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Bio 5488 Genomics

Course Web Site. http://www.genetics.wustl.edu/bio5488/home.htmlLinux PrimerLecture notes (if available)Schedule (changes)Weekly Assignments and AnswersWeekly Readings. Computer Labs. 1

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Bio 5488 Genomics

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    1. Bio 5488 Genomics Mon, Wed 10:00-11:30 am, Rm 823 McDonnell Fri., 10:00-11:30 am, 12:00-1:30 pm, Rm 109 CCB

    2. Course Web Site http://www.genetics.wustl.edu/bio5488/home.html Linux Primer Lecture notes (if available) Schedule (changes) Weekly Assignments and Answers Weekly Readings

    3. Computer Labs 1 ½ hours each Friday (10:00-11:30, 12:00-1:30) Room 109 In the CCB, 700 S. Euclid Access to the bldg. through card key entrance Access to the room through card key on the door Weekly computer assignments

    4. Grading 4 credit ¼ midterm ¼ final ½ weekly assignments

    5. Today’s Outline Introduction to Genomics Being Quantitative A case study on the differences between humans and chimps

    6. Part I, Introduction to Genomics?

    7. Some History On Reading Genomes 1951, Fred Sanger, Amino Acid Sequence of Insulin 1960’s, Crick, Brenner, Yanofsky, Nirenberg, Matthaei, The Genetic Code 1972, Margret Dayhoff, First Protein Database 1977, Maxim/Gilbert and Fred Sanger, DNA sequencing 1977, Fred Sanger, Complete sequence of phage ?X174 1979, Walter Goad, First implementation of Genbank 1989, NHGRI, Human Genome Project initiated 1990, Altschul/Gish/Miller/Myers/Lipman, BLAST

    8. 169 Genomes Done! 788 more started! 1995, Haemophilus influenzae 1996, Methanococcus jannaschii 1997, Saccharomyces cerevisiae 1997, Escherichia coli 1998, Caenorhabditis elegans 2000, Drosophila melanogaster 2000, Arabidopsis thaliana 2001, Homo sapiens 2002, Schizosaccharomyces pombe 2002, Oryza sativa 2002, Plasmodium falciparum 2002, Mus musculus

    9. Host-Pathogen Interactions Anopheles, Plasmodium, Homo sapiens Horizontal Transfer Yersini pestis (plague) Alternative Energy Sources Chlorobium tepidum (green sulfur bacterium) Extremeophiles Halobacterium, Deinococcus radiodurans, Pyrococcus furiosis Genomics and the return of “cool” biology

    10. Thinking Genomics

    11. Part II, Thinking Quantitatively

    12. From Mendel To Matricies…. Biology Is A Quantitative Science!!! Mendel’s Laws Chargaff’s Rules

    13. Thinking Quantitatively Spaces Signal to Noise Ratio Distributions Parametric Versus Nonparametric Data The P value Statistics and Probability

    14. Spaces

    15. Signal to Noise

    16. Distributions (Histograms)

    17. Parametric Versus Nonparametric Data Parametric Distributions Can be described by a standard equation Examples. Normal, Poisson, Binomial Nonparametric Distributions Irregular or highly skewed distributions Usually analyzed by Chi-Square or by simulation (bootstrap)

    18. The P value *for discreet variables

    19. “There Are Three Kinds of Lies: Lies, Damned Lies, and Statistics” Comparing averages Comparing variation

    20. “The most important questions of life are …really only problems of probability.”

    21. Part III, What makes organisms different from each other?

    22. Humans and Chimps

    23. Chimps Are Resistant To Many Human Diseases

    24. Edward Tyson

    25. Sir Richard Owen

    27. The 20th Century Comparison of human and chimps

    28. Complexity, Genome Size and the C-value Paradox www.genomesize.com

    29. Complexity and Gene Number

    30. Gene Finding Is Still An Art de novo, in silico Comparative genomics ESTs and cDNAs

    31. What about human/chimp specific genes? Only 14 out of 731 genes on mouse chromosome 16 have no human homolog (Celera) Many genes specific to the mouse are olfactory receptors, also some differences in immunity and reproduction

    32. What about organism specific variants?

    33. FOXP2, The Human Speech Gene?

    34. Sialic Acid Biology an example of database mining Chou et al. (1998) Proc. Natl. Acad. Sci. USA 95, 11751-11756 Apes have lots of Neu5Gc, humans very little Neu5Gc is located on the surface of epithelial cells Neu5Gc is present in very low levels in the brain even in animals that have lots of Neu5Gc

    35. Differences in Gene Expression in the Brain?

    36. The Modern Family?

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