PCB 6596: Bioinformation and Genomics

Fall 2009, Tuesday and Thursday 3:00-4:15pm
Office hour: Tuesday and Thursday 2:00-3pm
Instructor: Xiaoman Li


This course will introduce basic concepts and tools in bioinformatics. Topics include gene information retrieval, DNA sequence analysis, cis-regulatory analysis, ChIP-seq data analysis, microarray data analysis, epigenetics, and so on. Different from classical Bioinformatics courses that focus on method development, this course is more like a computational biology lab course, which enables students to be familiar with the useful tools and resources for their biomedical or bioinformatics research.

This course is for the advanced level Biomedical Science graduate students and Computer Science graduate students. All Biomedical Science students and all computer science students can take this applied bioinformatics course. If you are not sure whether you can take this course, you are welcome to talk with the instructor.

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

Assignments and grading: choose one topics and read four papers (30%), due on Oct 15. 50-minute presentation and discussion (20%). 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 Dec 8. 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

08/25 Welcome

Retrieval of gene information
08/27 The gene information at NCBI for one gene
09/01 when they are multiple genes
09/03 when the gene is not well annotated

Sequence analysis
09/08 Alignment ABC: local and global,pariwise and multiple
09/10 How to use BLAST
09/15 UCSC genome browser
09/17 Ensembl Genome Browser

Gene regulation analysis at the transcriptional level
09/22 Gene regulation basics
09/24 MATCH for known motif identification
09/29 MEME, CONSENSUS and others for novel motifs
10/01 TGS and others for multiple species
10/06 Genome-wide study for individual motifs
10/08 Cis-regulatory modules: MOPAT and others
10/13 Genome-wide cis-regulatory modules

Next generation sequencing and ChIP-seq
10/15 ChIP-seq
10/20 The comparison of ChIP-chip and ChIP-seq
10/22 Caveat in analyzing ChIP-seq data
10/27 RNA-seq

10/29 what is a gene?
11/03 replication pattern and replication origin
11/05 Protein microarray
11/10 regulatory SNP
11/12 Epigenetics

Microarray Data Analysis
11/17 Microarray basics: types, problems, and resources
11/19 Identify differentially expressed genes
11/24 Clustering analysis
12/01 Gene ontology analysis
12/03 Feature selection