Grading

The course will be graded by performance on in-class assignments (four times – 25% for each assignment). The eight lab sessions will be divided into four topics. Within each topic, 20% of the assignment will be given to the first lab session while 80% of the assignment will be given to the second lab session.

Missing classes

Please contact the instructor and TA to make arrangement for fulfilling the assignments.

Notice

The class meets at Rm.400AB of the Prior Health Library every Wednesday.

Course syllabus

Date	Lecture	Instructor	Lab	TA	Notes
01/09/07	Introduction to biomedical informatics	Huang	Search on gene and protein databases		Slides
01/16/07	Sequence alignment: dynamical programming, BLAST algorithm	Huang	BLAST	Keen	Lecture Slides Lab Slides Handout
01/23/07	Protein structure classification, prediction and alignment	Huang	BLAST, Multiple sequence alignment and ClustalW	Keen	Lecture Slides Lab Slides Assignment 1
01/30/07	Microarray – principle, analysis, and applications	Huang	Protein structure (PDB, SCOP) and structure alignment (VAST)	Keen	Lecture Slides Lab Slides Handout
02/06/07	Biological networks	Huang	Protein structure (PDB, SCOP) and structure alignment (VAST)	Keen	Lecture Slides Lab Slides Assignment 2 (in the lab slides)
02/13/07	Imaging informatics – Computer-aided diagnosis	Gurcan	Gene expression (GEO database) - I	Keen	Lab Slides Handout
02/20/07	Translational informatics	Payne	Gene expression (GEO database) - II	Keen	Assignment 3
02/27/07	Infectious disease tracking	Janies	Pathway and molecular interaction databases - I	Huang/Cooper	Lab Slides Handout
03/05/07	System biology	Parvin	Pathway and molecular interaction databases - II	Huang/Cooper	Lab Slides Assignment 4

Textbook and references

Recommended (not required) textbook: Bioinformatics, sequence and genome analysis, 2^nd Ed., David W. Mount, Cold Spring Harbor Laboratory Press, 2004.