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

AATTCATGAAAATCGTATACTGGTCTGGTACCGGCTGAGAAAATGGCAGAGCTCATCGCTAAAGGTATCTGGTAAAGACGTCAACACCATCAACGTGTCACATCGATGAACTGCTGAACGAAGATATCCTGTTGCTCTGCCATGGGCGATGAAGTTCTCGAGG

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

Sample Topic 1: Sequence Alignment

Multiple sequence alignment of 7 neuroglobins using clustalx

Sample Topic 2: Population Genetics

Brothers!

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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!