Introduction to Bioinformatics Lecture for CS 498 CXZ

Introduction to Bioinformatics (Lecture for CS 498 -CXZ Algorithms in Bioinformatics) Aug. 25, 2005 Cheng. Xiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign

Outline • What is bioinformatics? • Why is bioinformatics important? • Bioinformatics and other fields • Topics in bioinformatics

What is Bioinformatics • • • No standard definition! Our definition: Management & Exploitation of Biological Information – Biological information (DNA, Gene expression, Proteins, Literature…. ) – Information management (search, organization, classification) – Information exploitation (pattern analysis, data mining) Other definitions – (Broader) Computer Science + Biology, would cover • Computational Biology (biosimulation) • Bioimaging, etc – (Biased/Narrow) Only refers to one of the following • Information management tool development • Analysis of biology data http: //www. colorbasepair. com/what_is_bioinformatics. html

Why is Bioinformatics Important? • Biology perspective – More and more biological information is available – Need for effectively accessing and using the information – Information analysis supplements (even may replace) web lab experiments • Computer science perspective – Excellent application domain – Poses special computational challenges – Brings computer science closer to scientific discovery • Currently growing …

The Growing Field of Bioinformatics • Research: Universities are expanding research programs in bioinformatics • Education: New degree programs are being launched • Industry: Pharmaceutical industry has a great interest in bioinformatics • Many job and funding opportunities Tour of the Course Resource Web Page

Bioinformatics and Other Fields Biology Computer Science Information Management Biochemistry Molecular Bioinformatics Biology Biophysics Numerical Computing Theoretical CS Machine Learning Data Mining Applied Mathematics & Statistics

Topics in Bioinformatics …In this paper, we report the discovery of a new gene that affects DNA reproduction in … Genes Biology Literature … Gene expression & regulation DNA Sequences Microarray data AATTCATGAAAATCGTATACTGGT ACCGGC TGAGAAAATGGCAGAGCTCATCGCTA AAGGTA TCTGGTAAAGACGTCAACACCATCAA CGTGTC ACATCGATGAACTGCTGAACGAAGAT ATCCTG TTGCTCTGCCATGGGCGATGAAGTTC TCGAGG Genomics Transcriptomics … Text Mining Proteins (Function) Protein Sequences MKIVYWSGTGNTEKMAELIAKGIIE SGKDV DELLNEDILILGCSAMGDEVLEESE FEPFIE KVALFGSYGWGDGKWMRDFEER MNGYG PDEAEQDCIEFGKKIANI Proteomics

Sample Topic 1: Sequence Alignment Multiple sequence alignment of 7 neuroglobins using clustalx

Sample Topic 2: Microarray data clustering

Take Away Messages • Bioinformatics is a growing field • Many job/funding opportunities • Many open problems to be solved • It’s never too late to learn about bioinformatics