Latest lectures and other course materials will be available at
URL
http://www.cs.gmu.edu/~ashehu/?q=CS444_Fall2012
|
Instructor Location and Time Office Hours |
Amarda Shehu , Room #4422 ENG, amarda\AT\gmu.edu Innovation Hall 136, TR 12:00-1:15 pm TBD |
This course will introduce students to the rising importance of computer science in the life sciences. The topics will focus on computational methods in molecular biology. An array of methods will be introduced for the purpose of understanding and characterizing the role of molecules in cells and man-made constructs. Topics will be presented as three-week units, focusing on sequence alignment, gene and motif finding, structure and function prediction and modeling, covering both nucleic acids and proteins. Selected research topics will also be presented.
Material will be disseminated in the form of lectures. Students will be tested on comprehension through homeworks, some of which will contain simple programming assignments. Students can program in their language of choice.
A class make-up of students with different backgrounds, encompassing biology, chemistry, statistics, computer science, and electrical engineering, will give students a glimpse of the interdisciplinary and highly-collaborative work between the exact sciences and life sciences. This environment and team work will enhance the experience of each individual student in the class.
Students will work in two- to three-member teams towards their final topic presentation. To encourage independent research in computational biology, students will have the opportunity to choose and review interesting topics from existing literature. The in-class presentation of selected research articles on a chosen topic will conclude their course work.
At the end of this course, students will be able to implement alignment algorithms on protein sequences, modify and implement gene and motif finding algorithms, gather and present statistics on protein structures, implement simple geometric manipulations of protein chains, implement energy functions to rank structures of a protein chain, implement search algorithms to compute protein structures, and apply existing software to dock structures of proteins and ligands.
Material will be disseminated through lectures developed by the instructor, which will be posted online prior to each class. Lectures will combine online modules developed as part of the connexions project and the following textbook: Introduction to Bioinformatics by A. Lesk, Oxford University Press, 3rd Edition (2008). (1999).
C or better in CS 310.
| Date | Topic | Chapters | Assignments |
|---|---|---|---|
| Aug. 28, 30 | Introduction Molecular Biology Biological Databases | 1, 3 [pdf] | Student Info [pdf] |
| Sep. 4, 6 | Analyzing Sequences (Alignment) | 5, [pdf] | Hw1 Out [pdf] |
| Comparing Sequences and Structures | |||
| Sep. 11, 13 | Multiple Sequence Alignment | 5, pdf | |
| Sep. 18, 20 | Visualizing and Analyzing Protein Architecture | 1, 6, m1, pdf | |
| Sep. 25, 27 | Protein Classification and More: Hidden Markov Models | 6, pdf | Hw1 Due Hw2 Out pdf |
| Protein Folding and Structure Prediction | |||
| Oct. 2, 4 | Biomolecular Simulations: Molecular Dynamics, Monte Carlo | m2, pdf | Simulation and Proteins [pdf] |
| Oct. 11 | Structure Prediction and CASP | 6, m3, pdf | Hw2 Due Hw3 Out [pdf], script |
| Oct. 16, 18 | Comparative Modeling and Threading | 6, m4, pdf | |
| Oct. 23, 25 | Comparative Modeling and Threading | 6, m4, pdf | |
| Oct. 30, Nov. 1 | Ab-initio Methods - Fragment-based Assembly | 6, m5, pdf | Hw3 Due Hw4 Out [pdf] |
| Characterizing Protein Associations | |||
| Nov. 06, 08 | Docking Rigid Structures | 6, m6, m7, [pdf] | Article on Molecular Surface [pdf] |
| Nov. 13, 15 | Docking Flexible Structures | m6, m7, [pdf] | Reading and Presenting |
| Systems Biology | |||
| Nov. 20, 27 | Overview of Systems Biology | 7, [pdf] | Hw4 Due Interim Topic Report |
| Nov. 29, Dec. 04 | Analysis of High-throughput Data | 7, [pdf] | |
| Dec. 6 | Topic Presentations | ||
The class enforces the GMU Honor Code . Violations of academic honesty will not be tolerated.
If a disability or other condition affects your academic performance, document it with the Office of Disability Services.