Courses:

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Course readings.

Lec #	TOPICS	READINGS
1	Introduction: Brief Introduction to Biomedical Informatics and Outline of the Course - Dr. M. F. Ramoni	Shortliffe, Edward H., and Leslie E. Perreault, ed. Medical Informatics: Computer Applications in Health Care and Biomedicine. Gio Wiederhold, and Lawrence M. Fagan (associated editors). 2nd ed. New York, NY: Springer, 2003. ISBN: 9780387984728 .
2	Bioinformatics: Introduction to the Bioinformatics Module. Central Dogma of Molecular Biology. Short Biology Primer. Human Genome Project. The Role of Computational Sciences in the New Biology - Dr. M. F. Ramoni	Sebastiani, P., E. Gussoni, I. S. Kohane, and M. F. Ramoni. "Statistical challenges in functional genomics (with discussion)." Stat Science 18, no. 1 (2003): 33-70.
3	Structural Genomics: Human Variations. Genetic and Genomic Studies. Evolutionary Pressure and Selection. SNPs and Haplotypes. Haplotype-tagging - Dr. M. F. Ramoni	Wang, D. G., et al. "Large scale identification, mapping, and genotyping of single nucleotide polymorphisms in the human genome." Science 280 (1998): 1077-82. Sebastiani, P., R. Lazarus, S. T. Weiss, L. M. Kunkel, I. S. Kohane, and M. F. Ramoni. "Minimal haplotype tagging." Proc Nat Acad Sci U.S.A. 100, no. 17 (2003): 9900-05.
4	Human Variations: Human Variations. Analysis of Human Variations. Association Studies. Complex Traits. The Genomic Study of the Future - Dr. M. F. Ramoni	Lander, E. S., et al. "Genetic dissection of complex traits." Science 256 (1994): 2037-48. Sebastiani, P., M. F. Ramoni, V. Nolan, C. T. Baldwin, and M. H. Steinberg. "Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia." Nat Genet 37, no. 4 (2005): 435-40.
5	Sequencing: Genome Sequencing at the Human Genome Project - Dr. R. Nicol
6	Genome-wide Genomic: SNP Microarrays and High-density Genotyping - Dr. S. Monti	Janne, P. A., et al. "High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines." Oncogene 23 (2004): 2716-2726. Garraway, et al. "Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma." Nature 436 (2005): 117-122.
7	Functional Genomics - Dr. A. Kho
8	Expression Microarrays: Meta Elements of Transcriptome Profiling - Dr. A. Kho
9	Annotation Databases: This Lecture will Present the Most Important Public Databases of Genomic Knowledge Currently Available. Using the Flow of Information Inside a Cell (DNA - RNA - Proteins) as our Guiding Principle, We will Highlight the Specific Features and Characteristics of Each Resource, their Limitations, and How they Relate to Each Other - Dr. A. Riva	Stein, L. D. "Integrating biological databases." Nat Rev Genet 4, no. 5 (May 2003): 337-45.
10	Genomic Privacy - Dr. C. Cassa	Lin, Zhen, Art B. Owen, and Russ B. Altman. "Genomic Research and Human Subject Privacy." Science 305, no. 5681 (July 9, 2004): 183. (Washington) Sweeney, L. "k-anonymity: a model for protecting privacy." International Journal on Uncertainty, Fuzziness and Knowledge-based Systems 10, no. 5 (2002): 557-570. Malin, B., and L. Sweeney. "Inferring Genotype from Clinical Phenotype Through a Knowledge-based Algorithm." Pacific Symposium on Biocomputing (January 2002): 41-52. Malin, B. "Protecting DNA Sequence Anonymity with Generalization Lattices." Methods of Information in Medicine 44, no. 5 (2005): 687-692. Lin, Z., M. Hewett, and R. B. Altman RB. "Using binning to maintain confidentiality of medical data." Proc AMIA Symp (2002): 454-8.
11	Pharmacogenomics - Dr. S. Weiss
12	Proteomics: Introduction to the Proteomics Module. Old Proteomics: Western Blot, SDS-PAGE, etc. New Proteomics: Automation/parallel High-throughput Analysis with Mass Spectrometry (SELDI, MS/MS), Yeast Two-hybrid, and Protein Microarrays - Dr. G. Alterovitz	Alterovitz, G., E. Afkhami, J. Barillari, and M. Ramoni. "Proteomics." In Wiley Encyclopedia of Biomedical Engineering. Edited by Metin Akay. Vol. 1. Hoboken, NJ: John Wiley & Sons, 2006. ISBN: 9780471740377 .
13	Proteomics: Interactome: Introduction to the biological networks with focus on interactomes. Common themes and fundamental algorithm considerations underlying networks are explored with interactome examples such as the human massome network. Different types of biological networks are outlined as well as corresponding mathematical representations and related analysis. Recent developments in scale-free networks and analysis are described - Dr. G. Alterovitz	Alterovitz, G., E. Afkhami, J. Barillari, and M. Ramoni. "Proteomics." In Wiley Encyclopedia of Biomedical Engineering. Edited by Metin Akay. Vol. 1. Hoboken, NJ: John Wiley & Sons, 2006. ISBN: 9780471740377 .
14	Clinical Informatics: Computing Support for the Academic Healthcare Enterprise - Dr. D. Nigrin
15	Telemedicine - Dr. H. Fraser	Fraser, H. S., D. Jazayeri, P. Nevil, Y. Karacaoglu, P. E. Farmer, E. Lyon, M. K. Fawzi, F. Leandre, S. S. Choi, and J. S. Mukherjee. "An information system and medical record to support HIV treatment in rural Haiti." BMJ 329, no. 7475 (November 13, 2004): 1142-6. Fraser, H. S., P. Biondich, D. Moodley, S. Choi, B. W. Mamlin, and P. Szolovits. "Implementing electronic medical record systems in developing countries." Inform Prim Care 13, no. 2 (2005): 83-95.
16	Decision Support Systems: Introduction to Decision Support Systems and Artificial Intelligence Applications in Biomedical Sciences - Dr. M. F. Ramoni	Shortliffe, Edward H., and Leslie E. Perreault, ed. Medical Informatics: Computer Applications in Health Care and Biomedicine. Gio Wiederhold, and Lawrence M. Fagan (associated editors). 2nd ed. New York, NY: Springer, 2003. ISBN: 9780387984728 .
17	Patient Confidentiality: Slightly Controlled Information Exhibitionism in the Genetic Age - Dr. I. S. Kohane
18	Revision Class - Dr. M. F. Ramoni
	Mid-term Exam
19	Geographic Health Information: Slightly Controlled Information Exhibitionism in the Genetic Age - Dr. J. Brownstein
20	Medical Image Processing: Image Guided Therapy and the National Alliance for Medical Image Computing - Dr. R. Kikinis
21	Biosurveillance - Dr. K. Mandl
22	Pharmacoeconomics - Dr. S. Finkelstein
23	Public Health Informatics - Dr. B. Reis
24	Student Presentations
25	Student Presentations (cont.)