BE561 Protein and DNA Sequence Analysis
The goal of this course is to teach the mathematical and computational techniques to make biological inferences from the DNA and protein sequences. Pairwise sequence comparison is studied in detail. The algorithm is extended to deal with more general cases and applied to RNA structure prediction. Multiple sequence alignment and conserved sequence pattern recognition (sequence profile analysis) are studied extensively. Methods of using phylogenetic trees to study the molecular evolution are described. Methods of identifying coding regions in genomic data are considered. Mathematical models and computational algorithms for genetic regulation are described. An introduction to protein 3-dimentional structure prediction is given. This course is offered every Fall.
I have been teaching this course every Fall since 1997. Here is the home page of the course with details you ever want to know.
BE777 Computational Genomics
A case-study approach to current topics in computational genomics. Mathematical and engineering tools for analyzing genomic data are reviewed. The relationships between sequence, structure, and function in complex biological networks are studied using quantitative modeling. Whole genome analysis is performed. Completion of a series of projects emphasizing real-life data, integrated approaches, practical applications, hands-on analysis, and collaboration. Course projects aim at improving current approaches and involve C and/or PERL programming to interface with existing software packages. The course is offered in a computer laboratory equipped with one laptop per student. This course is offered every Spring.
I co-taught the course with Prof. Bob Berwick in 2000, and with Prof. Kasif in 2001 . Prof. Kasif taught it by himself in 2002. Here is the home page of the course in 2001. Here is the up-to-date homepage of the course.
BE768 Biological Database Analysis
Describes relational data models and database management systems; Teaches the theories and techniques of constructing relational databases to store various biological data, including sequences, structures, genetic linkages and maps, and signal pathways. Introduces relational database query language SQL and the ORACLE database management system, with an emphasis on answering biologically important questions. Summarizes currently existing biological databases. Describes Web based programming tools to make databases accessible. Addresses questions in data integration and security. The future directions for biological database development are also discussed.
I co-taught the course with Prof. Temple Smith in the spring of 1998. Prof. Smith taught it alone in the spring of 1999. If you want to access some of the materials I used in 1998, here is where you can go. Prof. Bob Berwick taught the course in 2000. Currently Prof. Simon Kasif is teaching the course and here is the course homepage.