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. Theoretical CS CompBio and Other Fields Molecular Biology Machine Learning Data Mining Information Management Biophysics Bioinformatics/ CompBio 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. 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!