1. Components of a Cell (Eukaryotes) Picture from on-line biology book,on-line biology book, http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html ~70% water 4% small molecules 15-20% proteins 2-7% DNA/RNA 4-7% membrane

2. Biological databases Data explosion - 96 new 83 updates of well established databases in 201196 new 83 updates - exponential growth of the quantity, complexity and diversity of biological data Protein Data Bank (www.pdb.org) - An example of a neuron databaseAn example of a neuron database How to minimize the representation? Earlier individual research oriented databases vs. large scale industrial like databases

3. Biological databases Primary Databases : - nucleic acid sequences including whole genomes - amino acid sequences of proteins - protein and nucleic acid structures - small molecule crystal structures - protein functions - expression of genes - networks: of metabolic pathways, of gene and protein interactions, of control cascades - publications Specialized Databases

4. Computations in Proteomics Introduction to MSIntroduction Newer Techniques Mass spectrometry (MS) - large scale of study of proteins - anytime, any cells Determination of the content in a complex of proteins Determination of protein-protein interactions

5. Computations in Proteomics Enright et al., Nature 402 p86-90 Protein-protein interactions - Use genomic sequences fusion event detection through computation Modeling gene regulatory networkgene regulatory network - nodes: genes/proteins - edges: biological events - inputs: proteins (eg. transcription factors) - outputs: gene expression

6. Microarry Data Microarray technologyMicroarray Microarray gene expression databases (eg. GEO GSE17913), interested in co-expression of genes, relationship of genes,GEO system biologysystem biology, pathways PubMed literature databasesPubMed Extract the knowledge from literatures, text mining Literature Data

7. Computations in 3D images Imaging techniques - Magnetic Resonance Images (MRI) – good tissue contrast, tumor detection, 2003 Nobel Price (Paul Lauterbur, Sir Peter Mansfield)Paul LauterburSir Peter Mansfield - CT - Electron tomography (eg. portal proteins)portal proteins 3D Volumetric data - pattern recognition, registration, classification, image retrieval, image data miningpattern recognition

8. Helix Tracer Helix, density map Helix, true structure Protein 1BM1 Del Palu, A., He. J., Pontelli, E., Lu, Y. “Identification of  -helices from Low Resolution Protein Density Map” Proceedings of Computational Systems Bioinformatics (CSB) 2006, p89-98, Stanford University, Aug. 2006.