Leming Zhou

From GEP Wiki
Jump to: navigation, search

University of Pittsburgh, School of Health and Rehabilitation Sciences, Department of Health Information Management

Course: HRS-1425 Genomics and Personalized Care in Health Systems

Credits: 3

Time: Spring 2010/2011/2012/2013, Monday, 5pm - 8pm

Instructor: Dr. Leming Zhou, (412) 383-6653, lzhou1@pitt.edu

Course Description

This course focuses on general introduction to genomics, gene structure and annotation, and gene and disease association. These topics are presented and discussed in details. Other topics such as RNA and protein structure, microarray experiments, and DNA sequencing technologies will also be briefly covered. Students will understand gene structure and annotation by working on novel gene annotation projects.

Course Objectives

Upon completion of this course, students should be able to:

1. Explain eukaryotic gene structure and molecular biology central dogma
2. Demonstrate the skills of annotating eukaryotic genes using online tools
3. Demonstrate the skills of performing sequence similarity search using blast
4. Demonstrate the skills of collecting evidence from UCSC genome browser
5. Describe major DNA and protein databases and the method of extracting data from them
6. Explain major gene finding methods, their advantages and disadvantages
7. Describe different types of genetic diseases and the relationship between genetic variations and diseases
8. Demonstrate the skills of determining protein and RNA secondary structures using online tools
9. Explain basic ideas behind microarray and DNA sequencing technologies

Methods of Presentation

Each new topic will be presented and explained. This will be substantiated by the use of the materials of text books, handouts, web sites, case studies, and class discussion.

In-Class Laboratory Session:
In-class lab sessions will be arranged so that students get familiar with online data mining and gene annotation tools.

Student Project and Presentation:
Each student will work on one gene annotation project. Each student will write a report about the project and present his/her results in the last class of the course.

Lab Visit:
A visit to the Genomics and Proteomics Core Laboratories will be arranged. Students will be able to see the procedures of DNA sequencing, PCR, microarray experiments.

Grading Scale

A 90 - 100%
B 80 - 89%
C 70 - 79%
D 60 - 69%
F 00 - 59%

Methods of Evaluations

The final grade for students will be composed of the following:

Class Participation           10%
Homework Assignments   30%
Gene Annotation Project  30%
Final Exam                     30%

Required Textbooks

• Bioinformatics and Functional Genomics, by Jonathan Pevsner, 2nd Edition, Wiley-Blackwell. ISBN: 978-0-470-08585-1
• Genes and Disease, by National Center for Biotechnology Information (NCBI), http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/gnd/gnd.pdf

Course Schedule

Week 1: Overview of the course and introduction to DNA, RNA, and protein.
Week 2: Molecular biology databases
Week 3: Sequence Alignment (Pairwise and Multiple Sequence Alignment) and Phylogenetic Analysis
Week 4:  Blast Search
Week 5: Genome Browsers
Week 6: Gene Finding Methods
Week 7: GEP Gene Annotation Techniques (GEP materials)
Week 8: Gene Annotation Lab 1 (GEP materials)

Week 9: Gene Annotation Lab 2 (GEP materials)
Week 10: Genomic Variations and Disease
Wekk 11: Protein, RNA structure and Pharmacogenomics
Week 12: High-throughput technologies: Microarray and Next-Generation Sequencing
Week 13: Genomics and Proteomics Lab visitt
Week 14 Student Presentations and Course Review
Week 15 Final Exam