same as: CHPR 278

GENE 279. Pediatric and Adult Genetic Counseling. 1 Unit.

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.
Same as: CHPR 279

GENE 280. Metabolic Genetic Counseling. 1 Unit.

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.
Same as: CHPR 280

GENE 281. Cancer Genetic Counseling. 1 Unit.

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.
Same as: CHPR 281

GENE 282A. Genetic Counseling Research Seminar. 1 Unit.

For genetic counseling students only. Facilitated discussions on identifying a topic and mentor for genetic counseling departmental research projects.

GENE 282B. Genetic Counseling Research Seminar. 1 Unit.

For genetic counseling students only. Lectures and facilitated discussions on research methodology for genetic counseling departmental research projects. Prerequisite: GENE 282A.

GENE 283. Genetic Counseling Research. 1-8 Unit.

Genetic counseling students conduct clinical research projects as required by the department for graduation. May be repeated for credit. Pre- or corequisite: GENE 282.

GENE 284. Medical Genetics Seminar. 1-2 Unit.

Presentation of research and cases. Students enrolling for 2 units also attend and report on external seminars. May be repeated for credit. Non-GC students: please contact the instructor when you enroll.
Same as: CHPR 284

GENE 285A. Genetic Counseling Seminar. 2-3 Units.

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. Extra paper required for 3 units.

GENE 285B. Genetics Counseling Seminar. 2 Units.

Year-long seminar primarily for genetic counseling students. Winter: the impact of chronic illness and genetic disease in a developmental manner.

GENE 285C. Genetic Counseling Seminar. 2 Units.

Year-long seminar primarily for genetic counseling students. Spring: applying therapeutic counseling approaches to the practice of genetic counseling.

GENE 286. Advanced Genetic Counseling Seminar. 2 Units.

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.

GENE 287. CARDIOVASCULAR GENETICS. 1 Unit.

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.
Same as: CHPR 287

GENE 299. Directed Reading in Genetics. 1-18 Unit.

Prerequisite: consent of instructor.

GENE 399. Graduate Research. 1-18 Unit.

Investigations sponsored by individual faculty members. Prerequisite: consent of instructor.

GENE 801. TGR Project. 0 Units.

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GENE 802. TGR Dissertation. 0 Units.

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