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Introduction to Bioinformatics

Technology
1 of 22
Bioinformatics ,[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Outline http://gila.engr.uic.edu/bioinformatics/
DNA Protein Nucleotides sequence Gene expression = Protein production
Exons & Introns STOP F R L
Biological Diversity Bacteria Fruit Fly Human Yeast
The Genetic Code ,[object Object],[object Object]
From protein sequence to Structure ,[object Object],=
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Bioinformatics http://gila.engr.uic.edu/bioinformatics/
[object Object],[object Object],[object Object],[object Object],[object Object],Bioinformatics in BioE http://gila.engr.uic.edu/bioinformatics/
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Research
Gene expression Computational analysis of cDNA microarray expression profiles ~26,000 genes in one experiment
Functional correlation in clusters 1. Cell division 2. cell signaling/cell communication 3. cell structure/motility 4. cell/organism defense 5. gene/protein expression 6. metabolism 7. unclassified ,[object Object],[object Object]
How Proteins Interfaces with Other Molecules ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Research – structure & function
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Structural genomics/proteomics
Voronoi Diagram and Delaunay Triangulation Geometry based approach for functional motifs Discrete Flow
3D alpha shapes (HIV-1 protease)‏
What is an algorithm? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Are computers fast enough? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Pockets in Ribonuclease A
A Server for Identification of Protein Pockets & Cavities CASTp http://cast.engr.uic.edu/ Users of CASTp: Columbia, Harvard, Mayo Clinic, Princeton, Stanford, U Penn, SUNY Stony Brook, Texas A&M, UCIrvine, UBC, Virginia Tech, Yale, Abbott Lab, Pfizer, SmithKline Beecham, ... Agouron, Emisphere, Vertex, ... Kyoto U, Cambridge, European Molecular Biology Lab, INRA (France), Pasteur-Lille, Uppsala, Weizman,... Brazil, Czech, Korea, Turkey, ...
CASTp Results ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],http://cast.engr.uic.edu/
THANK YOU

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Bioinformatics

  • 1.
  • 2.
  • 3. DNA Protein Nucleotides sequence Gene expression = Protein production
  • 4. Exons & Introns STOP F R L
  • 5. Biological Diversity Bacteria Fruit Fly Human Yeast
  • 6.
  • 7.
  • 8.
  • 9.
  • 10.
  • 11. Gene expression Computational analysis of cDNA microarray expression profiles ~26,000 genes in one experiment
  • 12.
  • 13.
  • 14.
  • 15. Voronoi Diagram and Delaunay Triangulation Geometry based approach for functional motifs Discrete Flow
  • 16. 3D alpha shapes (HIV-1 protease)‏
  • 17.
  • 18.
  • 20. A Server for Identification of Protein Pockets & Cavities CASTp http://cast.engr.uic.edu/ Users of CASTp: Columbia, Harvard, Mayo Clinic, Princeton, Stanford, U Penn, SUNY Stony Brook, Texas A&M, UCIrvine, UBC, Virginia Tech, Yale, Abbott Lab, Pfizer, SmithKline Beecham, ... Agouron, Emisphere, Vertex, ... Kyoto U, Cambridge, European Molecular Biology Lab, INRA (France), Pasteur-Lille, Uppsala, Weizman,... Brazil, Czech, Korea, Turkey, ...
  • 21.