Moore Notes 5 11 15

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Group Call

  • Participants: Katie, Tom, Jonathan, Sarah, Patrick, Dongying, Stephen
  • GBMF:
    • Software release report:
      • Last June
      • Post new things to wiki
    • Progress report
    • No-cost extension
  • Shotmap revisions
    • Expanded IBD analysis with population of additional samples
      • CD separates out from UC and healthy in PCA plot
      • No longer see lower functional richness
      • Patrick will repeat statistical tests
    • Tom working on software items
    • Stephen is handling simulation items
  • Tom: clade distributions project
    • Phylogeny aware microbial distributions
    • Motivation:
      • Sparsity (correlations maybe more meaningful at less granular level)
      • Multiple testing correction (fewer tests if use ancestral vs. leaf nodes)
      • Properties of clades (versus OTUs)
      • Identifying core taxa
      • Co-diversification of microbiome with host/environment
      • Hypotheses about interacting clades
    • Related work:
    • Proof-of-principal study with Muegge et al (2011) data on six non-human primates
      • 11 clades common to all samples (one within Prevotella)
      • Clades co-vary across samples
    • Tree building and traversal is slow and error prone
      • Traverse reference tree
      • Place reads (slow)
        • Iterate over phyla?
        • Classify reads into reference OTUs (green genes tree)
        • Need to validate accuracy
      • Build clade abundance matrix from edge to clade matrix
        • KP: Use pplacer probabilities rather than hard assignments
        • Patrick: non-independence of tests
    • JE: Apply to marker genes in metagenomes, not just 16S, for more novelty and resolution