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Instructor Location and Time Office Hours |
Amarda Shehu , Room #4422 ENG, amarda\AT\gmu.edu West Building #1004, R, 4:30pm - 7:10 pm T 4:00 - 6:00 pm |
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. Students with little prior programming experience are encouraged to use Matlab.
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.
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. Tramontano, CRC Press, 1st Edition (2006). Additional textbooks that are recommended but not required include: Computational Molecular Biology: An Introduction by P. Clote and R. Backofen, Wiley, 1st Edition (2000); Introduction to Protein Structure by Carl Branden, Routledge, 2nd Edition (1999).
CS 499 is cross-listed as BINF 401 and ECE 499. No hard prerequisites are needed for this course beyond a programming course.
| Date | Topic | Chapters | Assignments |
|---|---|---|---|
| Jan. 21 | Introduction Molecular Biology Biological Databases | 1.2, [pdf] | Student Info [pdf] |
| Jan. 28 | Analyzing Sequences (Alignment) | 1.2, 2.4.1, 4.2.4, [pdf] | Hw1 Out [pdf] |
| Comparing Sequences and Structures | |||
| Feb. 4 | Multiple Alignments; Visualizing and Analyzing Protein Architecture | 1.4, m1, pdf | |
| Feb. 11 | Protein Classification and More: Hidden Markov Models | 2.4, pdf | Hw1 Due Hw2 Out pdf |
| Simulating Protein Folding | |||
| Feb. 18 | Biomolecular Simulations | m2, pdf | Simulation and Proteins [pdf] |
| Feb. 25 | Trajectory-based Exploration: Molecular Dynamics and Monte Carlo | m2, pdf | Survey article [pdf] |
| Protein Structure Determination | |||
| Mar. 04 | CASP and Prediction Quality | 6, 9, m3, pdf | Hw2 Due Hw3 Out [pdf], script |
| Mar. 11 | Spring Break | Topic Selection | |
| Computing Structure(s) of Similar and Novel Sequences | |||
| Mar. 18 | Comparative Modeling and Threading | 7, m4, pdf | |
| Mar. 25 | Ab-initio Methods - Fragment-based Assembly | 9, m5, pdf | Hw3 Due Hw4 Out [pdf] |
| Characterizing Protein Associations | |||
| Apr. 01 | Docking Rigid Structures | 6.5, m6, m7, [pdf] | Article on Molecular Surface [pdf] |
| Apr. 08 | Docking Flexible Structures | m6, m7, [pdf] | Reading and Presenting |
| Systems Biology | |||
| Apr. 15 | Overview of Systems Biology | articles [pdf] | Hw4 Due Interim Topic Report |
| Apr. 22 | Analysis of High-throughput Data | articles [pdf] | |
| Apr. 29 | 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.
Latest lectures and other course materials will be available at
URL
http://www.cs.gmu.edu/~ashehu/?q=CS499_Spring2010