everything.study
HST.950

Medical Computing

Graduate · Historical course

Fall 2010 · Biomedical Computing

Analyzes computational needs of clinical medicine reviews systems and approaches that have been used to support those needs, and the relationship between clinical data and gene and protein measurements. Topics: the nature of clinical data; architecture and design of healthcare information systems; privacy and security issues; medical expertsystems; introduction to bioinformatics. Case studies and guest lectures describe contemporary systems and research projects. Term project using large clinical and genomic data sets integrates classroom topics.

Readings

Spring 2003

Topics

  • Introduction: Nature of Modern Medicine and Medical Practice
  • Nature of Medical Data: Where it is and Where it is Not
  • Genomics in Medicine: Centrality of Bioinformatics
  • Patient Identification
  • Countering Bioterrorism
  • Workflow, Decision Support and Data Gathering
  • Computing Support for the Enterprise
  • Diagnosis, Standards, Codification
  • Patient Data Confidentiality and Security
  • Decreasing Variability in Health Care
  • Computerized Physician Order Entry: Using Technology To Improve Patient Safety
  • Integration and Data Sharing or Medical Data for Quality Improvement
  • Telemedicine
  • Genomic Medicine I: Population Genetics in the Post Genomic Era
  • Genomic Medicine II: Expression Arrays, Gene Clustering and Distance Metrics
  • Decision Analysis and Decision Support
  • Getting to Causality in Functional Genomics
  • Advanced Expert Systems
  • Patient Monitoring
  • Genomic Medicine III: Introduction to Genomics
  • Genomic Medicine IV: Linking Genotypes and Phenotypes
  • Genomic Medicine V: Reverse Engineering
  • Student Presentations

Readings

  • The following text is required for the course and is referenced in the calendar of readings listed in the table below. Shortliffe, E. H., L. E. Perreault, G. Wiederhold, and L. M. Fagan. Medical Informatics: Computer Applications in Health Care and Biomedicine . 2nd ed. New York, NY: Springer, 2003. ISBN: 9780387984728.
    Listed reading
  • LEC #: 1 · TOPICS: Introduction: Nature of Modern Medicine and Medical Practice · READINGS: Read Chapters 1 & 2 of Shortliffe.
    Reading assignment
  • LEC #: 2 · TOPICS: Nature of Medical Data: Where it is and Where it is Not · READINGS: Read Chapters 9 & 10 of Shortliffe.
    Reading assignment
  • “Initial Sequencing and Analysis of the Human Genome.” International Human Genome Sequencing Consortium, 409 (2001): Macmillan Magazines Ltd.
    Listed reading
  • Chakravarti, Aravinda. “Population Genetics — Making Sense Out of Sequence.” Nature Genetics Supplement 21 (Jan 1999): Ohio: Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland.
    Listed reading
  • Brown, Patrick O., and David Botstein. “Exploring the New World of the Genome with DNA Microarrays.” Nature Genetics Supplement 21 (Jan 1999): Stanford , California : Departments of Biochemistry and Genetics, and the Howard Hughes Medical Institute, Stanford University School of Medicine.
    Listed reading
  • “Distinct Types of Diffuse Large B-cell Lymphoma Identified by Gene Expression Profiling.” Nature 403 (3 Feb. 2000): Macmillan Magazines Ltd.
    Listed reading
  • LEC #: 4 · TOPICS: Patient Identification · READINGS: Fellegi, Ivan P., and Allen B. Sunter. “A Theory for Record Linkage.” Journal of American Statistical Association 64 (328) (Dec 1969): 1183-1210.
    Reading assignment
  • LEC #: 5 · TOPICS: Countering Bioterrorism · READINGS: Chapter 11 of Shortliffe.
    Reading assignment
  • Coiera, Enrico. “Clinical Communication: A New Informatics Paradigm.” Jamia (1996): UK.
    Listed reading
  • Coiera, Enrico. “When Conversation is Better than Computation.” Jamia (14 Jan. 2000): Washington DC.
    Listed reading
  • Kohane, Isaac S., Philip Greenspun, James Fackler, Christopher Cimino, and Peter Szolovits. “Application of Technology in Building National Electronic-Medical Record Systems via the World Wide Web.” Journal of the American Medical Informatics Association 3 (3) (May/Jun 1996).
    Listed reading
  • LEC #: 8 · TOPICS: Diagnosis, Standards, Codification · READINGS: Chapters 6, 12 and 14 of Shortliffe.
    Reading assignment
  • Chapter 7 of Shortliffe.
    Listed reading
  • Barrows, Randolph. C. Jr., Paul D. Clayton. “Privacy Confidentiality and EMR.” Journal of the American Medical Informatics Association 3 (2) (Mar/Apr 1996).
    Listed reading
  • For the Record. Protecting Electronic Health Information. Washington D.C. : National Academy Press, 1997.
    Listed reading
  • LEC #: 13 · TOPICS: Telemedicine · READINGS: Chapter 14 of Shortliffe.
    Reading assignment
  • Lander, Eric S. “Array of hope.” _Nature Genetics Supplement _ 21 (1999): Cambridge, Massachusetts: America Inc.
    Listed reading
  • -—–., and Nicholas J. Schork. “Genetic Dissection of Complex Traits.” Science , New Series, 265 (5181) (30 Sep. 1994): 2037-2048.
    Listed reading
  • “Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome.” Science 280 (15 May 1998): 1077. http://www.sciencemag.org ↗
    Listed reading
  • LEC #: 15 · TOPICS: Genomic Medicine II: Expression Arrays, Gene Clustering and Distance Metrics · READINGS: Michael, P. S. Brown, William Noble Grundy, David Lin, Nello Cristianini, Charles Walsh Sugnet, Terence S. Furey, Manuel Ares, Jr., and David Haussler. “Knowledge-based Analysis of Microarray Gene Expression Data by Using Support Vector Machines.” PNAS 97 (1) (4 Jan. 2000): 262-267.
    Reading assignment
  • Chapters 15 and 16 of Shortliffe.
    Listed reading
  • Szolovits, P. “Uncertainty and Decisions in Medical Informatics.” Methods of Information in Medicine 34 (1995): 111–21.
    Listed reading
  • “The Transcriptional Program in the Response of Human Fibroblasts to Serum.” Science 283 (1 Jan. 1999). www.sciencemag.org ↗
    Listed reading
  • Ramoni, Marco F., Paola Sebastiani, and Isaac S. Kohane. “Cluster Analysis of Gene Expression Dynamics.” PNAS. Edited by Louis M. Kunkel.
    Listed reading
  • LEC #: 18 · TOPICS: Advanced Expert Systems · READINGS: Chapters 12 and 13 of Shortliffe.
    Reading assignment
  • LEC #: 22 · TOPICS: Genomic Medicine V: Reverse Engineering · READINGS: Zoltan. “The Perils and Promises of Massively Parallel Biology.” Chap. 5 in Genetic Network Analysis, 2002: pp. 23.
    Reading assignment
  • Shortliffe, E. H., L. E. Perreault, G. Wiederhold, and L. M. Fagan. Medical Informatics: Computer Applications in Health Care and Biomedicine . 2nd ed. New York, NY: Springer, 2003. ISBN: 9780387984728 .
    Required
Sources