CS 177: Introduction to Bioinformatics

Course Homepage: Fall 2003

NOTE: CS 177 will be also be offered in Spring 2004.

Announcements:

NOTE: For Fall 2003, registration priority will be given to students in the MS Bioinformatics program. Typically, there are about 15 students in the program. Following that, we will offer registration on a first-come-first-served basis to other students.
There will be an offering of CS 177 in Spring 2004, for which undergraduates will have the higher registration priority.
Please get Tompkins 405 accounts by filling out an application in the TA room on the 4th floor of Tompkins.

Fall 2003 information:

Instructor: Dr. Tom Wilke (mtmtxw@gwumc.edu). Co-instructor: Prof. Rahul Simha
Office Hours:
- Dr. Wilke: by appointment (send email: mtmtxw@gwumc.edu).
- Prof. Simha: Tue 1.30-3.30pm.

Class Time/Place:

CS 177: Mondays, 3.30 - 6.10 pm, Tompkins 405
CRN: 75881

Prerequisites:

Permission of instructor. To get permission, please show up the first day of class.

To get permission: CS students can also send an email to Prof. Simha explaining your background, why you want to take the course and why you ought to be selected. Bio/Med-school students can send a similar email to Dr. Wilke.

Course description:

This course will provide a broad introduction to the area of bioinformatics. Topics include: biochemistry overview, databases, the alignment problem, proteins and protein structure-function, introductory phylogenetics, and use of public databases.

Textbook: S.M.Brown. Bioinformatics: A Biologist's Guide to Biocomputing and the Internet. Eaton Publishing.

Supplementary (optional) textbooks:

D.W.Mount. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Lab Press.
C.Gibas and P.Gambeck. Developing Bioinformatics Computer Skills. O'Reilly.

Lecture schedule:

Lecture 1 (Sep 8): Introduction (Powerpoint slides)
- Motivating problem: manufacture of the Polio virus
- Informal "information perspective" of problem: string searching
- History: Traditional biology vs. new information-based biology
- What is bioinformatics? Narrow (genomics) definition and broad definition.
- Example using GenBank.
- The future: bioinformatics careers.
- Course goals.
Lecture 2 (Sep 15): DNA/RNA overview (Powerpoint slides)
- DNA overview.
- RNA overview.
- PCR, sequencing.
- Mutations.
Lecture 3 (Sep 22): Nucleotide and protein databases (Powerpoint slides)
- Public sequence databases.
- Sequence retrieval and examples.
- Similarity searching.
- Gene identification.
- Genetic and physical map.
- Protein databases.
- Data exchange and management.
Lecture 4 (Sep 29): Hands-on lab with databases (Powerpoint slides)
- Motivating problem: a paper from the literature.
- Review nucleotide and protein databases.
- Sequence formats.
- Lab exercises in using GenBank
Lecture 5 (Oct 6): The Alignment problem (Powerpoint slides)
- Pairwise alignment problem.
- Dynamic programming algorithm.
- Multiple alignment.
- Editing and formatting alignments.
Lecture 6 (Oct 13): The new biology lab (Powerpoint slides - Part I) (Powerpoint slides- Part II)
- PCR, sequencing.
- Microarrays.
- Crystallography.
- Mass-spec.
Lecture 7 (Oct 20): Proteins I, Structure-Function Relationships (Powerpoint slides)
- Review of protein structure and function.
- Review of experimental techniques to determine structure
- Protein databases.
- Database similarity search.
- Protein family analysis.
Lecture 8 (Oct 27): Proteins II, Computational modeling
- Structural analysis.
- 3D comparative modeling.
- 3D structural analysis in lab.
- Protein interactions.
Lecture 9 (Nov 3): Phylogenetics I (Powerpoint slides)
- Evolution: overview.
- Taxonomy and phylogenetics.
- Phylogenetic trees.
- Cladistic vs Phenetic analyses.
- Models of sequence evolution.
Lecture 10 (Nov 10): Phylogenetics II (Powerpoint slides)
- Phylogenetic trees and networks.
- Cladistic vs Phenetic analyses.
- Computer software and demos.
Lecture 11 (Nov 17): Algorithms and simulations
Lecture 12 (Nov 24): (Powerpoint slides)
Lecture 13 (Dec 1): Field trips.
Lecture 14 (Dec 8): Student presentations