Genomics

Johns Hopkins Bloomberg School of Public Health 260.605.01

This eight-week course begins Friday October 27, 2006 (room W4019). It is offered jointly by the Depts. of Molecular Microbiology & Immunology and Biostatistics. All graduate students and postdocs enrolled in the School of Public Health or School of Medicine are also welcome to attend.

Description

A genome is the collection of DNA that comprises an organism, and genomics is the study of the function of DNA including genes. This course explores genomes across the tree of life, using the tools of bioinformatics. The topics include viruses; bacteria and archaea; protozoa (e.g. Plasmodium); plants (with a focus on Arabidopsis and rice); the fungi; the metazoans (Drosophila, C. elegans, the rodents, the primates, and human). Each lecture highlights features of the relevant genome(s), key websites and bioinformatics tools, the phylogenetic context in which to understand the significance of the organism, and genomics-based approaches to human disease. Weekly computer labs introduce students to genomics software available on the internet, including tools for genome annotation, comparison, and analysis.

Learning objectives

After successfully completing this course, you will be able to do the following:

· Define the main features of viral, prokaryotic, and eukaryotic genomes

· Define the relevance of various genomes to human disease

· Use web-based tools for genome analysis (e.g. annotation and comparison)

· Read papers on the sequencing of the human genome and other genomes, and evaluate the quality and limitations of the analytic approaches

Prerequisites

Introduction to Bioinformatics (260.602.01) or Bioinformatics (ME:800.707) are prerequisites, or obtain consent of instructor. Students may sign up with the Registrar's Office (School of Public Health) to take the course for credit. Computer lab (offered each Friday) is required if the course is taken for credit. Auditors (including postdoctoral fellows and graduate students) are welcome but are requested to register as auditors.

Format

·Monday and Wednesday lectures 10:30-11:50 a.m. (room W4019)
·Friday 10:30-11:50 computer lab (room W3025)
· Note: the first class on Friday October 27 meets at 10:30 in W4019)

Instructor

J. Pevsner (443-923-2686; pevsner@kennedykrieger.org).

Textbook

J. Pevsner, Bioinformatics and Functional Genomics (John Wiley & Sons, 2003). About five copies will be on reserve at Welch Medical Library (checkout for two hours at a time). To buy the book, visit Wiley.com to save 15%. Your discount will be applied automatically upon checkout. If you do you not see the discount being applied, please enter code aff15 in the Promotion Code field and click the Apply Discount button. Also, you can buy it through the Matthews Johns Hopkins Medical Book Center (i.e. the bookstore) or order it at Amazon or Barnes & Noble. You can also find used copies on-line (e.g. Abebooks). Website for textbook: http://www.bioinfbook.org.

Moodle site!!!

Visit the moodle site to get class information, including powerpoints!

Grading

40% of grade is based on a written report on a gene and a genome of your choice. 30% of grade is based on a final exam (in-class closed-book exam on December 20). 30% of grade is based on moodle quizzes.

Teaching assistants

Hugh Cahill, Jennifer Turney, and Meg Zupancic.

Course sponsors

Dept. of Molecular Microbiology and Immunology and Dept. of Biostatistics, Johns Hopkins Bloomberg School of Public Health. Thanks also to: The Kennedy Krieger Institute and Welch Medical Library, Division of Biomedical Information Sciences

Related courses of interest

—Bioinformatics (260.602.01); offered each September/October
—Bioinformatics (BCMB Core Course, M.E:800.707); offered November 17 to December 8, 2006.
—Analysis of Biological Sequences (140.638.01) 2nd term, 2003-2004, 3 units.
—BIOCOMPUTING I:PERL FOR BIOINFORMATICS (140.636.01) 2nd term.
—PROTEIN BIOINFORMATICS (260.841.01) 4th term.

Week

Monday

Wednesday

Friday

1

November 1
Viral genomes: focus on HIV and influenza
Chapter 13

2

November 6
Bacteria and archaea (part 1)
Chapter 14

November 8
Bacteria and archaea (part 2)
Lecture by Egbert Hoiczyk
Chapter 14

3

November 17
Computer lab 3
The fungi

4

November 20
The eukaryotic chromosome
Chapter 16

5

November 29
Eukaryotic genomes: plants
Chapter 16
Lecture by Judith Bender

December 1
Computer lab 4
Protozoans, plants

6

December 6
Eukaryotic genomes: vertebrates (fish, mouse, chimp)
Chapter 16

December 8
Computer lab 5
metazoans

7

December 11
The human genome
Chapter 17

December 15
Computer lab 6
human genome

December 18
Human disease
Chapter 18
Lecture by Dave Valle

December 20
Final exam (in class)