PCB 6938: Structure Bioinformatics

Spring 2010, Monday and Wednesday 3:00-4:15pm, BA126
Office hour: Monday and Wednesday 2:00-3pm, HEC210
Instructor: Xiaoman Li


This course focuses on tools and resources in bioinformatics. Topics include miRNA, RNA structure, protein motifs, protein structure, protein-DNA interaction, and so on. Different from classical Bioinformatics courses that target on method development, this course aims to teach students useful tools and resources in bioinformatics, and the idea behind these tools and resources, which will benefit their research.

There is no pre-requisite for the course. Any graduate students from BSBS, EECS, or Biology can take this course.

Textbook: No required textbook. All class contents are provided in the lecture slides and published papers.

Assignments and grading: choose one topics and read three to four papers (20%), ppt slides due on March 31. 50-minute presentation and discussion (30%). Write a review paper based on the four papers and theirs references. The review must include the background, what have been done and at least two points about what can be done for future research (40%). The review is due on April 26. The attendance accounts for 10% of the final score.

Academic Mis-conduct:
Absolutely no cheating is allowed. Please read the policy on Academic misconduct and cheating on http://www.goldenrule.sdes.ucf.edu/2e_Rules.html

Tentative schedule

01/11 Welcome
01/13 UCSC genome browser and Ensembl genome browser: some useful tools from PCB6596

01/20 miRNA
01/25 Predict miRNA target genes
01/27 Predict miRNA host genes

Predict RNA structure
02/01 RNA secondary structure
02/03 Estimating "energy" parameters
02/08 Align and fold
Align then fold

Predict protein motifs
02/10 EMI and prosite motifs
02/15 Insight from minimotif and minimotif miner
02/17 How to predict protein motifs
02/22 The disorder regions of proteins

Predict protein structure
02/24 Importance, CASP, and structure genomics, X-ray crystallography or NMR spectroscopy
03/01 Ab initio protein modelling
03/03 Comparative protein modeling: Homology modeling
03/15 Comparative protein modeling: Protein threading
03/17 Macromolecular docking
03/22 Molecular dynamics

Homology modeling for protein-DNA interaction
03/24 Protein-DNA docking
03/29 Connecting protein structure with predictions of regulatory site
03/31 Ab initio prediction of transcription factor targets using structural knowledge

04/05 Genomes
04/07 Epigentics
04/12 Alternative splicing
04/14 RNA-seq
04/19 Metagenomics
04/21 coding project presentations