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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 | Grading: Medical Satisfactory/No Credit

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. Only available to MD and MOM students.
Terms: Aut | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Bernstein, J. (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, 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.
Terms: Aut | Units: 3-4 | Grading: Medical Option (Med-Ltr-CR/NC)

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

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.
Terms: Aut, Win, Spr | Units: 1 | Repeatable for credit | Grading: Medical Satisfactory/No Credit

GENE 217: Translational Bioinformatics (BIOE 217, BIOMEDIN 217, CS 275)

Computational methods for the translation of biomedical data into diagnostic, prognostic, and therapeutic applications in medicine. Topics: multi-scale omics data generation and analysis, utility and limitations of public biomedical resources, machine learning and data mining, issues and opportunities in drug discovery, and mobile/digital health solutions. Case studies and course project. Prerequisites: programming ability at the level of CS 106A and familiarity with biology and statistics.
Terms: Aut | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)

GENE 219: Current Issues in Genetics

Current Issues in Genetics is an in-house seminar series that meets each Academic Quarter tor one hour per week (Friday, 4:00-5:00) and features talks by Genetics Department faculty, students, and postdoctoral fellows (with occasional visiting speakers from other Stanford departments). Thus, over the Academic Year, it provides a comprehensive overview of the work going on in the Department. Student attendance at the seminars will be required, with short written assignments (typically three per Quarter) to encourage thinking about the material presented in the talks.
Terms: Aut, Win, Spr | Units: 1 | Grading: Medical Satisfactory/No Credit

GENE 224: Principles of Pharmacogenomics (BIOMEDIN 224)

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.
Terms: Aut, Win, Spr, Sum | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

GENE 236: Deep Learning in Genomics and Biomedicine (BIODS 237, BIOMEDIN 273B, CS 273B)

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 CS 109, and basic machine learning such as CS 229. No prior knowledge of genomics is necessary.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Kundaje, A. (PI); Zou, J. (PI)

GENE 271: Human Molecular Genetics (CHPR 271)

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. Non-GC students: Please contact the instructor when you enroll.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Hanson-Kahn, A. (PI)

GENE 272: Introduction to Medical Genetics (CHPR 272)

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 | Grading: Medical Option (Med-Ltr-CR/NC)

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 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. Non-GC students: Please contact the instructor when you enroll.
Terms: Aut | Units: 2 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Hanson-Kahn, A. (PI)

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 specialty settings.
Terms: Aut | Units: 2 | Grading: Medical Satisfactory/No Credit
Instructors: ; Ormond, K. (PI)

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: 1-7 | Repeatable for credit | Grading: Medical Option (Med-Ltr-CR/NC)

GENE 278: Prenatal Genetic Counseling (CHPR 278)

Online course for genetic counseling students, graduate students in genetics, medical students, residents, fellows, and nurses interested in prenatal genetics. Genetic counseling students should take this course in conjunction with their initial prenatal genetics rotation. Topics include: prenatal screening and diagnostic testing, ultrasound, genetic carrier screening, teratology, fetal treatment and intervention, perinatal loss, termination, and infertility. Non-GC students: Please contact the instructor when you enroll.
Terms: Aut, Win, Spr | Units: 1 | Grading: Medical Satisfactory/No Credit

GENE 279: Pediatric and Adult Genetic Counseling (CHPR 279)

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: clinical reasoning in medical genetics, techniques to prepare for the medical genetics visit, assessment of child development and medical history in the context of a genetic workup, dysmorphology, development of a differential diagnosis, and resources for case management and family support. Non-GC students: Please contact the instructor when you enroll.
Terms: Aut, Win, Spr | Units: 1 | Grading: Medical Satisfactory/No Credit
Instructors: ; Hanson-Kahn, A. (PI)

GENE 280: Metabolic Genetic Counseling (CHPR 280)

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. Non-GC students: Please contact the instructor when you enroll.
Terms: Aut, Win, Spr | Units: 1 | Grading: Medical Satisfactory/No Credit
Instructors: ; Hanson-Kahn, A. (PI)

GENE 281: Cancer Genetic Counseling (CHPR 281)

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.Non-GC students: Please contact the instructor when you enroll.
Terms: Aut, Win, Spr | Units: 1 | Grading: Medical Satisfactory/No Credit
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 | Grading: Medical Satisfactory/No Credit

GENE 284: Medical Genetics Seminar (CHPR 284)

Presentation of genetics research and cases from the medical genetics and biochemical genetics services. Course may be completed online or in-person. Non-GC students: Please contact the instructor when you enroll.
Terms: Aut, Win, Spr | Units: 1 | Repeatable for credit | Grading: Medical Satisfactory/No Credit

GENE 285A: Genetic Counseling Seminar

Year-long seminar primarily for genetic counseling students. Fall: An introduction to genetic counseling principles, techniques, and professional development.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

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 for credit | Grading: Medical Option (Med-Ltr-CR/NC)

GENE 287: CARDIOVASCULAR GENETICS (CHPR 287)

Online course for genetic counseling students, graduate students in genetics, medical students, residents, fellows, and nurses interested in inherited cardiovascular conditions. 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; psychological issues related to sudden death conditions.nnNon-GC students: Please contact the instructor when you enroll.
Terms: Aut, Win, Spr | Units: 1 | Grading: Medical Satisfactory/No Credit

GENE 288: Neurogenetics

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 neurogenetics rotation. Topics include: introduction to neurology for beginners, including an overview of neurologic exam and localization, to provide non-neurologist trainees a foundation for understanding the differential diagnosis process in neurology; common and exemplary neurogenetics disorders spanning the adult and pediatric neurologic sub-specialties; key genetic concepts such as triple repeat disorders and FSHD; ethical and psychological topics as well as gene-targets therapeutics. Medical students and graduate students outside of genetic counseling should obtain permission from instructor prior to enrollment. No prerequisite for genetic counseling students, genetics or neurology residents/fellows or post-docs. Non-GC students: Please contact the instructor when you enroll.
Terms: Aut, Win, Spr | Units: 1 | Grading: Medical Satisfactory/No Credit
Instructors: ; Ormond, K. (PI)

GENE 346: Advanced Seminar on Prokaryotic Molecular Biology (BIO 346, CSB 346)

Enrollment limited to PhD students associated with departmental research groups in genetics or molecular biology.
Terms: Aut, Win, Spr | Units: 1 | Grading: Satisfactory/No Credit
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