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TTh  11:00-12:15 in Clark S361 Profs: Serafim Batzoglou, Gill Bejerano

TTh  11:00-12:15 in Clark S361 Profs: Serafim Batzoglou, Gill Bejerano TAs: George Asimenos, Cory McLean. Lecture 13. Insulators in the Human Genome Discuss Project Co-option. Insulators: A Reminder. CTCF. [Ohlsson et al., 2001]. The Glass Ceiling. [Ohlsson et al., 2001].

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TTh  11:00-12:15 in Clark S361 Profs: Serafim Batzoglou, Gill Bejerano

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  1. TTh  11:00-12:15 in Clark S361 Profs: Serafim Batzoglou, Gill Bejerano TAs: George Asimenos, Cory McLean http://cs273a.stanford.edu [Bejerano Spr06/07]

  2. Lecture 13 • Insulators in the Human Genome • Discuss Project • Co-option http://cs273a.stanford.edu [Bejerano Spr06/07]

  3. Insulators: A Reminder http://cs273a.stanford.edu [Bejerano Spr06/07]

  4. CTCF [Ohlsson et al., 2001] http://cs273a.stanford.edu [Bejerano Spr06/07]

  5. The Glass Ceiling [Ohlsson et al., 2001] http://cs273a.stanford.edu [Bejerano Spr06/07]

  6. ChIP-chip reminder http://cs273a.stanford.edu [Bejerano Spr06/07]

  7. Breaking the Glass Ceiling [Kim et al., 2007] http://cs273a.stanford.edu [Bejerano Spr06/07]

  8. A known locus http://cs273a.stanford.edu [Bejerano Spr06/07]

  9. More & less interesting correlations http://cs273a.stanford.edu [Bejerano Spr06/07]

  10. Outliers http://cs273a.stanford.edu [Bejerano Spr06/07]

  11. Consensus! http://cs273a.stanford.edu [Bejerano Spr06/07]

  12. Not all are captured http://cs273a.stanford.edu [Bejerano Spr06/07]

  13. From in vitro to in silico [Xie et al., 2007] http://cs273a.stanford.edu [Bejerano Spr06/07]

  14. http://cs273a.stanford.edu [Bejerano Spr06/07]

  15. http://cs273a.stanford.edu [Bejerano Spr06/07]

  16. http://cs273a.stanford.edu [Bejerano Spr06/07]

  17. http://cs273a.stanford.edu [Bejerano Spr06/07]

  18. Genomic Distribution of Ultraconserved Elements • exonic • non • possibly Origins? http://cs273a.stanford.edu [Bejerano Spr06/07]

  19. Uniquely Abundant in Coelacanth Upto 80%id between Coelacanth instances and some human instances, inc uc.338. ? x 100 diverged copies in a Gigabase 60 highly similar copies in a Megabase http://cs273a.stanford.edu [Bejerano Spr06/07]

  20. Repeats / obile Elements ("selfish DNA") Human Genome: 3*109 letters 1.5% known function >50% junk http://cs273a.stanford.edu [Bejerano Spr06/07]

  21. The LF SINE (for Lobefin Fish / “Living Fossil”) not similar to any known repeat out back Reconstruction target site duplications http://cs273a.stanford.edu [Bejerano Spr06/07]

  22. To Be Continued…. http://cs273a.stanford.edu [Bejerano Spr06/07]

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