Instructor:         Mohammed J. Zaki
Office:               Lally Bldg 307
Phone:               x6340
Email:                zaki.AT.cs.rpi.edu
Class Hours:     Low 4034, MR 10:00-11:50am
Office Hours:    Mondays 12-2pm, or by appointment
Web Page:         http://www.cs.rpi.edu/~zaki/bioinfo/
 

Introduction
Bioinformatics is the science of storing, extracting, organizing, analyzing, and interpreting biological data. Its importance has increased with the technology of DNA sequencing, microarrays, as well as the widespread understanding that genes and proteins act in networks. This in turn renders high performance data analysis algorithms central to this task. The goal of this course is to introduce the main principles of bioinformatics. The coverage will include traditional concepts like sequence alignments, phylogenetic trees, and structure prediction, as well as emerging topics like high dimensional indexing, database support, text mining, microarray data analysis, and data mining.

Text
The following book is required for the course: Bioinformatics: Sequence and Genome Analysis, by David W. Mount, Cold Spring Harbor Laboratory Press, 2001 (ISBN: 0-87969-608-7). Additional reading material will be handed out in class as required.

Class Format and Requirements

Requirements: Discrete Math and Data Structures and Algorithms are required. A course in probability and statistics will be helpful. Programming skill in Perl is indispensable. Prior knowledge of molecular biology is not assumed; all necessary concepts will be covered in class.

There will be two exams. All exams are closed book, closed notes. See class schedule for tentative dates. There will be no final exam.

On occasion students may be required to read some classic or latest papers in bioinformatics to supplement class material.

There will be about 5-7 homework assignments to be done either individually or in groups. Some of these will involve algorithm implementation and performance study, while others might involve application of techniques to some bioinfo problem. Some of the assignments may be fairly involved, almost like a mini-project. Students will be assigned into groups of 2 for the group assignments.

The final grade will be determined as follows:
    50% exams (25% per exam)
    50% homeworks

Timeline for Topics
See the course website for a tentative timeline. There might be a change in the topics as we progress during the semester.

Academic Integrity
The school takes cases of academic dishonesty very seriously, resulting in an automatic "F" grade for the course if anyone is caught cheating. Students should familiarize themselves with the relevant portion of the Rensselaer Handbook on this topic.