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BME 695 Advanced Biomolecular Engineering

Course Overview
This 3-credit advanced BME graduate course is aimed at understanding the principles and tools necessary to collect and analyze genome-wide experimental data in genomics and proteomics. The course covers interdisciplinary materials and methods encompassing gene regulation, protein interactions, linear algebra, biostatistics, etc.

Prerequisite
Students should be able to use matrices (linear algebra) and some software programming tools (e.g., Matlab, C, Visual Basic, etc.). Prior knowledge of structure and function of DNA and proteins, and gene regulation is highly recommended. Consultation with the instructor is encouraged.

Course Description
One of the most challenging tasks for the current biomedical engineers is to extract biologically important information from a large amount of data such as genomic DNA sequences and mRNA/protein expression data. Using examples in human genomics and proteomics, this course describes cutting-edge biomolecular technologies, computational algorithms, and mathematical models. The first half is genomics focusing on experimental designs with microarrays and analyses of microarray-derived data, and the second half is proteomics focusing on the principles of mass spectrometry and analyses of protein expression data. The subjects include structure of human genome, DNA microarrays, cluster analyses, singular value decomposition, modeling and voting, mass spectroscopy, protein arrays, systems biology, and biostatistics.

Required Textbooks
There are no required textbooks. Handouts and journal articles are made available to the students.

Recommended Reading
Ideker, T. et al. Ann. Rev. Gen. Hum. Genet. 2:343-372 (2001)
Ideker, T. et al. Science 292:929-934 (2001)
Churchill, G.A. et al. Nature Genetics 32:490-495 (2002)
Eisen, M.B. et al. PNAS 95:14863-14868 (1998)
Khan, J. et al. Cancer Res. 58:5009-5013 (1998)
Alter, O. et al. PNAS 97:10101-10106 (2000)
Shipp, M.A. et al. Nature Medicine 8:68-74 (2002)
Yates, J.R. TIG 16:5-8 (2000)
Griffin , T.J., and Aebersold, R. JBC 276:45497-45500 (2001)
Harris, R.A. Proteomics 2:212-223 (2002)
Haab et al. Genome Biology 2:4.1-4.13 (2001)
Tong, A.H.Y. et al. Science 295:321-324 (2002)
Ho et al. Nature 415:180-183 (2002)