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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

Algorithms in Computational Biology

Tanya Berger-Wolf

Compbio.cs.uic.edu/~tanya/teaching/CompBio

January 13, 2006


Outline

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

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

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

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


Compbio and other fields

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


Topics in bioinformatics

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


Sample topic 1 sequence alignment

Sample Topic 1: Sequence Alignment

Multiple sequence alignment of 7 neuroglobins using clustalx


Sample topic 2 population genetics

Sample Topic 2: Population Genetics

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Brothers!

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Take away messages

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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