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Algorithms in Computational BiologyAlgorithms in Computational Biology
Tanya Berger-WolfTanya Berger-WolfCompbio.cs.uic.edu/~tanya/teaching/CompBioCompbio.cs.uic.edu/~tanya/teaching/CompBio
January 13, 2006January 13, 2006
Outline
• What is computational biology?
• Computational Biology vs Bioinformatics
• Why is computational biology important?
• CompBio and other fields
• Topics in CompBio
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
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 …
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
Theoretical CS
CompBio and Other Fields
MolecularBiology
Machine LearningData Mining
Information Management
Biophysics
Bioinformatics/CompBio
Biochemistry
Applied Mathematics & Statistics
Biology Computer Science
Numerical Computing
Topics in Bioinformatics
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MKIVYWSGTGNTEKMAELIAKGIIESGKDVDELLNEDILILGCSAMGDEVLEESEFEPFIEKVALFGSYGWGDGKWMRDFEERMNGYGPDEAEQDCIEFGKKIANI
Genes Proteins (Function)Gene expression & regulation
Microarray dataDNA Sequences
1.2 2.2 ...1.53.2 2.0 ...5.6....0.5 1.5 ... 4.3
Protein Sequences
…In this paper, we report the discovery of a new gene that affects DNA reproduction in …
……Biology Literature
Genomics ProteomicsTranscriptomics
Text Mining