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Miracles can be achieved by mixture modelling of messy data..

Miracles can be achieved by mixture modelling of messy data. Chromopainter/FineSTRUCTURE/Globetrotter. Mixture modelling of an English palette. How does the information from metagenomics compare with what we would know if we had full genome sequences?. Not quite a metagenomics experiment.

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Miracles can be achieved by mixture modelling of messy data..

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  1. Miracles can be achieved by mixture modelling of messy data.. Chromopainter/FineSTRUCTURE/Globetrotter

  2. Mixture modelling of an English palette

  3. How does the information from metagenomics compare with what we would know if we had full genome sequences?

  4. Not quite a metagenomics experiment Qizhi Cao, Jianzhong Zhang, China CDC, Xavier Didelot, Imperial College

  5. 18 Helicobacter pylori sequenced from the same biopsy. All of them were different. 2 clades = 2 infections.

  6. Reconstruction of recombination and mutation using ClonalFrame. Average import size 940bp Years in past

  7. Interspersions in recombination events

  8. Functional characterization of recombination events Proportion of genes recombined

  9. Ancestral sequences show interactions between strains in the past And suggest longer mixed infection.

  10. Classical metagenomic questions How many different infections? What proportion of the population does each infection account for? Microevolutionary questions What diversification has each infection undergone? What is the functional effect of diversification? Heroic questions How many infections were there in the past?

  11. Ecological questions Which strains thrive in the same environment? Which strains thrive in the presence of each other? Which strains competitively exclude one another? What determines patterns of „succession“? What determines infection rates by different strains? Ecological genetic questions How do strains adapt to new environments?

  12. Campylobacter in chickens Fran Colles, University of Oxford

  13. Epidemiology of infection amongst a free-range broiler breeder flock: two stages of infection Colles et al. (2011) PLoS One 6(12):e22825

  14. A rapid turnover of Campylobacter STs amongst individual birds Sequence types: Colles et al, Unpublished

  15. Clonal complexes isolated from a broiler breeder flock over time Colles et al, Unpublished

  16. Strains are sampled from a population...

  17. Vibrio parahaemolyticus with Yujun Cui and Ruifu Yang

  18. SNP density in 1Kbp windows All the strains in CG1 The strains in CG1+S093 The strains in CG1+S093+CG2 The strains in CG1+S093+CG2 +1 unrelated strain

  19. Oceanic gene pools

  20. Amongst 53 unrelated strains, strong non-random associations between loci are almost entirely due to close genetic linkage

  21. Not all populations are that simple...

  22. Host-restricted and multihost lineages of C. jejuni

  23. Multihost lineages of C. coli and C. jejuni

  24. Association study Method: Word analysis ST-45 complex

  25. 9034 host associated words in ST-45 complex Map to 99 genes in total but 76% of words map to 10 contiguous genes (region 3)

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