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Introduction to Bioinformatics

Introduction to Bioinformatics. (Lecture for CS498-CXZ Algorithms in Bioinformatics) Aug. 25, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign. Outline. What is bioinformatics? Why is bioinformatics important? Bioinformatics and other fields

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Introduction to Bioinformatics

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

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

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

  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

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