CS174 Bioinformatics

Instructor: Xiaohui S. Xie
   Email: xhx@ics.uci.edu
   Office Hour: Tue/Thur after class

Meeting information: TT 3:30-4:50pm    Room: DBH 1423

Lecture schedule

Homework assignments

Philosophy

Prerequisites

Subject requirements

Textbooks

Philosophy

Recent breakthroughs in sequencing technology, genomics, gene expression profling, and compuational science have changed the face of modern biology, transforming it into a largely information-based science. This course introduces the state-of-the-art computational methods used in studying modern biological systems. We study the principles of algorithm design for biological datasets, analyze commonly used algorithms, and apply them to solve real-life problems.

The course serves as an introductory course to the rapidly growing field of computational biology and bioinformatics, and emphasizes basic concepts and applications of bioinformatics.

Prerequisites

• familiarity with multivariate calculus, probability theory and basic biology

Subject requirements

• problem sets
• final exam

Textbooks

• N.C. Jones and P.A. Pevzner.   An Introduction to Bioinformatics Algorithms
• Supplementary reading:  R. Durbin, S. Eddy, A. Krogh and G. Mitchison.   Biological Sequence Analysis

Both books will be placed on reserve at the UCI Science Library.

• Supplemental texts, free online at the NCBI Bookshelf (click title to view):

  • Molecular Biology of the Cell, by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. Garland Publishing, 2002.
  • Genomes, by T.A. Brown, BIOS Scientific Publishers, 2002
  • The Python Tutorial
  • The Python Standard Library
  • Biopython
  • http://aspn.activestate.com/ASPN/Python/Cookbook/
  • http://ivory.idyll.org/articles/advanced-swc/
  • http://www.diveintopython.org/
  • http://docs.python.org/ref/ref.html
  • http://www.doughellmann.com/projects/PyMOTW/
  • Python course in Bioinformatics