Moore Notes 5 19 10

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Group Call

  • June meeting:
    • fly in Weds evening June 23
    • start Weds morning June 24
    • finish by 4pm June 25
  • Katie: Report on Cold Spring Harbor Biology of Genomes meeting
    • Metagenomics talks:
      • HMP DACC (Jennifer Wortman)
      • Vibrio speciation: ecotypes driven by just a few genes (Jesse Shapiro/Martin Polz)
      • H. pylori - human signaling, loss of H. pylori and allergies vs. cancer (Martin Blaser - key note)
    • posters: viral enrichment (Bjorn Andersson), GPU blastx (Wash U), HMP summary (Erica Sodergren/George Weinstock)
    • new collaborations/contacts: HMP, Eric Alm's lab
  • James' Ecology Letters paper was highlighted in Nature's journal club, is posted on GBMF website
  • Amber Hartman's WATERS workflow paper was accepted
  • Jessica will visit Bay Area week of July 12
  • Tom: OTU paper draft
    • feedback on methods/results requested
    • intro/discussion plan
      • phylogeny based clustering (vs. tree to get distance matrix), PD (vs. OTUs)
      • necessity of phylogenetic distance vs. benefit over % identity in terms of recapitulating taxonomy (and not overestimating diversity)
      • Hans Peter Klank paper
  • Josh: distance-decay paper draft
    • Steve: could do model selection to see what parameters are necessary to get good model fit
    • Steve: do the models depend mostly on proportion of shared species, is this a "natural metric"? What about metrics that aren't based on the quantities you model?