Biomedical Informatics for Medicine
Biomedin 205
Offered Aut, Spr
2 units
Instructor: Atul Butte
Primarily for M.D. students; open to others. Emphasis is on practical applications of bioinformatics and medical informatics for medicine, health care, clinicians, and medical research. 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, and pharmacogenomics. Applications such as BLAST (sequence alignment), PharmGKB (matches allelic variation to drug response), and statistical packages such as R. Background in programming or medicine not required. May be repeated for credit. We will provide lunch for all class sessions.
Class Details
Wednesdays, 11:45 AM-1:05 PM
Location: Alway, M114
| Date | Speaker | Topic
|
|---|---|---|
| 2-Apr-08 | Cells Taking Shape | Julie Theriot |
| 9-Apr-08 | Sick Patients with Healthy Genes: The control layer of the human genome | Gill Bejerano |
| 16-Apr-08 | Imaging Informatics: Computing with Pictures | Daniel Rubin |
| 23-Apr-08 | Challenges in the Informatics of Immunology | PJ Utz |
| 30-Apr-08 | Modeling the Early Detection of Cancer | Sylvia Plevritis |
| 7-May-08 | Bioinformatics and Biostatistics for Personalized Medicine | Michael Walker |
| 14-May-08 | Immunogenomics: Discovering Allogeneic Antigens with Integrated Bioinformatics | David Miklos |
| 21-May-08 | Bioinformatics Analysis of Human and Pathogen Metabolic Networks | Peter Karp |
| 28-May-08 | Deciphering the Cancer Genome | Howard Chang |
Finals |
||
Prerequisites
No formal prerequisites
Supplementary Material
The level of the class is introductory but some background is helpful. To get everyone started, we offer "courselets", small sets of lectures devoted to essential prerequisite information for biomedical informatics. There are four lectures on the essential biology needed for bioinformatics and two lectures which introduce basic medicine. To view the complete list of courselets, see:
http://scpd.stanford.edu/scpd/courses/courselets/list_auth.asp
Recommended Textbooks - Biology
"Genomes 3", by Terry Brown, 2006. A great non-overwhelming reference on molecular biology, with specific focus on novel genome-era measurement tools, such as microarrays. A previous edition of this text is available free at NCBI at http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes.TOC&depth=2.
"Molecular Biology of the Cell" is a useful basic biology textbook written by Alberts, et. al. The first six chapters are most essential for the bioinformatics portion of the class. The four biology courselets cover the most significant material from these chapters using the fourth edition.
Recommended TextBooks - Medical Informatics
Medical Informatics by Shortliffe et. al. is an introductory textbook. The second edition is adequate for these lectures (3rd is the latest edition). (http://www.dbmi.columbia.edu/shortliffe/textbooks.shtml)
Other Resources
You may be interested in supplementing your readings with Biomedin 202 Introductory Biomedical Informatics or Biomedin 204 Pharmacogenomics. This is a series of lectures available over the Internet which cover medical informatics, bioinformatics and pharmacogenomics. The lectures are available for class credit, as an audit or you may sign up out of interest. You may access the lectures by signing onto Coursework and adding these classes to your Coursework page.
Class Registration and Access
Register for Biomedin 205 via Axess.
Class materials will be distributed via the Coursework site. Login to Coursework and add biomedin 205 to your Coursework page.
Contact amy.erickson@ stanford.edu if you have further questions.