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Introduction to bioinformatics
- 1. Introduction to Bioinformatics Monthly technical Session Philipp Weber 2014.10.24
- 2. Table of Contents ● Definition ● Recent History ● Basics ● Applications
- 3. Definition Wikipedia: Bioinformatics an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics and engineering to study and process biological data.1 1 http://en.wikipedia.org/wiki/Bioinformatics
- 4. Basics ● What is a cell and how does it work? The nucleus Mitochondrion The lysosome ER - Electroplasmatic reticulum The DNA Ribosome http://www.wormbook.org/chapters/www_intromethodscellbiology/cellfig10.jpg Cytoplasm mRNA
- 5. Basics ● Genetics o 1953 Watson & Crick uncovered DNA α-helix structure o ~ 3’000’000’000 base pairs in human genome o living organisms inherit their genetic properties from their parents o Molecular clock hypothesis o Through comparing DNA in an alignment we can deduce a similarity measure and a common ancestor
- 6. Basics o DNA is packed very tightly o Genetic Code - 3 bases code for one amino-acid o Hundreds of amino-acids code for one protein 29lifescience.wikispaces.com/file/view/ChromosomeStructure.jpg/57692504/659x261/ChromosomeStructure.jpg
- 7. Basics ● Translation from mRNA to a protein The nucleus Mitochondrion The lysosome ER - Electroplasmatic reticulum The DNA Ribosome http://www.wormbook.org/chapters/www_intromethodscellbiology/cellfig10.jpg Cytoplasm mRNA
- 8. Basics ● Translation from mRNA to a protein The nucleus The DNA Ribosome mRNA
- 9. Basics ● Translation detail http://2.bp.blogspot.com/- a1idohPVPFM/UNQ9KqrQHoI/AAAAAAAAASY/rvpAqwKn_ic/s1600/figure+1.pn g
- 10. Basics ● A Protein
- 11. Recent History ● 1978 - Nussinov Algorithm ● 2000 - Human Genome Project ● 2010 - 1000 Genomes Project ● 2014 - First time synthesis of an artificial yeast chromosome http://www.sciencemag.org/content/291/5507/F1.medium.gif
- 12. Applications ● Sequence: o Phylogeny o Gene Finding ● Structure: o Drug Design o Protein Dynamics ● Systems: o Microarrays o Protein Network Inference
- 13. Applications - Phylogeny ● DNA Sequence similarities ● (Re-)construct the evolutionary history ● Problem: Multiple Sequence Alignment Phylogenetic Tree of Life
- 14. Applications - Phylogeny ● Example: o Given a set of taxa X={x1,x2,...,xn} and a distance function d(xi,xj), reconstruct an evolutionary tree 1 2 4 5 3 8 9 6 7 1 2 3 4 5 UPGMA
- 15. Applications - Drug Design ● What is Drug Design? o Design: Deliberate creative act o Drug Design: Design of a drug for a specific (medical) application
- 16. Applications - Drug Design ● Key question: What to put into a pill? ● Problem: Molecular dynamics and optimization
- 17. Applications - Drug Design ● Drug Discovery Pipeline Biol. Data Target ID Lead ID Optimization Testing Approval Accelerated by Bioinformatics
- 18. Applications - Microarrays http://sgugenetics.pbworks.com/f/1366505822/cDNAarray.gif
- 19. Applications - Microarrays ● Samples labeled o Experimental o Control o When same expression level: Yellow https://genome.unc.edu/images/microarray.jpg
- 20. Applications - PPIs ● Combining multiple experiments to a graph ● Problem: Network Inference
- 21. Applications ● Solution to high complexity / runtime problems: Use heuristical methods and dynamic programming ● Metropolis Monte Carlo ● => Blast
- 22. Applications “And thats why we need a Computer”
- 23. Thank you for your attention!
- 24. Sources: 1 http://en.wikipedia.org/wiki/Bioinformatics 2 Narayana Annaluru et al.: Total Synthesis of a Functional Designer Eukaryotic Chromosome. In: Science. 344, Nr. 6179, 2014, S. 55–58
- 25. Applications ● How hard / complex are these problems? ● Multiple Sequence Alignment: o NP-complete - O(length#sequences) ● Molecular Dynamics simulation: o naive scales O(#particles2)
Notes de l'éditeur
- Simple Model of a cell - a lot of things going on in different parts of the cell and what kind of cell we are looking at Care most about Nucleus with DNA, Ribosomes and Cytoplasm on the right is a less simplified version of a cell
- 1869 dicovered nuclein in Tuebingen, 1953 Watson and Crick
- Next: History
- Simple Model of a cell - a lot of things going on in different parts of the cell and what kind of cell we are looking at Care most about Nucleus with DNA, Ribosomes and Cytoplasm on the right is a less simplified version of a cell
- Simple Model of a cell - a lot of things going on in different parts of the cell and what kind of cell we are looking at Care most about Nucleus with DNA, Ribosomes and Cytoplasm on the right is a less simplified version of a cell
- Simple Model of a cell - a lot of things going on in different parts of the cell and what kind of cell we are looking at Care most about Nucleus with DNA, Ribosomes and Cytoplasm on the right is a less simplified version of a cell
- Simple Model of a cell - a lot of things going on in different parts of the cell and what kind of cell we are looking at Care most about Nucleus with DNA, Ribosomes and Cytoplasm on the right is a less simplified version of a cell
- Human Genome Project 300 Mio $ - 13 years - new technologies have emerged and we are even able to replicate an artificial yeast chromosome - next: Applications
- MSA - length#sequences complexity,
- Clustering problem, reconstruction of trees - NEXT Another application of Bioinformatics
- NP-complete problem - Dynamic Programming to the rescue
- Disease we want to cure, like a special kind of cancer. Target is a special cancer supressor protein p53, examine possible substances that increase effectiveness of p53 - try to optimize them 10 - 15 years and costs of up to 870 Million US$ - NEXT Application Microarrays