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Abstract/Syllabus:
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Kohane, Isaac, Lucila Ohno-Machado, and Peter Szolovits, HST.950J Medical Computing, Spring 2003. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed 09 Jul, 2010). License: Creative Commons BY-NC-SA
Chart of the medical cycle. (Image by Prof. Peter Szolovits.)
Course Highlights
A number of assignments and lecture notes are available for this course.
Course Description
The focus of the course is on medical science and practice in the age of automation and the genome, both present and future.
It includes an analysis of the computational needs of clinical medicine, a review systems and approaches that have been used to support those needs, and an examination of new technologies.
Technical Requirements
Any number of development tools can be used to compile and run the .java files found on this course site. Please refer to the course materials for any specific instructions or recommendations.
Java® is a trademark or registered trademark of Sun Microsystems, Inc. in the United States and other countries.
*Some translations represent previous versions of courses.
Syllabus
Topics and Format
The following topics are covered in the course:
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the nature of clinical data
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architecture and design of healthcare information systems
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privacy and security issues
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medical expert systems
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introduction to genomic medicine and its techniques.
Case studies of contemporary systems are used in lecture sessions. Term project is required. The project involves using a large pseudonymized clinical dataset to integrate classroom topics.
We plan to give a handful of modest homework assignments to complement and reinforce material taught in the class. You must do the homework problems on your own. Of course you may ask for help and advice from classmates, but the final work that you turn in and all the words used to describe it must be your own.
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, 2001. ISBN: 0387984720.
The last four class sessions will be an opportunity for students to present the results of significant research projects done for the class. We encourage you to team up (in teams of two or three students) to work on projects, and teams that span students with different interests, skills and approaches are encouraged.
Calendar
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TOPICS |
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KEY DATES |
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1 |
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Introduction: Nature of Modern Medicine and Medical Practice |
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2 |
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Nature of Medical Data: Where it is and Where it is Not |
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3 |
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Genomics in Medicine: Centrality of Bioinformatics |
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4 |
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Patient Identification |
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HW1 Out
Other HW1 Resources |
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5 |
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Countering Bioterrorism |
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HW1 Due |
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6 |
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Workflow, Decision Support and Data Gathering |
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HW2 Out |
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7 |
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Computing Support for the Enterprise |
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Diagnosis, Standards, Codification |
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9 |
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Patient Data Confidentiality and Security |
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10 |
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Decreasing Variability in Health Care |
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HW2 Due |
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11 |
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Computerized Physician Order Entry: Using Technology To Improve Patient Safety |
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12 |
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Integration and Data Sharing or Medical Data for Quality Improvement |
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13 |
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Telemedicine |
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No Classes |
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HW3 Out |
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14 |
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Genomic Medicine I: Population Genetics in the Post Genomic Era |
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HW3 Addendum |
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15 |
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Genomic Medicine II: Expression Arrays, Gene Clustering and Distance Metrics |
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HW3 Due |
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16 |
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Decision Analysis and Decision Support |
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Sign up for Final Presentation |
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17 |
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Getting to Causality in Functional Genomics |
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Project Proposals Due |
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18 |
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Advanced Expert Systems |
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Patient Monitoring |
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20 |
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Genomic Medicine III: Introduction to Genomics |
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21 |
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Genomic Medicine IV: Linking Genotypes and Phenotypes |
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22 |
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Genomic Medicine V: Reverse Engineering |
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23 |
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Student Presentations |
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24 |
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Student Presentations |
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25 |
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Student Presentations |
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26 |
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Student Presentations |
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Further Reading:
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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, 2001. ISBN: 0387984720.
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LEC # |
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TOPICS |
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READINGS |
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1 |
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Introduction: Nature of Modern Medicine and Medical Practice |
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Read Chapters 1 & 2 of Shortliffe. |
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2 |
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Nature of Medical Data: Where it is and Where it is Not |
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Read Chapters 9 & 10 of Shortliffe. |
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3 |
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Genomics in Medicine: Centrality of Bioinformatics |
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"Initial Sequencing and Analysis of the Human Genome." International Human Genome Sequencing Consortium, 409 (2001): Macmillan Magazines Ltd.
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.
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.
"Distinct Types of Diffuse Large B-cell Lymphoma Identified by Gene Expression Profiling." Nature 403 (3 Feb. 2000): Macmillan Magazines Ltd.
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4 |
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Patient Identification |
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Fellegi, Ivan P., and Allen B. Sunter. "A Theory for Record Linkage." Journal of American Statistical Association 64 (328) (Dec 1969): 1183-1210. |
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5 |
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Countering Bioterrorism |
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Chapter 11 of Shortliffe. |
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6 |
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Workflow, Decision Support and Data Gathering |
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Mueller, Ganslandt, Frankewitsch, Krieglstein, Senninger, and Prokosch. "Workflow Analysis and Evidence-Based Medicine: Towards Integration of Knowledge-Based Functions in Hospital Information Systems." Germany: University of Muenster.
Coiera, Enrico. "Clinical Communication: A New Informatics Paradigm." Jamia (1996): UK.
Coiera, Enrico. "When Conversation is Better than Computation." Jamia (14 Jan. 2000): Washington DC.
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).
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7 |
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Computing Support for the Enterprise |
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8 |
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Diagnosis, Standards, Codification |
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Chapters 6, 12 and 14 of Shortliffe. |
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9 |
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Patient Data Confidentiality and Security |
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Chapter 7 of Shortliffe.
Barrows, Randolph. C. Jr., Paul D. Clayton. "Privacy Confidentiality and EMR." Journal of the American Medical Informatics Association 3 (2) (Mar/Apr 1996).
Optional
- For the Record. Protecting Electronic Health Information. Washington D.C. : National Academy Press, 1997.
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10 |
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Decreasing Variability in Health Care |
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11 |
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Computerized Physician Order Entry: Using Technology To Improve Patient Safety |
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12 |
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Integration and Data Sharing or Medical Data for Quality Improvement |
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13 |
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Telemedicine |
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Chapter 14 of Shortliffe. |
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14 |
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Genomic Medicine I: Population Genetics in the Post Genomic Era |
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Lander, Eric S. "Array of hope." Nature Genetics Supplement 21 (1999): Cambridge, Massachusetts: America Inc.
------., and Nicholas J. Schork. "Genetic Dissection of Complex Traits." Science, New Series, 265 (5181) (30 Sep. 1994): 2037-2048.
"Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome." Science 280 (15 May 1998): 1077.
http://www.sciencemag.org
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15 |
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Genomic Medicine II: Expression Arrays, Gene Clustering and Distance Metrics |
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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. |
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16 |
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Decision Analysis and Decision Support |
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Chapters 15 and 16 of Shortliffe.
Szolovits, P. "Uncertainty and Decisions in Medical Informatics." Methods of Information in Medicine 34 (1995): 111–21.
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17 |
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Getting to Causality in Functional Genomics |
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"The Transcriptional Program in the Response of Human Fibroblasts to Serum." Science 283 (1 Jan. 1999).
www.sciencemag.org
Ramoni, Marco F., Paola Sebastiani, and Isaac S. Kohane. "Cluster Analysis of Gene Expression Dynamics." PNAS. Edited by Louis M. Kunkel.
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18 |
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Advanced Expert Systems |
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Chapters 12 and 13 of Shortliffe. |
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19 |
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Patient Monitoring |
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20 |
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Genomic Medicine III: Introduction to Genomics |
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21 |
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Genomic Medicine IV: Linking Genotypes and Phenotypes |
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22 |
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Genomic Medicine V: Reverse Engineering |
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Zoltan. "The Perils and Promises of Massively Parallel Biology." Chap. 5 in Genetic Network Analysis, 2002: pp. 23. |
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23 |
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Student Presentations |
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24 |
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Student Presentations |
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25 |
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Student Presentations |
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26 |
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Student Presentations |
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