CS 685-001/PPA 784-003/STA 695-001 Fall 2009
Phylogenetic Analysis and Molecular Evolution
- Time and Date: Tue and Thurs, 3:30pm to 4:45pm
- Room: Whitehall Classroom Bldg-Rm.233-CB
- Course Number: CS 685 - 001/STA 695 - 001/PPA 784 - 003
- Instructors: Drs R. Yoshida, C. Schardl, and J. Jaromczyk
- Website: www.cophylogeny.net/courses/F09
- Teaching Assistant: Dr. David Haws
- Office Hours: at 5:00PM to 5:50PM on Tue/Thurs at CB307
Course Description
One of the key tasks to study molecular sequence data is phylogenetics, the study of evolutionary relatedness among various groups of organisms from molecular sequence data. Finding out evolutionary relatedness among various groups of organisms and the reconstruction of the ancestral relationships have applications including predicting evolution of fast evolution species, such as Human Immunodeficiency Virus (HIV), finding the origin of life (the tree of life project, http://www.tolweb.org/tree/) and coevolutions among different species. This highly interdisciplinary course is self-contained and is designed to introduce graduate and advanced undergraduate-level students (permission to enroll is required) to the fast growing field of Bioinformatics (with a lot of research opportunities and funding).
The course will cover methods underlying molecular phylogeny studies of protein and nucleic acid sequences to elucidate evolutionary histories and relationships of genes and organisms, as summarized in phylogenetic trees. Students will learn theory of molecular sequence evolution, methods of data acquisition, utilization of sequence databases, methods of phylogenetic analysis, and the interpretation and evaluation of phylogenetic trees.
The course will be interdisciplinary and collaborative in nature, with students and instructors from three relevant disciplines: statistics, computer science, and the life sciences. Students will be introduced to the basics of phylogenetics and phylogenomics from the perspectives of all three disciplines, and will gain more in-depth knowledge through instruction and assignments tailored to their own areas of specialization. Projects that team students with complementary skills will illustrate the interdisciplinary nature of this science and the potential that can be realized through such collaborations.
Hand-outs
Selected topics
- Dogma of molecular biology (information flow)
- Nature of mutations
- Neutral theory
- Homology
- Evolution models (such as GTR, HKY, JC etc)
- Hidden Markov Model and Alignment problem
- Maximum likelihood phylogeny inference
- Distance based methods such as NJ method, BME method, and UPGMA.
Grading
There will be graded homework, using/applying bioinformatics tools, reviewing a recent paper in bioinformatics (write a five page report), and a final group project: these will count 25%, 25%, 15%, and 35% of your grade, respectively.
No homework will be made up for credit, but it is important to make it up for your own benefit. Late homework will not be accepted. No make up final. Correctness, completeness and presentation of turned-in assignments affects the grade.
Recommended books
- R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Biological Sequence Analysis, Cambridge University Press (1998)- Application of graphical models to problems in biological sequence analysis.
- J. Felsenstein, Inferring Phylogenies, Sinauer Associates, Sunderland, Mass (2004).
Suggested final project topics
They are flexible. We will be working with you to modify the projects to make them more in tune with individual needs. For more details please go to: LINK Final date is on Dec 15th, Tue at 3:30PM to 5:30PM
Papers to read
Lecture notes
Passward is needed to access: LINK
Links
Predator and Prey model: LINK