Graduate courses in Biomedical Informatics

Series of colloquia offered by program faculty, students, and occasional guest lecturers. Credit available only to students in a Biomedical Informatics degree program. May be repeated three times for credit.

1 unit, Aut (Musen, M), Win (Musen, M), Spr (Musen, M)

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. Credit available only to students in a Biomedical Informatics degree program. May be repeated three times for credit.

1 unit, Aut (Musen, M), Win (Musen, M), Spr (Musen, M)

BIOMEDIN 202. Introductory Biomedical Informatics

Via Internet. Current research problems and computational approaches to them. Topics include medical security and privacy, electronic medical records, controlled terminologies and biomedical ontologies, electronic retrieval, technology-assisted learning environments, medical decision making and support, sequence analysis, phylogenetics, biological networks and pathways, microarray analysis, natural language processing, and protein structural analysis and prediction. Graduate students in the Biomedical Informatics training program may not take this class for credit.

1 unit, Aut (Fagan, L; Cheng, B), Win (Fagan, L; Cheng, B), Spr (Fagan, L; Cheng, B), Sum (Fagan, L; Cheng, B)

BIOMEDIN 204. Pharmacogenomics

Via Internet. 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 BIO 41, 42, 43, and 44X,Y or consent of instructor.

1 unit, Aut (Cheng, B; Fagan, L), Win (Cheng, B; Fagan, L), Spr (Cheng, B; Fagan, L), Sum (Cheng, B; Fagan, L)

BIOMEDIN 205. Biomedical Informatics for Medicine

Primarily for M.D. students; open to others. 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. May be repeated for credit. Prerequisite: background in biomedicine. Recommended: background in programming.

2 units, Aut (Butte, A), Spr (Butte, A)

BIOMEDIN 210. Introduction to Biomedical Informatics: Fundamental Methods

(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 (Musen, M)

BIOMEDIN 211. Introduction to Biomedical Informatics: Principles of Systems Design

(Same as CS 271.) Focus is on undertaking design and implementation of computational and information systems for life scientists and healthcare providers. Case studies illustrate what design factors lead to success or failure in building systems in complex biomedical environments. Topics: requirements analysis, workflow and organizational factors, functional specification, knowledge modeling, data heterogeneity, component-based architectures, human-computer interaction, and system evaluation. Prerequisite: 210, or consent of instructor.

3 units, Win (Das, A)

BIOMEDIN 212. Introduction to Biomedical Informatics Research Methodology

(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, or consent of instructor.

3 units, Aut (Altman, R; Cheng, B; Klein, T)

BIOMEDIN 214. Representations and Algorithms for Computational Molecular Biology

(Same as BIOE 214, CS 274, GENE 214.) Topics: algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, computing with networks of genes, 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, graphical display of biological data, machine learning (clustering and classification), and natural language text processing. Prerequisites: programming skills; consent of instructor for 3 units.

3-4 units, Spr (Altman, R)

BIOMEDIN 216. Lectures on Representations and Algorithms for Molecular Biology

Lecture series for BIOMEDIN 214. Recommended: familiarity with biology.

1 unit, Spr (Altman, R)

BIOMEDIN 217. Translational Bioinformatics

(Same as 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.

4 units, Win (Butte, A)

BIOMEDIN 218. Translational Bioinformatics

Same content as 217; for medical and graduate students who attend lectures and participate in limited assignments and final project. 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 at the level of CS 106A; familiarity with statistics and biology.

2 units, Win (Butte, A)

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 (Brutlag, D)

BIOMEDIN 231. Computational Molecular Biology

(Same as BIOC 218.) Via Internet. 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 http://biochem218.stanford.edu/. Prerequisites: introductory molecular biology course at level of BIO 41 or consent of instructor.

3 units, Aut (Brutlag, D), Win (Brutlag, D), Spr (Brutlag, D)

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 (Sainani, K)

BIOMEDIN 238. Computational Proteomic Biology

(Same as BIOC 238.) Application of computational protein analysis to biological problems. Topics include: protein sequence analysis and comparison including protein sequence databases, amino acid composition, protein alignment, protein motifs, protein families, and probabilistic models of families; protein structure including structure comparison and superposition methods, structural motifs, and structure and domain databases; protein structure prediction including secondary structure, homology modeling, threading, and ab initio structure prediction; protein-protein interaction databases and protein-protein interaction prediction; and protein-DNA interaction motifs and protein-ligand docking. Prerequisite: An introductory course in computational bioloby such as BIOC 218, BIOMEDIN 214, or SBIO/BIOPHYS 228. Via Internet in Spring.

3 units, not given this year

BIOMEDIN 251. Outcomes Analysis

(Same as HRP 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 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 (Bhattacharya, J)

BIOMEDIN 256. Economics of Health and Medical Care

(Same as BIOMEDIN 156, ECON 126, HRP 256.) 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 (Bhattacharya, J)

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 (Batzoglou, S)

BIOMEDIN 273A. A Computational Tour of the Human Genome

(Same as CS 273A, DBIO 273A.) Computational biology through an exploration of human genome. Key genetic concepts from a bioinformatics perspective. Biomedical advances resulting from sequencing of human and related organisms. Genome sequencing: technologies, assembly, personalized sequencing. Functional landscape: genes, regulatory modules, repeats, RNA genes. Genome evolution: processes, comparative genomics, ultraconservation, co-option. Additional topics: population genetics and personalized genomics, ancient DNA, and metagenomics.

3 units, Aut (Batzoglou, S; Bejerano, G)

BIOMEDIN 299. Directed Reading and Research

For students wishing to receive credit for directed reading or research time. Prerequisite: consent of instructor.

1-18 units, Aut (Staff), Win (Staff), Spr (Staff), Sum (Staff)

BIOMEDIN 301. Special Topics in Biomedical Informatics

1-6 units, Sum (Staff)

BIOMEDIN 303. Statistics for Research

Statistical methods commonly used in research. Emphasis is on when and how to use the methods rather than on proofs. How to describe data and detect unusual values, compare treatment effects, interpret p-values, detect and quantify trends, detect and measure association and correlation, determine the sample size and power for an experiment, and choose statistical tests and software. Topics include descriptive statistics (mean, median, standard deviation, standard error), probability, paired and unpaired t-tests, analysis of variance, correlation, regression, chi-square, discriminant analysis, and power and sample size. Statistical analysis software including Excel and Statistica. (M. Walker)

1 unit, not given this year

BIOMEDIN 366. Computational Biology

(Same as STATS 166, STATS 366.) 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.

2-3 units, Spr (Wong, W)

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.

2-3 units, Spr (Batzoglou, S)

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 follow-up on projects they expect to perform. BIOMEDIN 390A, B, and C may each be taken only once. (Musen)

1 unit, Aut (Staff), Win (Staff), Spr (Musen, M), Sum (Musen, M)

BIOMEDIN 390B. Curricular Practical Training

1 unit, Aut (Staff), Win (Staff), Spr (Musen, M), Sum (Musen, M)

BIOMEDIN 390C. Curricular Practical Training

1 unit, Aut (Staff), Win (Staff), Spr (Musen, M), Sum (Musen, M)

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 (Garber, A; Owens, D)

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Stanford Bulletin, Archive 2008-09

Stanford Bulletin, Archive 2008-09

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Graduate courses in Biomedical Informatics