Introduction to Bioinformatics
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This document provides an introduction to the field of bioinformatics. It defines bioinformatics as the merging of biology, computer science, and information technology into a single discipline. The document outlines key topics in bioinformatics including what is bioinformatics, why it is needed due to the growth of sequencing data, common data types and analysis problems, careers in bioinformatics, and different sequencing technologies such as Illumina and SOLiD sequencing.
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Introduction to Bioinformatics
- 1. Introduction to Bioinformatics Niema Moshiri and Argus Athanas
- 4. Original Bioinformatics Definition • It seemed to us that one of the defining properties of life was information processing in its various forms, e.g., information accumulation during evolution, information transmission from DNA to intra- and intercellular processes, and the interpretation of such information at multiple levels. Hogeweg, P. The Roots of Bioinformatics in Theoretical Biology. PLoS Comput Bio. 2011.
- 5. National Center for Biotechnology Information (NCBI) • Bioinformatics – Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. • Computational Biology – The actual process of analyzing and interpreting data is referred to as computational biology.
- 6. Why Do We Need Bioinformatics? http://www.philcallaway.ab.ca/images/Cartoons/privacy%20cartoon2.jpg
- 8. Sequencing Data Types • DNA-Seq • RNA-Seq • ChIP-Seq • Methyl-C-Seq • Dnase Hypersensitivity • Hi-C • smRNA-Seq http://www.biomics.nl/images/illuminahiseq.jpg
- 12. Bioinformatics Problems • Sequence Alignment • Genetic Variation Detection • Phylogenetics • Gene Expression Analysis http://www.youtube.com/watch?v=RpuTps9OumQ&feature=related
- 13. Bioinformatics in the News • A New Bioinformatics System Improves Medical Diagnosis – http://www.sciencedaily.com/releases/2011/06/110628094833. htm • Pacific Biosciences Contributes Whole Genome Sequence Data for German E. Coli Outbreak Strain and 11 Related Strains for Comparative Analysis – http://www.marketwatch.com/story/pacific-biosciences- contributes-whole-genome-sequence-data-for-german-e-coli- outbreak-strain-and-11-related-strains-for-comparative-analysis- 2011-07-06?reflink=MW_news_stmp • Initiative Launched to Sequence 5,000 Insects – http://www.genomeweb.com/sequencing/initiative-launched- sequence-5000-insects
- 14. Preparing for a Career in Bioinformatics • Try a whole bunch of stuff! • Don’t give up on math • Learn/understand Computer Science • Don’t forget, the biology is what people care about http://www.youtube.com/watch?v=kZ3y8e676cw&feature=related
- 15. Where Can You Work In Bioinformatics? http://www.tomhcanderson.com/wp-content/uploads/2010/11/textminingacademia.jpg http://www.freefoto.com/images/13/53/13_53_21---Sunset--Teesside-Industry_web.jpg http://www.youtube.com/watch?v=ydXLP3MlO58 http://www.youtube.com/watch?v=dJrpSvsFXFI
- 16. Gene Patenting http://www.cbsnews.com/video/watch/?id=6362525n •Requirements for a patent •Novelty, Usefulness, and Nonobvious •Dr. Picard, through an intense genomic analysis of many patients, has recently isolated a gene from humans that is responsible for providing immunity to HIV. Recognizing the obvious therapeutic benefits this gene might hold, he files a patent request with the US patent office. •Should Dr. Picard’s patent be accepted? •If Dr. Picard’s patent is accepted, what should other researchers and companies be allowed to do with his gene (i.e., what kinds of research and products can they develop)? •What are the pros and cons of allowing Dr. Picard to patent his discovery?
- 18. Central Dogma of Biology http://library.thinkquest.org/C0122429/pictures/centraldogma2.gif The central dogma of molecular biology deals with the detailed residue- by-residue transfer of sequential information. It states that information cannot be transferred back from protein to either protein or nucleic acid. Crick F (August 1970). "Central dogma of molecular biology.". Nature 227 (5258): 561–3.
- 19. Molecule of Inheritance Image:http://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Griffith_experiment.svg/716px- Griffith_experiment.svg.png Experiment: Avery, MacLeod, and McCarty (1944). "Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III". Journal of Experimental Medicine 79 (1): 137–158.
- 20. The Case for DNA http://www.visionlearning.com/library/modules/mid149/Image/VLObject-3756-080922120939.jpg
- 21. The Structure of DNA Experiment: Watson J.D. and Crick F.H.C. (1953). "A Structure for Deoxyribose Nucleic Acid" (PDF). Nature 171 (4356): 737–738. Image: http://shs.westport.k12.ct.us/forensics/10-dna/dna_molecule.gif
- 23. The Organization of DNA http://www.med.unc.edu/~bstrahl/chromatin.png
- 27. What are the first 10 bases of this DNA sequence?
- 34. SOLiD Sequencing
- 35. SOLiD Sequencing
- 36. SOLiD Sequencing
- 37. Pacific Biosciences Sequencing • http://www.youtube.com/watch?v=v8p4ph2 MAvI
- 38. Other Sequencing Technologies • 454 • Oxford Nanopore • Ion Torrent