BICH/GENE 419 Computational Techniques for Evolutionary Analysis
Instructor: Sing-Hoi Sze
Meeting: TR 2:20-3:35 WCBA 110
Office Hours: TR 10-11 HRBB 328B or by appointment
- Midterm 1 (Oct. 17): sequence based analysis
- Midterm 2 (Nov. 30): higher-level analysis
As the increased availability of genome-scale data allows comparisons across
a large number of genomes, it becomes possible to study evolutionary mechanisms
in detail, which include conservation, duplication and specialization of genes
and proteins. The study of evolution becomes a sub-area within computational
biology, which involves the application of computational techniques to solve
problems in biology.
In the past, computational biology was considered to be a
sub-field within theoretical computer science, since many problems
employ techniques in algorithm analysis. More recently, multi-disciplinary
collaborations become the norm, which include participations of mathematicians,
statisticians, biologists and biochemists.
The course will investigate the types of questions that can be addressed
through the application of computational techniques, and algorithms for
construction and analysis of evolutionary relationships. No programming
experience is needed. The course will focus on understanding the main ideas
behind these approaches.
- Sequence alignment.
- Motif finding.
- Phylogenetic footprinting.
- Phylogenetic tree construction.
- Clustering and protein classification.
- Genome rearrangement.
- Gene clustering within genomes.
- Biological network analysis.
- High-throughput sequencing.
- Homework assignments (60%): short written assignments handed out every one
or two weeks.
- Two midterms (20% each).
- Junior or senior classification or approval of instructor.
- Jones N.C. and Pevzner P.A. (2004) An Introduction to Bioinformatics
Algorithms (Computational Molecular Biology). The MIT Press.
- Mount D.W. (2004) Bioinformatics: Sequence and Genome Analysis,
Second Edition. Cold Spring Harbor Laboratory Press.
- Cormen T.H., Leiserson C.E., Rivest R.L. and Stein C. (2009)
Introduction to Algorithms, Third Edition. The MIT Press.