american gut - omicron

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  1. 1. theRNAfortaxonomicubiquitousconserved and
  2. 2. A microbe dominated worldThe universal nature of biochemistry. Pace NR.Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):805-8.
  3. 3. A microbe dominated worldLozupone and Knight PNAS. 2007 Jul 3;104(27):11436-40
  4. 4. A microbe dominated worldLey et al Nat Rev Microbiol. Oct 2008; 6(10): 776788
  5. 5. How human are we, really?Hamady, 2009, PhD thesis
  6. 6. How human are we, really?Hamady, 2009, PhD thesis
  7. 7. How human are we, really?Hamady, 2009, PhD thesis
  8. 8. Costello et al. Science 326, 1694 (2009)
  9. 9. Photo credit: Steve Miller, CIRES
  10. 10. https://commons.wikimedia.org/wiki/File:Wallacea.png
  11. 11. Fierer et al. PNAS. 2010 Apr 6;107(14):6477-81
  12. 12. Fierer et al. PNAS. 2010 Apr 6;107(14):6477-81
  13. 13. Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7
  14. 14. Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7
  15. 15. HMP HMPYatsunenko et al. Nature. 2012 May 9;486(7402):222-7
  16. 16. Koeing et al. Proc Natl Acad Sci U S A. 2011 Mar 15;108
  17. 17. Video fun time!Full version here: http://www.youtube.com/watch?v=Pb272zsixSQ
  18. 18. HMP: Human Microbiome Project (2012, Nature 486: 202-214) GG: Global Gut (2012, Nature 486: 222-228) PGP: Personal Genome Project (unpublished) AGP: American Gut Project (unpublished)http://microbio.me/americangut/img/mod1_main.pdf
  19. 19. http://microbio.me/americangut/img/mod1_main.pdf
  20. 20. ICU Microbiome pilot International Nutritional Survey 5 sites around the world Multiple time points Rich patient metadata
  21. 21. Autism spectrum cohort of the American Gut 269 families to receive samples Conjunction with ASD-clinicians Donations for ASD-affected and neurotypical siblingscovered by Jack Gilbert
  22. 22. *
  23. 23. Analyses are executable, reproducible, andBSD-licensed
  24. 24. An Introduction to AppliedBioinformatics
  25. 25. The American Gut ConsortiumThe Knight LabProf. Rob KnightProf. Greg CaporasoProf. Jack GilbertProf. Tim SpectorDr. Victoria VazquezProf. Paul WischmeyerDr. Antonio GonzalezDr. Gail AckermannYoshiki Vzquez-BaezaDr. Jess MetcalfDr. Katie AmatoAcknowledgementsdaniel.mcdonald@colorado.eduTwitter: @mcdonadtGithub: @wasadewww: http://wasade.github.io
  26. 26. Links and questionsProjects of interest: Earth Microbiome Project (http://earthmicrobiome.org) American Gut Project (http://americangut.org) British Gut Project (http://britishgut.org)daniel.mcdonald@colorado.eduTwitter: @mcdonadtGithub: @wasadewww: http://wasade.github.ioKey labs: Knight Lab (http://knightlab.colorado.edu) Caporaso Lab (http://caporasolab.us) Spector Lab (http://www.tim-spector.co.uk/)Education: Courseras Gut Check (https://www.coursera.org/course/microbiome) Intro. to Appl. Bioinformatics (http://caporasolab.us/An-Introduction-To-Applied-Bioinformatics/)Useful software projects: Quantitative Insights into Microbial Ecology (http://qiime.org) Qiita (http://qiita.colorado.edu)* biocore (http://github.com/biocore) scikit-bio (http://scikit-bio.org) EMPeror (http://emperor.colorado.edu)*Soon to be opened for the general public