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
01/07/07	Introduction to biomedical informatics	Huang			Slides
01/14/07	Sequence alignment: dynamical programming, BLAST algorithm	Ozer	Search on gene and protein databases, BLAST	Cooper	Slides Lab slides Lab handout
01/21/07	Protein structure classification, prediction and alignment	Huang	BLAST, Multiple sequence alignment and ClustalW	Cooper	Slides
01/28/07	Cancelled due to snow weather	-	No lab	-
02/04/07	Microarray – principle, analysis, and applications	Huang	Protein database, structure (PDB, SCOP) and structure alignment (VAST)	Cooper	Slides Lab slides Lab handout
02/11/07	Systems biology / Cis-regulation and gene regulation network	Huang	Protein database, structure (PDB, SCOP) and structure alignment (VAST)	Cooper	Slides Lab slides
02/18/07	Infectious disease tracking	Janies	Gene expression (GEO database) - I	Cooper	Lab slides Lab handout
02/25/07	Translational informatics	Payne	Gene expression (GEO database) - II	Cooper	Lab slides
03/04/07	Massive parallel sequencing and its applications	Huang	Pathway and molecular interaction databases - I	Cooper	Slides Lab slides Lab handout
3/11/07	Imaging informatics – Computer-aided diagnosis	Huang	Pathway and molecular interaction databases - II	Cooper	Slides Lab handout

Textbook and references

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