IBGP/BMI 705 Introduction to Biomedical Informatics (Winter 2008)

Wednesday 4-6pm  Prior Health Library 400AB

 

Instructor: Kun Huang, Ph.D.

Rm.204 BRT

E-mail: khuang@bmi.osu.edu

Phone: 292-5607

 

TA: Lee Cooper, Abhsiek Cooper (IBGP705@gmail.com)

 

Course website http://www.bmi.osu.edu/~khuang/IBGP705.htm

 

Office hours: By appointment

 

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, 2nd Ed., David W. Mount, Cold Spring Harbor Laboratory Press, 2004.