BIOE 212:
Introduction to Biomedical Informatics Research Methodology (BIOMEDIN 212, CS 272, GENE 212)
Capstone Biomedical Informatics (BMI) experience. Handson 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.
Terms: Spr

Units: 35

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 156:
Economics of Health and Medical Care (BIOMEDIN 256, ECON 126, HRP 256)
Institutional, theoretical, and empirical analysis of the problems of health and medical care. Topics: demand for medical care and medical insurance; institutions in the health sector; economics of information applied to the market for health insurance and for health care; measurement and valuation of health; competition in health care delivery. Graduate students with research interests should take ECON 249. Prerequisites: ECON 50 and either ECON 102A or STATS 116 or the equivalent. Recommended: ECON 51.
Terms: Spr

Units: 5

UG Reqs: WAYSI

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 200:
Biomedical Informatics Colloquium
Series of colloquia offered by program faculty, students, and occasional guest lecturers. May be repeated three times for credit.
Terms: not given this year

Units: 1

Repeatable for credit

Grading: Medical Satisfactory/No Credit
BIOMEDIN 201:
Biomedical Informatics Student Seminar
Participants report on recent articles from the Biomedical Informatics literature or their research projects. Goals are to teach critical reading of scientific papers and presentation skills. May be repeated three times for credit.
Terms: Aut, Win, Spr, Sum

Units: 1

Repeatable for credit

Grading: Medical Satisfactory/No Credit
BIOMEDIN 205:
Precision Practice with Big Data
Primarily for M.D. students; open to other graduate students. Provides an overview of how to leverage large amounts of clinical, molecular, and imaging data within hospitals and in cyberspacebig datato practice medicine more effectively. Lectures by physicians, researchers, and industry leaders survey how the major methods of informatics can help physicians leverage big data to profile disease, to personalize treatment to patients, to predict treatment response, to discover new knowledge, and to challenge established medical dogma and the current paradigm of clinical decisionmaking based solely on published knowledge and individual physician experience. May be repeated for credit. Prerequisite: background in biomedicine. Background in computer science can be helpful but not required.
Terms: Aut

Units: 1

Repeatable for credit

Grading: Medical Satisfactory/No Credit
BIOMEDIN 206:
Informatics in Industry
Effective management, modeling, acquisition, and mining of biomedical information in healthcare and biotechnology companies and approaches to information management adopted by companies in this ecosystem. Guest speakers from pharmaceutical/biotechnology companies, clinics/hospitals, health communities/portals, instrumentation/software vendors. May be repeated for credit.
Terms: Spr

Units: 1

Repeatable for credit

Grading: Medical Satisfactory/No Credit
BIOMEDIN 207:
Digital Medicine: How health IT is changing the practice of medicine
The widespread use of health IT, such as electronic health records, and of health applications by patients, will radically alter the practice of medicine in the coming decades. This seminar, comprised of guest lectures from industry and academia, will highlight the practical challenges and successes of how health IT has transformed care delivery programs. The seminar will cover current efforts in clinical decision support, patientcentered design, integration with community care, Big Data, and the innovation pipeline for healthcare delivery organizations.
Terms: not given this year

Units: 1

Grading: Medical Satisfactory/No Credit
BIOMEDIN 208:
Clinical Informatics Literature Review Seminar
Focus is on reading and discussing seminal papers in clinical and health informatics. Topics include biomedical informatics methods, systems design, implementation and evaluation. Limited enrollment.
Terms: Win

Units: 1

Grading: Medical Satisfactory/No Credit
BIOMEDIN 210:
Modeling Biomedical Systems: Ontology, Terminology, Problem Solving (CS 270)
Methods for modeling biomedical systems and for building modelbased software systems. Emphasis is on intelligent systems for decision support and Semantic Web applications. Topics: knowledge representation, controlled terminologies, ontologies, reusable problem solvers, and knowledge acquisition. Students learn about current trends in the development of advanced biomedical software systems and acquire handson experience with several systems and tools. Prerequisites: CS106A, basic familiarity with biology.
Terms: Win

Units: 3

Grading: Letter or Credit/No Credit
BIOMEDIN 212:
Introduction to Biomedical Informatics Research Methodology (BIOE 212, CS 272, GENE 212)
Capstone Biomedical Informatics (BMI) experience. Handson 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.
Terms: Spr

Units: 35

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 214:
Representations and Algorithms for Computational Molecular Biology (BIOE 214, CS 274, 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, 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: 34

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 215:
Data Driven Medicine
With the spread of electronic health records and increasingly low cost assays for patient molecular data, powerful data repositories with tremendous potential for biomedical research, clinical care and personalized medicine are being built. But these databases are large and difficult for any one specialist to analyze. To find the hidden associations within the full set of data, we introduce methods for datamining at the internet scale, the handling of largescale electronic medical records data for machine learning, methods in natural language processing and textmining applied to medical records, methods for using ontologies for the annotation and indexing of unstructured content as well as semantic web technologies. Prerequisites: CS 106A; STATS 216. Recommended: one of CS 246, STATS 305, or CS 22
Terms: Aut

Units: 3

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 216:
Representations and Algorithms for Molecular Biology: Lectures
Lecture component of BIOMEDIN 214. One unit for medical and graduate students who attend lectures only; may be taken for 2 units with participation in limited assignments and final project. Lectures also available via internet. Prerequisite: familiarity with biology recommended.
Terms: Aut

Units: 12

Grading: Medical Satisfactory/No Credit
BIOMEDIN 217:
Translational Bioinformatics (BIOE 217, CS 275)
Computational methods for the translation of biomedical data into diagnostic, prognostic, and therapeutic applications in medicine. Topics: multiscale 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: Win

Units: 4

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 218:
Translational Bioinformatics Lectures
Same content as BIOMEDIN 217; for medical and graduate students who attend lectures and participate in limited assignments and final project. Computational methods for the translation of biomedical data into diagnostic, prognostic, and therapeutic applications in medicine. Topics: multiscale 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.nPrerequisites: programming ability at the level of CS 106A and familiarity with biology and statistics.
Terms: Win

Units: 2

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 219:
Mathematical Models and Medical Decisions
Analytic methods for determining optimal diagnostic and therapeutic decisions with applications to the care of individual patients and the design of policies applied to patient populations. Topics include: utility theory and probability modeling, empirical methods for disease prevalence estimation, probability models for periodic processes, binary decisionmaking techniques, Markov models of dynamic disease state problems, utility assessment techniques, parametric utility models, utility models for multidimensional outcomes, analysis of timevarying clinical outcomes, and the design of costconstrained clinical policies. Extensive problem sets compliment the lectures. Prerequisites: introduction to calculus and basic statistics.
Terms: Win

Units: 3

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 224:
Principles of Pharmacogenomics (GENE 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 (MedLtrCR/NC)
BIOMEDIN 225:
Data Driven Medicine: Lectures
Lectures for BIOMEDIN 215.With the spread of electronic health records and increasingly low cost assays for patient molecular data, powerful data repositories with tremendous potential for biomedical research, clinical care and personalized medicine are being built. But these databases are large and difficult for any one specialist to analyze. To find the hidden associations within the full set of data, we introduce methods for datamining at the internet scale, the handling of largescale electronic medical records data for machine learning, methods in natural language processing and textmining applied to medical records, methods for using ontologies for the annotation and indexing of unstructured content as well as semantic web technologies. Prerequisites: familiarity with statistics (STATS 216) and biology.
Terms: Aut

Units: 2

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 233:
Intermediate Biostatistics: Analysis of Discrete Data (HRP 261, STATS 261)
Methods for analyzing data from casecontrol and crosssectional studies: the 2x2 table, chisquare test, Fisher's exact test, odds ratios, MantelHaenzel methods, stratification, tests for matched data, logistic regression, conditional logistic regression. Emphasis is on data analysis in SAS. Special topics: crossfold validation and bootstrap inference.
Terms: Win

Units: 3

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 245:
Statistical and Machine Learning Methods for Genomics (BIO 268, CS 373, GENE 245, 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

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 251:
Outcomes Analysis (HRP 252, MED 252)
Methods of conducting empirical studies which use large existing medical, survey, and other databases to ask both clinical and policy questions. Econometric and statistical models used to conduct medical outcomes research. How research is conducted on medical and health economics questions when a randomized trial is impossible. Problem sets emphasize handson data analysis and application of methods, including reanalyses of wellknown studies. Prerequisites: one or more courses in probability, and statistics or biostatistics.
Terms: Spr

Units: 4

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 256:
Economics of Health and Medical Care (BIOMEDIN 156, ECON 126, HRP 256)
Institutional, theoretical, and empirical analysis of the problems of health and medical care. Topics: demand for medical care and medical insurance; institutions in the health sector; economics of information applied to the market for health insurance and for health care; measurement and valuation of health; competition in health care delivery. Graduate students with research interests should take ECON 249. Prerequisites: ECON 50 and either ECON 102A or STATS 116 or the equivalent. Recommended: ECON 51.
Terms: Spr

Units: 5

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 260:
Computational Methods for Biomedical Image Analysis and Interpretation (RAD 260)
The latest biological and medical imaging modalities and their applications in research and medicine. Focus is on computational analytic and interpretive approaches to optimize extraction and use of biological and clinical imaging data for diagnostic and therapeutic translational medical applications. Topics include major image databases, fundamental methods in image processing and quantitative extraction of image features, structured recording of image information including semantic features and ontologies, indexing, search and contentbased image retrieval. Case studies include linking image data to genomic, phenotypic and clinical data, developing representations of image phenotypes for use in medical decision support and research applications and the role that biomedical imaging informatics plays in new questions in biomedical science. Includes a project. Enrollment for 3 units requires instructor consent. Prerequisites: programming ability at the level of CS 106A, familiarity with statistics, basic biology. Knowledge of Matlab highly recommended.
Terms: Spr

Units: 34

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 262:
Computational Genomics
Applications of computer science to genomics, and concepts in genomics from a computer science point of view. Topics: dynamic programming, algorithms on strings and sequences, graphical models for sequence analysis. Applications of these tools to comparative genomics, DNA sequencing and assembly, genomic annotation, functional genomics, phylogeny and molecular evolution, population genomics, cancer genomics. Prerequisites: 161 or familiarity with basic algorithmic concepts. Recommended: basic knowledge of genetics.
Terms: not given this year

Units: 3

Grading: Letter or Credit/No Credit
BIOMEDIN 273A:
A Computational Tour of the Human Genome (CS 273A, DBIO 273A)
Introduction to computational biology through an informatic exploration of the human genome. Topics include: genome sequencing (technologies, assembly, personalized sequencing); functional landscape (genes, gene regulation, repeats, RNA genes, epigenetics); genome evolution (comparative genomics, ultraconservation, cooption). Additional topics may include population genetics, personalized genomics, and ancient DNA. Course includes primers on molecular biology, the UCSC Genome Browser, and text processing languages. Guest lectures from genomic researchers. No prerequisites. Seehttp://cs273a.stanford.edu/.
Terms: Aut

Units: 3

Grading: Letter or Credit/No Credit
BIOMEDIN 273B:
Deep Learning in Genomics and Biomedicine (BIODS 237, CS 273B, GENE 236)
Recent breakthroughs in highthroughput 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 highthroughput 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.
Terms: Aut

Units: 3

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 279:
Computational Biology: Structure and Organization of Biomolecules and Cells (BIOE 279, BIOPHYS 279, CME 279, CS 279)
Computational techniques for investigating and designing the threedimensional structure and dynamics of biomolecules and cells. These computational methods play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Course topics include protein structure prediction, protein design, drug screening, molecular simulation, cellularlevel simulation, image analysis for microscopy, and methods for solving structures from crystallography and electron microscopy data. Prerequisites: elementary programming background (CS 106A or equivalent) and an introductory course in biology or biochemistry.
Terms: Aut

Units: 3

Grading: Letter or Credit/No Credit
BIOMEDIN 290:
Biomedical Informatics Teaching Methods
Handson training in biomedical informatics pedagogy. Practical experience in pedagogical approaches, variously including didactic, inquiry, project, team, case, field, and/or problembased approaches. Students create course content, including lectures, exercises, and assessments, and evaluate learning activities and outcomes. Prerequisite: instructor consent.
Terms: Aut, Win, Spr, Sum

Units: 16

Repeatable for credit

Grading: Medical Option (MedLtrCR/NC)
Instructors: ;
Altman, R. (PI);
Ashley, E. (PI);
Bagley, S. (PI);
Bassik, M. (PI);
Batzoglou, S. (PI);
Bayati, M. (PI);
Bejerano, G. (PI);
Bhattacharya, J. (PI);
Blish, C. (PI);
Boahen, K. (PI);
Brandeau, M. (PI);
Brutlag, D. (PI);
Bustamante, C. (PI);
Butte, A. (PI);
Chang, H. (PI);
Cherry, J. (PI);
Cohen, S. (PI);
Covert, M. (PI);
Curtis, C. (PI);
Das, A. (PI);
Das, R. (PI);
Davis, R. (PI);
Delp, S. (PI);
Desai, M. (PI);
Dill, D. (PI);
Dumontier, M. (PI);
Elias, J. (PI);
Fagan, L. (PI);
Feldman, M. (PI);
Ferrell, J. (PI);
Fraser, H. (PI);
Gambhir, S. (PI);
Gerritsen, M. (PI);
Gevaert, O. (PI);
Goldstein, M. (PI);
Greenleaf, W. (PI);
Guibas, L. (PI);
Hastie, T. (PI);
Hlatky, M. (PI);
Holmes, S. (PI);
Ji, H. (PI);
Karp, P. (PI);
Khatri, P. (PI);
Kim, S. (PI);
Kirkegaard, K. (PI);
Klein, T. (PI);
Koller, D. (PI);
Krummel, T. (PI);
Kundaje, A. (PI);
Levitt, M. (PI);
Levitt, R. (PI);
Li, J. (PI);
Longhurst, C. (PI);
Lowe, H. (PI);
Mallick, P. (PI);
Manning, C. (PI);
McAdams, H. (PI);
Meng, T. (PI);
Menon, V. (PI);
Montgomery, S. (PI);
Musen, M. (PI);
Napel, S. (PI);
Nolan, G. (PI);
Olshen, R. (PI);
Owen, A. (PI);
Owens, D. (PI);
Paik, D. (PI);
Palacios, J. (PI);
Pande, V. (PI);
Petrov, D. (PI);
Plevritis, S. (PI);
Poldrack, R. (PI);
Pritchard, J. (PI);
Relman, D. (PI);
RiedelKruse, I. (PI);
Rivas, M. (PI);
Rubin, D. (PI);
Sabatti, C. (PI);
Salzman, J. (PI);
Shachter, R. (PI);
Shafer, R. (PI);
Shah, N. (PI);
Sherlock, G. (PI);
Sidow, A. (PI);
Snyder, M. (PI);
Tang, H. (PI);
Taylor, C. (PI);
Theriot, J. (PI);
Tibshirani, R. (PI);
Utz, P. (PI);
Walker, M. (PI);
Wall, D. (PI);
Winograd, T. (PI);
Wong, W. (PI);
Xing, L. (PI);
Zou, J. (PI);
Thompson, J. (GP)
BIOMEDIN 299:
Directed Reading and Research
For students wishing to receive credit for directed reading or research time. Prerequisite: consent of instructor. (Staff)
Terms: Aut, Win, Spr, Sum

Units: 118

Repeatable for credit

Grading: Medical Option (MedLtrCR/NC)
Instructors: ;
Altman, R. (PI);
Ashley, E. (PI);
Bagley, S. (PI);
Bassik, M. (PI);
Batzoglou, S. (PI);
Bayati, M. (PI);
Bejerano, G. (PI);
Bhattacharya, J. (PI);
Blish, C. (PI);
Boahen, K. (PI);
Brandeau, M. (PI);
Brutlag, D. (PI);
Bustamante, C. (PI);
Butte, A. (PI);
Chang, H. (PI);
Cherry, J. (PI);
Cohen, S. (PI);
Covert, M. (PI);
Curtis, C. (PI);
Das, A. (PI);
Das, R. (PI);
Davis, R. (PI);
Delp, S. (PI);
Desai, M. (PI);
Dill, D. (PI);
Dumontier, M. (PI);
Elias, J. (PI);
Fagan, L. (PI);
Feldman, M. (PI);
Ferrell, J. (PI);
Fraser, H. (PI);
Gambhir, S. (PI);
Gerritsen, M. (PI);
Gevaert, O. (PI);
Goldstein, M. (PI);
Greenleaf, W. (PI);
Guibas, L. (PI);
Hastie, T. (PI);
Hlatky, M. (PI);
Holmes, S. (PI);
Ji, H. (PI);
Karp, P. (PI);
Khatri, P. (PI);
Kim, S. (PI);
Kirkegaard, K. (PI);
Klein, T. (PI);
Koller, D. (PI);
Krummel, T. (PI);
Kundaje, A. (PI);
Levitt, M. (PI);
Li, J. (PI);
Longhurst, C. (PI);
Lowe, H. (PI);
Mallick, P. (PI);
Manning, C. (PI);
McAdams, H. (PI);
Meng, T. (PI);
Menon, V. (PI);
Montgomery, S. (PI);
Musen, M. (PI);
Napel, S. (PI);
Nolan, G. (PI);
Olshen, R. (PI);
Owen, A. (PI);
Owens, D. (PI);
Paik, D. (PI);
Palacios, J. (PI);
Pande, V. (PI);
Petrov, D. (PI);
Plevritis, S. (PI);
Poldrack, R. (PI);
Pritchard, J. (PI);
Relman, D. (PI);
RiedelKruse, I. (PI);
Rivas, M. (PI);
Rubin, D. (PI);
Sabatti, C. (PI);
Salzman, J. (PI);
Shachter, R. (PI);
Shafer, R. (PI);
Shah, N. (PI);
Sherlock, G. (PI);
Sidow, A. (PI);
Snyder, M. (PI);
Tang, H. (PI);
Taylor, C. (PI);
Theriot, J. (PI);
Tibshirani, R. (PI);
Tu, S. (PI);
Utz, P. (PI);
Walker, M. (PI);
Wall, D. (PI);
Winograd, T. (PI);
Wong, W. (PI);
Xing, L. (PI);
Zou, J. (PI);
Thompson, J. (GP)
BIOMEDIN 370:
Medical Scholars Research
Provides an opportunity for student and faculty interaction, as well as academic credit and financial support, to medical students who undertake original research. Enrollment is limited to students with approved projects.
Terms: Aut, Win, Spr, Sum

Units: 418

Repeatable for credit

Grading: Medical School MD Grades
Instructors: ;
Altman, R. (PI);
Ashley, E. (PI);
Bagley, S. (PI);
Bassik, M. (PI);
Batzoglou, S. (PI);
Bayati, M. (PI);
Bejerano, G. (PI);
Bhattacharya, J. (PI);
Blish, C. (PI);
Boahen, K. (PI);
Brandeau, M. (PI);
Brutlag, D. (PI);
Bustamante, C. (PI);
Butte, A. (PI);
Chang, H. (PI);
Cherry, J. (PI);
Cohen, S. (PI);
Covert, M. (PI);
Curtis, C. (PI);
Das, A. (PI);
Das, R. (PI);
Davis, R. (PI);
Delp, S. (PI);
Desai, M. (PI);
Dill, D. (PI);
Dumontier, M. (PI);
Elias, J. (PI);
Fagan, L. (PI);
Feldman, M. (PI);
Ferrell, J. (PI);
Fraser, H. (PI);
Gambhir, S. (PI);
Gerritsen, M. (PI);
Gevaert, O. (PI);
Goldstein, M. (PI);
Greenleaf, W. (PI);
Guibas, L. (PI);
Hastie, T. (PI);
Hlatky, M. (PI);
Holmes, S. (PI);
Ji, H. (PI);
Karp, P. (PI);
Khatri, P. (PI);
Kim, S. (PI);
Kirkegaard, K. (PI);
Klein, T. (PI);
Koller, D. (PI);
Krummel, T. (PI);
Kundaje, A. (PI);
Levitt, M. (PI);
Li, J. (PI);
Longhurst, C. (PI);
Lowe, H. (PI);
Mallick, P. (PI);
Manning, C. (PI);
McAdams, H. (PI);
Meng, T. (PI);
Menon, V. (PI);
Montgomery, S. (PI);
Musen, M. (PI);
Napel, S. (PI);
Nolan, G. (PI);
Olshen, R. (PI);
Owen, A. (PI);
Owens, D. (PI);
Paik, D. (PI);
Palacios, J. (PI);
Pande, V. (PI);
Petrov, D. (PI);
Plevritis, S. (PI);
Poldrack, R. (PI);
Pritchard, J. (PI);
Relman, D. (PI);
RiedelKruse, I. (PI);
Rivas, M. (PI);
Rubin, D. (PI);
Sabatti, C. (PI);
Salzman, J. (PI);
Shachter, R. (PI);
Shafer, R. (PI);
Shah, N. (PI);
Sherlock, G. (PI);
Sidow, A. (PI);
Snyder, M. (PI);
Tang, H. (PI);
Taylor, C. (PI);
Theriot, J. (PI);
Tibshirani, R. (PI);
Tu, S. (PI);
Utz, P. (PI);
Walker, M. (PI);
Wall, D. (PI);
Winograd, T. (PI);
Wong, W. (PI);
Xing, L. (PI);
Zou, J. (PI);
Thompson, J. (GP)
BIOMEDIN 371:
Computational Biology in Four Dimensions (BIOPHYS 371, CME 371, CS 371)
Cuttingedge research on computational techniques for investigating and designing the threedimensional structure and dynamics of biomolecules, cells, and everything in between. These techniques, which draw on approaches ranging from physicsbased simulation to machine learning, play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Course is devoted primarily to reading, presentation, discussion, and critique of papers describing important recent research developments. Prerequisite: CS 106A or equivalent, and an introductory course in biology or biochemistry. Recommended: some experience in mathematical modeling (does not need to be a formal course).
Terms: Win

Units: 3

Grading: Letter or Credit/No Credit
BIOMEDIN 374:
Algorithms in Biology
Algorithms and computational models applied to molecular biology and genetics. Topics vary annually. Possible topics include biological sequence comparison, annotation of genes and other functional elements, molecular evolution, genome rearrangements, microarrays and gene regulation, protein folding and classification, molecular docking, RNA secondary structure, DNA computing, and selfassembly. May be repeated for credit. Prerequisites: 161, 262 or 274, or BIOCHEM 218, or equivalents.
Terms: not given this year

Units: 23

Grading: Letter or Credit/No Credit
BIOMEDIN 390A:
Curricular Practical Training
Provides educational opportunities in biomedical informatics research. Qualified biomedical informatics students engage in internship work and integrate that work into their academic program. Students register during the quarter they are employed and must complete a research report outlining their work activity, problems investigated, key results, and any followup on projects they expect to perform. BIOMEDIN 390A, B, and C may each be taken only once.
Terms: Aut, Win, Spr, Sum

Units: 1

Grading: Medical Satisfactory/No Credit
BIOMEDIN 390B:
Curricular Practical Training
Provides educational opportunities in biomedical informatics research. Qualified biomedical informatics students engage in internship work and integrate that work into their academic program. Students register during the quarter they are employed and must complete a research report outlining their work activity, problems investigated, key results, and any followup on projects they expect to perform. BIOMEDIN 390A, B, and C may each be taken only once.
Terms: Aut, Win, Spr, Sum

Units: 1

Grading: Medical Satisfactory/No Credit
BIOMEDIN 390C:
Curricular Practical Training
Provides educational opportunities in biomedical informatics research. Qualified biomedical informatics students engage in internship work and integrate that work into their academic program. Students register during the quarter they are employed and must complete a research report outlining their work activity, problems investigated, key results, and any followup on projects they expect to perform. BIOMEDIN 390A, B, and C may each be taken only once.
Terms: Aut, Win, Spr, Sum

Units: 1

Grading: Medical Satisfactory/No Credit
BIOMEDIN 432:
Analysis of Costs, Risks, and Benefits of Health Care (HRP 392)
(Same as MGTECON 332) For graduate students. How to do cost/benefit analysis when the output is difficult or impossible to measure. How do M.B.A. analytic tools apply in health services? Literature on the principles of cost/benefit analysis applied to health care. Critical review of actual studies. Emphasis is on the art of practical application.
Terms: Aut

Units: 4

Grading: Medical Option (MedLtrCR/NC)
BIOMEDIN 801:
TGR Master's Project
Project credit for masters students who have completed all course requirements and minimum of 45 Stanford units.
Terms: Aut, Win, Spr, Sum

Units: 0

Repeatable for credit

Grading: TGR
Instructors: ;
Altman, R. (PI);
Ashley, E. (PI);
Bagley, S. (PI);
Bassik, M. (PI);
Batzoglou, S. (PI);
Bayati, M. (PI);
Bejerano, G. (PI);
Bhattacharya, J. (PI);
Blish, C. (PI);
Boahen, K. (PI);
Brandeau, M. (PI);
Brutlag, D. (PI);
Bustamante, C. (PI);
Butte, A. (PI);
Chang, H. (PI);
Cherry, J. (PI);
Cohen, S. (PI);
Covert, M. (PI);
Curtis, C. (PI);
Das, A. (PI);
Das, R. (PI);
Davis, R. (PI);
Delp, S. (PI);
Desai, M. (PI);
Dill, D. (PI);
Dumontier, M. (PI);
Elias, J. (PI);
Fagan, L. (PI);
Feldman, M. (PI);
Ferrell, J. (PI);
Fraser, H. (PI);
Gambhir, S. (PI);
Gerritsen, M. (PI);
Gevaert, O. (PI);
Goldstein, M. (PI);
Greenleaf, W. (PI);
Guibas, L. (PI);
Hastie, T. (PI);
Hlatky, M. (PI);
Holmes, S. (PI);
Ji, H. (PI);
Karp, P. (PI);
Khatri, P. (PI);
Kim, S. (PI);
Kirkegaard, K. (PI);
Klein, T. (PI);
Koller, D. (PI);
Krummel, T. (PI);
Kundaje, A. (PI);
Levitt, M. (PI);
Li, J. (PI);
Longhurst, C. (PI);
Lowe, H. (PI);
Mallick, P. (PI);
Manning, C. (PI);
McAdams, H. (PI);
Meng, T. (PI);
Menon, V. (PI);
Montgomery, S. (PI);
Musen, M. (PI);
Napel, S. (PI);
Nolan, G. (PI);
Olshen, R. (PI);
Owen, A. (PI);
Owens, D. (PI);
Paik, D. (PI);
Palacios, J. (PI);
Pande, V. (PI);
Petrov, D. (PI);
Plevritis, S. (PI);
Poldrack, R. (PI);
Pritchard, J. (PI);
Relman, D. (PI);
RiedelKruse, I. (PI);
Rivas, M. (PI);
Rubin, D. (PI);
Sabatti, C. (PI);
Salzman, J. (PI);
Shachter, R. (PI);
Shafer, R. (PI);
Shah, N. (PI);
Sherlock, G. (PI);
Sidow, A. (PI);
Snyder, M. (PI);
Tang, H. (PI);
Taylor, C. (PI);
Theriot, J. (PI);
Tibshirani, R. (PI);
Tu, S. (PI);
Utz, P. (PI);
Walker, M. (PI);
Wall, D. (PI);
Winograd, T. (PI);
Wong, W. (PI);
Xing, L. (PI);
Zou, J. (PI);
Thompson, J. (GP)
BIOMEDIN 802:
TGR PhD Dissertation
Terms: Aut, Win, Spr, Sum

Units: 0

Repeatable for credit

Grading: TGR
Instructors: ;
Altman, R. (PI);
Ashley, E. (PI);
Bagley, S. (PI);
Bassik, M. (PI);
Batzoglou, S. (PI);
Bayati, M. (PI);
Bejerano, G. (PI);
Bhattacharya, J. (PI);
Blish, C. (PI);
Boahen, K. (PI);
Brandeau, M. (PI);
Brutlag, D. (PI);
Bustamante, C. (PI);
Butte, A. (PI);
Chang, H. (PI);
Cherry, J. (PI);
Cohen, S. (PI);
Covert, M. (PI);
Curtis, C. (PI);
Das, A. (PI);
Das, R. (PI);
Davis, R. (PI);
Delp, S. (PI);
Desai, M. (PI);
Dill, D. (PI);
Dumontier, M. (PI);
Elias, J. (PI);
Fagan, L. (PI);
Feldman, M. (PI);
Ferrell, J. (PI);
Fraser, H. (PI);
Gambhir, S. (PI);
Gerritsen, M. (PI);
Gevaert, O. (PI);
Goldstein, M. (PI);
Greenleaf, W. (PI);
Guibas, L. (PI);
Hastie, T. (PI);
Hlatky, M. (PI);
Holmes, S. (PI);
Ji, H. (PI);
Karp, P. (PI);
Khatri, P. (PI);
Kim, S. (PI);
Kirkegaard, K. (PI);
Klein, T. (PI);
Koller, D. (PI);
Krummel, T. (PI);
Kundaje, A. (PI);
Levitt, M. (PI);
Li, J. (PI);
Longhurst, C. (PI);
Lowe, H. (PI);
Mallick, P. (PI);
Manning, C. (PI);
McAdams, H. (PI);
Meng, T. (PI);
Menon, V. (PI);
Montgomery, S. (PI);
Musen, M. (PI);
Napel, S. (PI);
Nolan, G. (PI);
Olshen, R. (PI);
Owen, A. (PI);
Owens, D. (PI);
Paik, D. (PI);
Palacios, J. (PI);
Pande, V. (PI);
Petrov, D. (PI);
Plevritis, S. (PI);
Poldrack, R. (PI);
Pritchard, J. (PI);
Relman, D. (PI);
RiedelKruse, I. (PI);
Rivas, M. (PI);
Rubin, D. (PI);
Sabatti, C. (PI);
Salzman, J. (PI);
Shachter, R. (PI);
Shafer, R. (PI);
Shah, N. (PI);
Sherlock, G. (PI);
Sidow, A. (PI);
Snyder, M. (PI);
Tang, H. (PI);
Taylor, C. (PI);
Theriot, J. (PI);
Tibshirani, R. (PI);
Tu, S. (PI);
Utz, P. (PI);
Walker, M. (PI);
Wall, D. (PI);
Winograd, T. (PI);
Wong, W. (PI);
Xing, L. (PI);
Zou, J. (PI);
Thompson, J. (GP)
CS 272:
Introduction to Biomedical Informatics Research Methodology (BIOE 212, BIOMEDIN 212, GENE 212)
Capstone Biomedical Informatics (BMI) experience. Handson 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.
Terms: Spr

Units: 35

Grading: Medical Option (MedLtrCR/NC)
GENE 212:
Introduction to Biomedical Informatics Research Methodology (BIOE 212, BIOMEDIN 212, CS 272)
Capstone Biomedical Informatics (BMI) experience. Handson 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.
Terms: Spr

Units: 35

Grading: Medical Option (MedLtrCR/NC)
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 genomescale measurements in molecular biology and genomic medicine; analysis of microarray data; analysis of polymorphisms, proteomics, and protein interactions; linking genomescale 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

Grading: Medical Option (MedLtrCR/NC)