Introduction to Bioinformatics

Johns Hopkins Bloomberg School of Public Health 260.602.01

This eight-week course begins Friday August 31, 2007 (room W4019 on Mondays and Wednesdays; the first meeting is the in the computer lab, W3025). It is a core course in the new "Master of Health Science in Bioinformatics" program at the School of Public Health. All graduate students and postdocs enrolled in the School of Medicine are also welcome to attend. (Click here for the JHSPH webpage for this course.)

Description

The use of computers has revolutionized biological research. This course provides an introduction to bioinformatics, the combined field of biology and informatics (information science and technology). The course focuses on the analysis of proteins, genes, and genomes.

Prerequisites

None. 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) are welcome but are requested to register.

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 August 31 meets at 10:30 in the computer lab

Instructor

J. Pevsner (443-923-2686; pevsner@kennedykrieger.org). Additional lectures by Ingo Ruczinski and Sarah Wheelan.

Textbook

I will distribute chapters from the upcoming second edition of J. Pevsner, Bioinformatics and Functional Genomics (John Wiley & Sons, first ed. 2003). For the first edition, 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 take weekly quizzes and get class information! You can create an account now, and you will get the "key" to log in on Friday, September 1. Note: only people registered for this course will be able to see the quizzes.

Grading

30% of grade is based on discovery of a novel gene by the final day of the course. 30% of grade is based on a final exam (in-class closed-book exam on October 25). 40% of grade is based on ten web-based moodle quizzes.

Teaching assistant

Megan Szymanski

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

—Genomics; this newly-offered course immediately follows Introduction to Bioinformatics and covers the tree of life
—Bioinformatics (BCMB Core Course, M.E:800.707); I will give seven lectures beginning December 2, 2005.
—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

2

3

September 19
Molecular phylogeny (part 1)
Chapter 11

4

September 24
Molecular phylogeny (part 2)
Chapter 11 Microarrays: SNPs and aCGH

5

October 3
Gene expression: microarray data analysis
Chapter 7

6

October 10
Hidden Markov models

7

October 15
Protein structure (part 1) by Ingo Ruczinski
Chapter 9

October 22
Functional genomics

October 24
Final exam (in class)
Find-a-gene project due