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Bioinformatics For MNW 2 nd Year

This document outlines the Integrative Bioinformatics course for 2nd year MNW students at VU, offered in Spring 2003. It covers essential topics including pattern recognition, supervised and unsupervised learning, protein structure prediction, and molecular interactions. The course emphasizes data analysis techniques such as sequence alignment, clustering, and principal component analysis, along with applications in genomics and proteomics. Students will engage with bioinformatics method development, programming, and computational challenges throughout the curriculum, fostering a comprehensive understanding of bioinformatics in the life sciences.

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Bioinformatics For MNW 2 nd Year

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  1. Bioinformatics For MNW 2nd Year Jaap Heringa FEW/FALW Integrative Bioinformatics Institute VU (IBIVU) heringa@cs.vu.nl, www.cs.vu.nl/~ibivu, Tel. 47649, Rm R4.41

  2. Current Bioinformatics Unit • Jens Kleinjung (1/11/02) • Victor Simosis – PhD (1/12/02) • Radek Szklarczyk - PhD (1/01/03) • John Romein (1/12/02, Henri Bal)

  3. Bioinformatics course 2nd year MNW spring 2003 • Pattern recognition • Supervised/unsupervised learning • Types of data, data normalisation, lacking data • Search image • Similarity tables • Clustering • Principal component analysis • Discriminant analysis

  4. Bioinformatics course 2nd year MNW spring 2003 • Protein • Folding • Structure and function • Protein structure prediction • Secondary structure • Tertiary structure • Function • Post-translational modification • Prot.-Prot. Interaction -- Docking algorithm • Molecular dynamics/Monte Carlo

  5. Bioinformatics course 2nd year MNW spring 2003 • Sequence analysis • Pairwise alignment • Dynamic programming (NW, SW, shortcuts) • Multiple alignment • Combining information • Database/homology searching (Fasta, Blast, Statistical issues-E/P values)

  6. Bioinformatics course 2nd year MNW spring 2003 • Gene structure and gene finding algorithm • Omics • DNA makes RNA makes protein • Expression data, Nucleus to ribosome, translation, etc. • Metabolomics • Physiomics • Databases • DNA, EST • Protein sequence • Protein structure

  7. Bioinformatics course 2nd year MNW spring 2003 • Microarray data • Protein structure (PDB) • Proteomics • Mass spectrometry/NMR/X-ray?

  8. Bioinformatics course 2nd year MNW spring 2003 • Bioinformatics method development • IPR issues • Programming and scripting languages • Web solutions • Computational issues • NP-complete problems • CPU, memory, storage problems • Parallel computing • Bioinformatics method usage/application • Molecular viewers (RasMol, MolMol, etc.)

  9. Gathering knowledge Rembrandt, 1632 • Anatomy, architecture • Dynamics, mechanics • Informatics (Cybernetics – Wiener, 1948) (Cybernetics has been defined as the science of control in machines and animals, and hence it applies to technological, animal and environmental systems) • Genomics, bioinformatics Newton, 1726

  10. Bioinformatics Chemistry Biology Molecular biology Mathematics Statistics Bioinformatics Computer Science Informatics Medicine Physics

  11. Bioinformatics “Studying informational processes in biological systems” (Hogeweg, early 1970s) • No computers necessary • Back of envelope OK “Information technology applied to the management and analysis of biological data” (Attwood and Parry-Smith) Applying algorithms with mathematical formalisms in biology (genomics) -- USA

  12. Bioinformatics in the olden days • Close to Molecular Biology: • (Statistical) analysis of protein and nucleotide structure • Protein folding problem • Protein-protein and protein-nucleotide interaction • Many essential methods were created early on (BG era) • Protein sequence analysis (pairwise and multiple alignment) • Protein structure prediction (secondary, tertiary structure)

  13. Bioinformatics in the olden days (Cont.) • Evolution was studied and methods created • Phylogenetic reconstruction (clustering – NJ method

  14. The Human Genome -- 26 June 2000

  15. The Human Genome -- 26 June 2000 Dr. Craig Venter Celera Genomics -- Shotgun method Sir John Sulston Human Genome Project

  16. Human DNA • There are about 3bn (3  109) nucleotides in the nucleus of almost all of the trillions (3.5  1012 ) of cells of a human body (an exception is, for example, red blood cells which have no nucleus and therefore no DNA) – a total of ~1022 nucleotides! • Many DNA regions code for proteins, and are called genes (1 gene codes for 1 protein in principle) • Human DNA contains ~30,000 expressed genes • Deoxyribonucleic acid (DNA) comprises 4 different types of nucleotides: adenine (A), thiamine (T), cytosine (C) and guanine (G). These nucleotides are sometimes also called bases

  17. Human DNA (Cont.) • All people are different, but the DNA of different people only varies for 0.2% or less. So, only 2 letters in 1000 are expected to be different. Over the whole genome, this means that about 3 million letters would differ between individuals. • The structure of DNA is the so-called double helix, discovered by Watson and Crick in 1953, where the two helices are cross-linked by A-T and C-G base-pairs (nucleotide pairs – so-called Watson-Crick base pairing).

  18. Tot hier 03/02/2003 – 10.45-12.30

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