Moore Notes 5 19 10

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?