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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

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

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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