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Algorithms in Computational Biology

Algorithms in Computational Biology. Tanya Berger-Wolf Compbio.cs.uic.edu/~tanya/teaching/CompBio January 13, 2006. Outline. What is computational biology? Computational Biology vs Bioinformatics Why is computational biology important? CompBio and other fields Topics in CompBio.

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Algorithms in Computational Biology

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  1. Algorithms in Computational Biology Tanya Berger-Wolf Compbio.cs.uic.edu/~tanya/teaching/CompBio January 13, 2006

  2. Outline • What is computational biology? • Computational Biology vs Bioinformatics • Why is computational biology important? • CompBio and other fields • Topics in CompBio

  3. What is Computational Biology? • No standard definition! • Our definition: computational techniques for biological problems • Data acquisition, management and representation (bioinformatics) • Pattern analysis and data mining (bioinformatics) • Data analysis and optimization • Using bio data to solve other problems (medicine, public policy, etc.) • Computational biology touches all parts of computer science • Databases • Data streaming • HPC and systems • Networking • Algorithms • Privacy and security • Image processing • Visualization http://www.colorbasepair.com/what_is_bioinformatics.html

  4. Why is CompBio Important? • Biology perspective • More and more biological information is available => need for effectively accessing and using the information • As more detailed information is available different questions can be asked (models of evolution) => requires new math • Computer science perspective • Excellent application domain • Poses special computational challenges • Brings computer science closer to scientific discovery • Currently growing …

  5. The Growing Field of CompBio • Research: Universities are expanding research programs in bioinformatics/compbio • Education: New degree programs are being launched • Industry: Pharmaceutical industry has a great interest in bioinformatics • Many job and funding opportunities

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

  7. Topics in Bioinformatics Text Mining Genomics Proteomics Transcriptomics 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. Sample Topic 1: Sequence Alignment Multiple sequence alignment of 7 neuroglobins using clustalx

  9. Sample Topic 2: Population Genetics ? Brothers! ?

  10. Take Away Messages • Computational Biology is a growing field • Many job/funding opportunities • Many open problems to be solved • Actually can do something good for the humanity? – Nah!

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