q        ANNOUNCEMENT: The project presentations schedule are as given below. Mail me a powerpoint file at least 6 hours before your presentation. If you give me your slides printed 6 on a page, I can make copies for the class before your presentation. You may also print out a page with your project summary, highlights, and important findings for the convenience of the audience. Your final reports (including source code) are due on December 1. The audience will evaluate these presentations.  

q        ANNOUNCEMENT: The final exam is scheduled for Thursday, Dec 4, 11AM. The room will be announced soon.  Sample questions.

q        Course Outline: CAP 5991; CGS 5991.

q         Text: Bioinformatics, by  Baxevanis & Ouelette, 2nd Edition, ISBN: 0-471-38391-0.

q         Text: Bioinformatics, by  David Mount, CSHL Press, 2002, Paperback, ISBN: 0-879-69608-7

q         Reading Material: Click Here.

q         Homework: Homework #1 (Due 18 Sept); Homework #2 (Due 21 Oct); 

q         Lecture Transparencies

• Lecture 1 (08/26): Overview; [Reading]

• Lecture 2 (09/02): Fundamentals of CS and Stats; Sequence Alignment; [Reading]

• Lecture 3 (09/09): Sequence alignment; Internet resources, BioPerl; [Reading]

• Lecture 4 (09/16): BioPerl; Multiple Alignment; [Reading]

• Lecture 5 (09/25): Hidden Markov Models; [Reading]

• Lecture 6 (09/30): HMM Applications, Gene Prediction; Protein Structure[Reading]

• Lecture 7 (10/7): Protein Structures; Motif Detection [Reading]

• Lecture 8 (10/14): Protein Classifications; Microarrays [Reading] 

• Lecture 9 (10/21): Neural Networks; SVMs; Genommics; Proteomics [Reading] 

• Lecture 10 (10/28): Decision Trees; Machine Learning; Project Briefs [Reading] 

• Lecture 11 (11/4): Shotgun Sequencing and SBH 

• (11/11): Holiday - Veteran's Day.

• Lecture 12 (11/18): Phylogenetic Trees; Protein Structure Prediction 

• Project Presentations I (11/25): Indulkar, Marathe, Nachev, Sautter.

• Project Presentations II (12/2): Alava, Archer-Farrow, Chavez, Zeng.

• Exam (12/4, 11AM, 1 hour).

 

q        Fall 2002 Course Information: Click Here. 

q        ANNOUNCEMENT: There will be no class on Tuesday, Sept 23. Instead, we will meet at the same time on Thursday, Sept 25.

 

Page last modified: November 18, 2003.