BCMB 8210: Computational Methods in Bioinformatics

Fall 2004 (Tue/Thur; 12:30 - 13:45pm)

Credit hours: 3

Prerequisite: basic programming skill and a strong interest in bioinformatics

Text book: Tao Jiang, Ying Xu, Michael Q Zhang, Current Topics in Computational Molecular Biology, MIT 2002

Course overview -- Dr. Ying Xu

Introduction to bio-database: mySQL -- Dr. Peng Wang

Computational Genomics

- bio-sequence comparison and BLAST search -- Dr. Jessie Kissinger

- computational gene finding -- Dr. Ying Xu

- prediction of transcription regulatory binding sites -- Dr. Victor Olman

- microarray data analysis -- Dr. Eileen Kraemer

Computational Proteomics

- functional prediction of proteins -- Dr. Youxing Qu

- protein identification through mass spectrometry data analysis -- Dr. Will York

Mid-term: project progress report/presentation/discussion -- Dr. Ying Xu

Structural Bioinformatics

- RNA secondary structure prediction and applications to RNA gene finding -- Dr. Liming Cai

- protein structure prediction -- Dr. Juntao Guo

- MD simulation of proteins and interactions -- Dr. Rob Woods

Computational systems biology

- comparative genome analysis for microbial genomic structure prediction -- Dr. Zhenchang Su

- prediction of microbial regulatory networks -- Dr. Ying Xu

- dynamics simulation of biological networks -- Dr. Bernd Schuttler

Final Exam: project presentation