1. Introduction to Bioinformatics (Lecture for CS498-CXZ Algorithms in Bioinformatics) Aug. 25, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign

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

3. 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

4. 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 …

5. 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

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

7. Topics in Bioinformatics AATTCATGAAAATCGTATACTGGTCTGGTACCGGC TGAGAAAATGGCAGAGCTCATCGCTAAAGGTA TCTGGTAAAGACGTCAACACCATCAACGTGTC ACATCGATGAACTGCTGAACGAAGATATCCTG TTGCTCTGCCATGGGCGATGAAGTTCTCGAGG MKIVYWSGTGNTEKMAELIAKGIIESGKDV DELLNEDILILGCSAMGDEVLEESEFEPFIE KVALFGSYGWGDGKWMRDFEERMNGYG PDEAEQDCIEFGKKIANI GenesProteins (Function) Gene expression & regulation Microarray data DNA Sequences Protein Sequences …In this paper, we report the discovery of a new gene that affects DNA reproduction in … … … Biology Literature GenomicsProteomics Transcriptomics Text Mining

8. Topics in Bioinformatics AATTCATGAAAATCGTATACTGGTCTGGTACCGGC TGAGAAAATGGCAGAGCTCATCGCTAAAGGTA TCTGGTAAAGACGTCAACACCATCAACGTGTC ACATCGATGAACTGCTGAACGAAGATATCCTG TTGCTCTGCCATGGGCGATGAAGTTCTCGAGG MKIVYWSGTGNTEKMAELIAKGIIESGKDV DELLNEDILILGCSAMGDEVLEESEFEPFIE KVALFGSYGWGDGKWMRDFEERMNGYG PDEAEQDCIEFGKKIANI GenesProteins (Function) Gene expression & regulation Microarray data DNA Sequences Protein Sequences …In this paper, we report the discovery of a new gene that affects DNA reproduction in … … … Biology Literature GenomicsProteomics Transcriptomics Text Mining

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

10. Sample Topic 2: Microarray data clustering

11. 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