Biomedical Information Technology
Fall 2008
This course teaches the design of contemporary information systems for biological and medical data. Examples are chosen from biology and medicine to illustrate complete life cycle information systems, beginning with data acquisition, following to data storage and finally to retrieval and analysis. Design of appropriate databases, client-server strategies, data interchange protocols, and computational modeling architectures. Students are expected to have some familiarity with scientific application software and a basic understanding of at least one contemporary programming language (e.g. C, C++, Java, Lisp, Perl, Python). A major term project is required of all students. This subject is open to motivated seniors having a strong interest in biomedical engineering and information system design with the ability to carry out a significant independent project. This course was offered as part of the {{% resource_link "394342a2-b1de-4c8f-9889-6f173f2f5b25" "Singapore-MIT Alliance" %}} (SMA) program as course number SMA 5304.
Readings
- Achard, F., et al. “XML, Bioinformatics and Data Integration.” Bioinformatics 17, no. 2 (2001): 115-125.
- Schweiger, R., et al. “Plug-and-Play XML: A Health Care Perspective.” Journal of the American Medical Informatics Association 9, no. 1 (January/February 2002): 37-48.
- Florescu, D., and D. Kossman. “Storing and Querying XML Data using an RDBMS.” Bulletin of the IEEE Computer Society Technical Committee on Data Engineering 22 (1999): 27-34. (See pp. 27-34 in ( PDF ))
- Lesser, U. “A Query Language for Biological Networks.” Bioinformatics 21, suppl. 2 (2005): ii33-ii39.
- Krishnamurthy, L., et al. “Pathways Database System: An Integrated System for Biological Pathways.” Bioinformatics 19, no. 8 (2003): 930-937.
- Stein, L. D. “Integrating Biological Databases.” Nature Reviews Genetics 4 (May 2003): 337-345.
- Searls, D. B. “Data Integration: Challenges for Drug Discovery.” Nature Reviews Drug Discovery 4 (January 2005): 45-48.
- Wilkinson, K., et al. “Efficient RDF Storage and Retrieval in Jena2.” Presented at 1st International Workshop on Semantic Web and Databases, September 7, 2003, Berlin, Germany.
- Zhou, J., et al. “Minerva: A Scalable OWL Ontology Storage and Inference System.” Proceedings of First Asian Semantic Web Conference, 2006, Beijing China.
- Kanaris, I., et al. “Building in-silico Pathway SBML Models from Heterogeneous Sources.” Proceedings of 8th IEEE International Conference on BioInformatics and BioEngineering (BIBE 2008), Athens Greece, October 8-10, 2008. Paper BI916. doi: 10.1109/BIBE.2008.4696730.
- Sharan, R., and T. Ideker. “Modeling Cellular Machinery Through Biological Network Comparison.” Nature Biotechnology 24, no. 4 (April 2006): 427-433.
- Kelley, Brian P., et al. “Conserved Pathways Within Bacteria and Yeast as Revealed by Global Protein Network Alignment.” PNAS 100, no. 20 (September 20, 2003): 11304-11309. doi: 10.1073/pnas.1534710100.
- Sharan, R., et al. “Conserved Patterns of Protein Interaction in Multiple Species.” PNAS 102, no. 6 (February 8, 2005): 1974-1979. doi:10.1073/pnas.0409522102.
- Fishman, M. C., and J. A. Porter. “A new grammar for drug discovery.” Nature 437 (22 September 2005): 491-493.
- Butcher, E. C., E. I. Berg and E. J. Kunkel. “Systems biology in drug discovery.” Nature Biotechnology 22, no. 10 (October 2004): 1253-1259.
- Huang, P. H., and F. M. White. “Phosphoproteomics: Unraveling the Signaling Web.” Molecular Cell 31 (September 26, 2008): 777-781.
Sources
- Course catalogue ↗Historical OpenCourseWare
- MIT OCW readings ↗
- MIT OCW syllabus ↗
- Historical MIT OpenCourseWare offering. Named reading entries and schedule topics are automatically extracted from the linked source pages.