Course Catalog

Biomedical Informatics Course Listing

Required courses for medical students are listed in purple.

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BIOMEDIN 109Q. Genomics: A Technical and Cultural Revolution
(Same as GENE 109Q) Stanford Introductory Seminar. Preference to sophomores. Concepts of genomics, high-throughput methods of data collection, and computational approaches to analysis of data. The social, ethical, and economic implications of genomic science. Students may focus on computational or social aspects of genomics. WRITE-2
3 units, Win (R. Altman)

BIOMEDIN 156/256. Economics of Health and Medical Care
(Same as ECON 126, HRP 256, HUMBIO 121A) Graduate students with research interests should take ECON 248. Graduate students with research interests should take ECON 248. Institutional, theoretical, and empirical analysis of the problems of health and medical care. Topics: institutions in the health sector; measurement and valuation of health; nonmedical determinants of health; medical technology and technology assessment; demand for medical care and medical insurance; physicians, hospitals, and managed care; international comparisons. Prerequisites: ECON 50 and ECON 102A or equivalent statistics. Recommended: ECON 51.
5 units, Aut (J. Bhattacharya)

BIOMEDIN 200. Biomedical Informatics Colloquium
Series of colloquia offered by program faculty, students, and occasional guest lecturers. May be repeated three times for credit.
1 unit, Aut, Win, Spr (M. Musen)

BIOMEDIN 201. Biomedical Informatics Student Seminar
Participants report on recent articles from the Biomedical Informatics literature or their research projects. Goal is to teach presentation skills. May be repeated three times for credit.
1 unit, Aut, Win, Spr (M. Musen)

BIOMEDIN 204. Pharmacogenomics
Genetically determined responses to drugs; applications focusing on the PharmGKB database, a publicly available Internet tool to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. Topics include: introduction to pharmacogenomics and pharmacology; the genome and genetics; human polymorphisms, frequencies, significance, and populations; informatics in pharmacogenomics; genotype to phenotype and phenotype to genotype approaches; drug discovery and validation; genomic variation discovery and genotyping; adverse drug reactions and interactions; pathways of drug metabolism; and cancer pharmacogenomics. Prerequisites: two of BIOSCI 41, 42, 43, and 44X,Y or consent of instructor.
1 unit, any quarter (B. Cheng, L. Fagan) Via internet

BIOMEDIN 205. Biomedical Informatics for Medicine
Primarily for M.D. students; open to other graduate students. Emphasis is on practical applications of bioinformatics and medical informatics for medicine, health care, clinicians, and biomedical research, focused on work at Stanford. Topics may include: methods to analyze genetic conditions¿ integrative methods for microarray, proteomic, and genomic data to understand the etiology of disease, clinical information systems in local healthcare facilities, cellular and radiology imaging, and pharmacogenomics. Enrollment for 2 units includes weekly assignments. Non-MD students may enroll for 1 unit. May be repeated for credit. Prerequisite: background in biomedicine. Recommended: background in programming.
1 to 2 units, Aut, Spr (A. Butte)

BIOMEDIN 206. Informatics in Industry
Effective management, modeling, acquistion, 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.
1 unit, Spr (N. Kotecha, N. Shah; sponsoring faculty R. Altman)

BIOMEDIN 207. Digital Medicine: Promise and Peril in the Age of Electronic Health Records
Topical discussions of the use of electronic health records in clinical care and clinical research. Lectures by faculty, students and guest speakers are augmented by site visits to local clinical institutions that have implemented electronic health records systems. Goal is exposure to practical challenges of system implementation and to research opportunities in clinical informatics.
1 unit, Sum (A. Das)

BIOMEDIN 210. Modeling Biomedical Systems: Ontology, Terminology, Problem Solving
(Same as CS 270). Methods for modeling biomedical systems and for making those models explicit in the context of building 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. Recommended: exposure to object-oriented systems, basic biology.
3 units, Aut (M. Musen)

BIOMEDIN 211. Effective Design in Clinical Informatics Systems
(Same as CS 271) Methods of designing and engineering software systems in complex clinical environments. Case studies illustrate factors leading to success or failure of systems. Project assignments involve focused team-based design work. Topics: user and organizational requirements, data and knowledge modeling, component-based system design, system prototyping, and human-systems interaction. Prerequisite: BIOMEDIN 210 recommended, or database or object-oriented programming course.
3 units, Win (A. Das)

BIOMEDIN 212. Biomedical Informatics Project Course
(Same as BIOE 212, CS 272, GENE 212) Hands-on software building. Student teams conceive, design, specify, implement, evaluate, and report on a software project in the domain of biomedicine. Creating written proposals, peer review, providing status reports, and preparing final reports. Guest lectures from professional biomedical informatics systems builders on issues related to the process of project management. Software engineering basics. Prerequisites: 210, 211 or 214, 217, or consent of instructor.
3 units, Aut (R. Altman, B. Cheng, T. Klein)

BIOMEDIN 214. Representations and Algorithms for Computational Molecular Biology
(Same as 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, 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.
3 to 4 units, Spr (R. Altman) Via internet.

BIOMEDIN 216. Lectures on Representations and Algorithms for Molecular Biology
Lecture series for BIOMEDIN 214. Prerequisite: familiarity with biology recommended:
1 unit, Spr (R. Altman) Via internet.

BIOMEDIN 217. Translational Bioinformatics
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.
3 to 4 units, Win (A. Butte)

BIOMEDIN 219. Mathematical Models and Medical Decisions
Analytic methods for determining the optimal diagnostic and therapeutic decisions for the care of individual patients and for the design of policies affecting the care of patient populations. Topics: utility theory and probability modeling, empirical methods for estimating disease prevalence, probability models for periodic processes, binary decision-making techniques, Markov models of dynamic disease state problems, utility assessment techniques, parametric utility models, utility models for multidimensional outcomes, analysis of time-varying clinical outcomes, and the design of cost-contstrained clinical policies. 2 units requires completion of a case study project. Prerequisites: introduction to calculus and basic statistics.
1 to 2 units, Win (M. Higgins; sponsoring faculty M. Musen)

BIOMEDIN 228. Computational Genomic Biology
(Same as BIOC 228) Application of computational genomics methods to biological problems. Topics include: assembly of genomic sequences; genome databases; comparative genomics; gene discovery; gene expression analyses including gene clustering by expression, transcription factor binding site discovery, metabolic pathway discovery, functional genomics, and gene and genome ontologies; and medical diagnostics using SNPs and gene expression. Recent papers from the literature and hands-on use of the methods. Prerequisites: introductory course in computational molecular biology or genomics such as BIOC 218, BIOMEDIN 214, or GENE 211.
3 units, Win (D. Brutlag) Not offered 2009-10.

BIOMEDIN 231. Computational Molecular Biology
(Same as BIOMEDIN 231) For molecular biologists and computer scientists. Representation and analysis of genomes, sequences, and proteins. Strengths and limitations of existing methods. Course work performed on web or using downloadable applications. See Prerequisites: introductory molecular biology course at level of BIOSCI 41 or consent of instructor.
3 units, Aut, Win, Spr (D. Brutlag) Via internet.

BIOMEDIN 233. Intermediate Biostatistics: Analysis of Discrete Data
(Same as HRP 261, STATS 261) Methods for analyzing data from case-control and cross-sectional studies: the 2x2 table, chi-square test, Fisher's exact test, odds ratios, Mantel-Haenzel methods, stratification, tests for matched data, logistic regression, conditional logistic regression. Emphasis is on data analysis in SAS. Special topics: cross-fold validation and bootstrap inference.
3 units, Win (K. Sainani)

BIOMEDIN 251. Outcomes Analysis
Introduction to 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 hands-on data analysis and application of methods, including re-analyses of well-known studies. Prerequisites: one or more courses in probability, and statistics or biostatistics.
3 units, Spr (J. Bhattacharya)

BIOMEDIN 262. Computational Genomics
(Same as CS 262). Applications of computer science to genomics, and concepts in genomics from a computer science point of view. Topics: dynamic programming, sequence alignments, hidden Markov models, Gibbs sampling, and probabilistic context-free grammars. Applications of these tools to sequence analysis: comparative genomics, DNA sequencing and assembly, genomic annotation of repeats, genes, and regulatory sequences, microarrays and gene expression, phylogeny and molecular evolution, and RNA structure. Prerequisites: 161 or familiarity with basic algorithmic concepts. Recommended: basic knowledge of genetics.
3 units, Win (S. Batzoglou)

BIOMEDIN 273A. A Computational Tour of the Human Genome
(Same as CS 273A, DBIO 273A) Biology through an exploration of Human Genome. Key genomic and genetic concepts from an informatics perspective. Biomedical advances resulting from the Genomics revolution. Topics: genome sequencing: technologies, assembly, personalized sequencing. Functional landscape: genes, gene regulation, repeats, RNA genes. Genome evolution: comparative genomics, ultraconservation, co-option. Additional topics: population genetics, personalized genomics, and ancient DNA. Course starts with primer in Biology and text processing languages. Ends with guest lectures from forefront of genomic research.
3 units, Aut (S. Batzoglou, G. Bejerano)

BIOMEDIN 299. Directed Reading and Research in Biomedical Informatics
Prerequisite: consent of instructor.
1 to 18 units, any quarter (Search for instructor in Axess)

BIOMEDIN 366. Computational Biology
(Same as STATS 366, STATS 166) Methods to understand sequence alignments and phylogenetic trees built from molecular data, and general genetic data. Phylogenetic trees, median networks, microarray analysis, Bayesian statistics. Binary labeled trees as combinatorial objects, graphs, and networks. Distances between trees. Multivariate methods (PCA, CA, multidimensional scaling). Combining data, nonparametric inference. Algorithms used: branch and bound, dynamic programming, Markov chain approach to combinatorial optimization (simulated annealing, Markov chain Monte Carlo, approximate counting, exact tests). Software such as Matlab, Phylip, Seq-gen, Arlequin, Puzzle, Splitstree, XGobi.
2 to 3 units, Spr (W. Wong)

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.
4 to 18 units, any quarter (Search for instructor in Axess)

BIOMEDIN 374. Algorithms in Biology
(Same as CS 374) 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 self-assembly. May be repeated for credit. Prerequisites: 161, 262 or 274, or BIOCHEM 218, or equivalents.
2 to 3 units, Spr (S.Batzoglou)

BIOMEDIN 390A,B,C. 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 follow-up on projects they expect to perform. BIOMEDIN 390A, B, and C may each be taken only once.
1 unit, Aut, Win, Spr, Sum (Staff)

BIOMEDIN 432. Analysis of Costs, Risks, and Benefits of Health Care
(Same as MGTECON 332, HRP 392) For graduate students. The principal evaluative techniques for health care, including utility assessment, cost-effectiveness analysis, cost-benefit analysis, and decision analysis. Emphasis is on the practical application of these techniques. Group project presented at end of quarter. Guest lectures by experts from the medical school, pharmaceutical industry, health care plans, and government.
4 units, Aut (A. Garber, D. Owens)


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