Computational Biology and Bioinformatics Course

CSCI 4961 Computational Biology and Bioinformatics

Spring 2007

Contact Information

Instructor:	Mohammed J. Zaki
Office:	Lally 307
Phone:	x6340
Email:	zaki.AT.cs.rpi.edu
Class Hours:	Lally 02, MR 10-11:50am
Office Hours:	MR 12-1pm, or by appointment
Web Page:	http://www.cs.rpi.edu/~zaki/bioinfo/

Course Information

Course Syllabus

Course Announcemens

4th April, 2007: The second homework has been posted: HW2. The due date is 16th April, before/during class. Please email me your solutions in doc/pdf format or bring the hard copy to class.
17th Feb, 2007: The first homework has been posted: HW1. The due date is 26th Feb, before midnight. Please email me your solutions in doc/pdf format.
18th Jan, 2007: Here are the powerpoint slides from todays lecture.
The Virtual Cell site has interesting animations of transcription and translation. See the links above for other interesting sites.

Class Topics

MONDAYS	THURSDAYS
Jan 15 - NO CLASS	Jan 18 - Overview
Jan 22 - SEQ: Sequence Alignment I	Jan 25 - SEQ: Sequence Alignment II
Jan 29 - SEQ: Evolution & Scoring Matrices	Feb 1 - SEQ: DNA Substitution Matrices
Feb 5 - SEQ: Database Search	Feb 8 - SEQ: Multiple Sequence Alignment
Feb 12 - SEQ: Suffix Trees	Feb 15 - SEQ: Suffix DAGs & Arrays
Feb 20(Tue) - SEQ: Motifs	Feb 22 - SEQ: Motifs & HMMs
Feb 26 - SEQ: HMMs	Mar 1 - EXAM I
Mar 5 - SPRING BREAK	Mar 8 - SPRING BREAK
Mar 12 - Guest Lecture (Prof. Chittibabu Guda, SUNY)	Mar 15 - Guest Lecture (Prof. Chris Bystroff)
Mar 19 - SEQ: Phylogenetics (Distance-based)	Mar 22 - SEQ: Phylogentics (Parsimony & Probabilistic)
Mar 26 - SEQ: Genome Evolution	Mar 29 - SEQ: Structure Alignment (Global)
Apr 2 - STR: Structure Alignment (Local)	Apr 5 - STR: Structural Motifs
Apr 9 - STR: Structure Alignment	Apr 12 - STR: Structure Predicton
Apr 16 - SB: Systems Biology & Biological Networks	Apr 19 - SB: Biological Networks
Apr 23 - SB: Network Motifs	Apr 27 - Review
Apr 30 - EXAM II	May 3 - NO CLASS

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