CS 167/290D – Introduction to Bioinformatics - Fall 2011

Prerequisites: Undergraduate/graduate course in algorithms and statistics or instructor’s permission

Lectures: MW 11-1 pm, Phelps 2510

Instructor: Ambuj K. Singh

Office Hours: T 11-12, HFH Rm. 3119, email: ambuj@cs.ucsb.edu

Enrollment Code: 50799 (167), 50815 (290D)

Units: 4.0, letter grade ONLY

Reference material:

1. Biological sequence analysis: probabilistic models of proteins and nucleic acids, Richard Durbin et al., Cambridge University Press.

2. Fundamental Concepts of Bioinformatics, D.E. Krane and M.L. Raymer, Pearson Education.

3. Bioinformatics: Sequence and genome analysis, D. Mount, Cold Spring Harbor Laboratory Press.

4. Algorithms on strings, trees, and sequences, D. Gusfield, Cambridge University Press.

5. Genes IX, B. Lewin, Oxford University Press.

6. Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health), W. J. Ewens and G. Grant, Springer.

Course Material:

Lecture outline

Projects (Suggested format)

List of topics and references

Paper presentation schedule

External websites:

Human Genome Primer

Public Human Genome Project Publication In Nature 15 February 2001

Commercial Human Genome Sequence Published in Science 16 February 2001

Conferences and journals:

· Bioinformatics

· Journal of computational biology

· Briefings in bioinformatics

· Nucleic Acids Research

· Genome research

· RECOMB (available from ACM digital library)

· BMC Bioinformatics

· ISMB (available through Bioinformatics journal)

· PSB

Class satisfies the following two areas for MS students: Applications, Foundations.