PCB 5596/ BSC 4434 Biomedical Informatics: Sequence Analysis

Fall 2012, Monday and Wednesday 3:00-4:15pm
Office hour: Monday and Wednesday 4:30-5:30pm
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, 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 useful tools and resources for their biomedical or bioinformatics research.

This course is for Biomedical Science undergraduate/graduate students and Computer Science undergraduate/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:
Graduates: choose one topics you are interested in and read three to four papers. The main paper must be from Science, Nature journals, or cell after 2008. The instructor should be informed of the selected topic before Sept 17 and the slides should be submitted by email no later than Oct 15 (30%). 60-minute presentation and discussion (35%). Write a 1~2 page summary of future directions of the topic you presented (35%). Due on Dec 1st, 2012. The review must include at least two points about what can be done for future research.
Undergraduates: choose one topics and read 1~2 papers. The main paper must be from Science, Nature Jounals, or cells after 2008. The instructor should be informed of the selected topic before Sept 17 and the slides should be submitted by Oct 15 (30%). 30-minute presentation of how we use the database for what research (35%). Write a 1 page description of what future directions of the topics you present (35%). Due on Dec 1st, 2012. The description must include why the directions are imporatant and novel.

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. Please also read the BSBS Academic Integrity Statement.

Tentative schedule

08/20 Welcome

Retrieval of gene information
08/22 The gene information at NCBI for one gene
08/27 when they are multiple genes
08/29 when the gene is not well annotated

Sequence analysis
09/05 Alignment ABC: local and global,pariwise and multiple
09/10 How to use BLAST
09/12 UCSC genome browser
09/17 Ensembl Genome Browser

Next generation sequencing and ChIP-seq
09/19 ChIP-seq
09/24 The comparison of ChIP-chip and ChIP-seq
09/26 Caveat in analyzing ChIP-seq data
10/01 RNA-seq
10/03 Metagenomics

Gene regulation analysis at the transcriptional level
10/09 Gene regulation basics
10/11 MATCH for known motif identification
10/16 MEME, CONSENSUS and others for novel motifs
10/18 TGS and others for multiple species
10/23 Genome-wide study for individual motifs
10/25 Cis-regulatory modules: MOPAT and others
10/30 Genome-wide cis-regulatory modules

Current trends in Bioinformatics
11/07 - 12/01