Summer 2010: July 19 to July 30

Helpful links

Information about the Instructor

Name: Sami Khuri, visiting professor from San José State University
Office: TBD.
Phone: TBD.
Office Hours: By appointment.
Email: khuri@cs.sjsu.edu

Course Description

The course is an introduction to Bioinformatics.
The need to understand the immense amount of data produced by large scale DNA sequencing is of paramount importance. Demands for sophisticated analysis of biological sequences are the driving force behind the rapidly expanding research area of bioinformatics.
This practical course provides an introduction to the main public domain tools, databases and methods in bioinformatics, including DNA and protein databases, such as Genbank and Swiss-Prot, software tools such as those at the National Center for Biotechnology Information (NCBI) and other web accessible applications. More precisely, the course introduces the methods for collecting, editing, and storing macromolecular sequences, for pairwise and multiple sequence alignments, for database searching for similar sequences, and for phylogenetic prediction. The course also covers microarray analysis; the use of SNPs and haplotypes in genomic variation, in pharmacogenomics, in genome-wide association studies and in personalized medicine.

No prior knowledge of Biology is required. In other words, biology is not a prerequisite for this course. But an interest in Biology is. I will spend the first lecture of the course going over some notions in molecular biology (mainly the following Biology Terms) that will be needed for the course.
We shall have lectures and hands-on exercises (praticals in British - travaux pratiques in French) conducted in a computer lab. We have two rooms at our disposal for the course S106 and S155. The lectures will be given in S106 and the hands-on exercises in S155. We shall probably spend 60% of the time on lectures and the rest in the computer lab, solving hands-on exercises. The purpose of the hands-on exercises is to develop your understanding of the material. You will get a hard copy of the slides.

Lecture Material and Schedule

Recommended Textbooks (Not required)