CS499 Bioinformatics and Computational Biology I (Spring 2009)

Information

Instructor: Amarda Shehu amarda\AT\cs.gmu.edu Place and Time: STI #120, R 1:30 - 4:10 pm
Office Hours: ENG #422, T 4:00 - 6:00 pm

Description

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.

Format

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.

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.

Objectives and Outcomes

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.

Prerequisites

CS 499 is cross-listed as BINF 401 and ECE 499. Prerequisities include BIOL 231, IT 108, IT 208, STAT 344.

Reading

The class material 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). The following textbooks are recommended but not required: 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).

Grade Breakdown

• Hw1: 10%
• Hw2: 25%
• Hw3: 25%
• Hw4: 25%
• Presentation: 15%

Syllabus

Date	Topic	Chapters	Assignments
Jan. 22	Introduction Molecular Biology Biological Databases	1.2, [pdf]	Student Info [pdf]
Jan. 29	Analyzing Sequences (Alignment)	1.2, 2.4.1, 4.2.4, [pdf], [pdf]	Hw1 Out [pdf]
Comparing Sequences and Structures
Feb. 5	Multiple Alignments; Visualizing and Analyzing Protein Architecture	1.4, m1 , [pdf], [pdf]
Feb. 12	Protein Classification and More: Hidden Markov Models	2.4, [pdf]	Hw1 Due Hw2 Out [pdf]
Simulating Protein Folding
Feb. 19	Biomolecular Simulations	m2 , [pdf]	Simulation and Proteins
Feb. 26	Trajectory-based Exploration: Molecular Dynamics and Monte Carlo	m2 , [pdf]	Survey article
Protein Structure Determination
Mar. 05	CASP and Prediction Quality	6, 9, m3 , [pdf]	Hw2 Due Hw3 Out [pdf] script
Mar. 12	Spring Break		Topic Selection
Computing Structure(s) of Similar and Novel Sequences
Mar. 19	Comparative Modeling and Threading	7, m4 , [pdf]
Mar. 26	Ab-initio Methods - Fragment-based Assembly	9, m5 , [pdf]	Hw3 Due Hw4 Out[pdf]
Characterizing Protein Associations
Apr. 02	Docking Rigid Structures	6.5, m6, m7, [pdf]	Article on Molecular Surface
Apr. 09	Docking Flexible Structures	m6, m7, [pdf]	Reading and Presenting
Systems Biology
Apr. 16	Overview of Systems Biology	articles 1 , 2 , [pdf]	Hw4 Due Interim Topic Report
Apr. 23	Analysis of High-throughput Data	articles 3 , 4 , [pdf]
Apr. 30	Topic Presentations

Honor Code

The class enforces the GMU Honor Code . Violations of academic honesty will not be tolerated.

Disability Statement

If a disability or other condition affects your academic performance, document it with the Office of Disability Services.