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Reframing Phylogenomics

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Unbiased comparative methods for environmental metagenomics sampling.

(NERC IRF Panel presentation, April 2014)

Published in: Science
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Reframing Phylogenomics

  1. 1. Reframing Phylogenetics Unbiased comparative methods for environmental metagenomics sampling Joe Parker
  2. 2. • My background & track record • Environmental metagenomics – existing problems • Phylogenomics Add Maximum Value To Datasets • Illustrative study Outline
  3. 3. Joe Parker: Novel methods for cutting-edge science High-throughput phylogenomics Parallelised analyses Bayesian statistics Information-theoretic measures NGS datasets Integrating clinical, genetic & molecular data Machine-learning and antigen modeling BaTS software >100 citations ‘000s downloads HADPACK framework in silico HIV vaccine design Clinical trial ABCDet API First genomic convergent evolution demonstration Nature Oct 2013 Public alpha
  4. 4. Throughput & Access Users Users Developers Developers
  5. 5. Mason et al. (2014) Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. The ISME J (epub ahead of print; 23rd Jan 2014; retrieved 1st Mar 2014): doi:10.1038/ismej.2013.254 Metagenomics of an environmental disaster
  6. 6. Comparative approaches
  7. 7. Homology
  8. 8. Deepwater Horizon, revisited Continuous analyses with immediate results Iterative sample collection / analysis; rapid cline detection Exploit phylogenetic methods Detect: population dynamics, adaptive evolution, migration Facilitate NGS Gene functions and Ecosystem services Explicitly model errors Account for paralogy & horizontal transfer Reduce ascertainment bias Unbiased taxon / gene discovery
  9. 9. Dr. Joe Parker Dr. Elizabeth Clare Environmental metagenomics Dr. Steve Rossiter Phylogenomics Prof. Richard Nichols Population genetics Prof. Steve Lloyd Parallel computing Prof. Mark Trimmer Biogeochemistry Dr. Jon Grey Aquatic ecology Prof. Alfried Vogler (NHM) Metagenomics & turbotaxonomy Mr. Tim Booth (NEBC) Bio-Linux & virtual machines Prof. Jonathan Eisen (US) Microbial phylogenomics Prof. Alexei Drummond (NZ) Bayesian phylogenetics, Geneious CSO Dr. Matthew Hahn (US) Genomics Dr. Aris Katzourakis (Oxford) Phylodynamics modelling GridPP HTC 3,000+ cores MidPlus HPC 2,000+ cores Genome Centre Sequencing expertise
  10. 10. Deepwater Horizon, revisited Continuous analyses with immediate results Iterative sample collection / analysis; rapid cline detection Exploit phylogenetic methods Detect: population dynamics, adaptive evolution, migration Facilitate NGS Gene functions and Ecosystem services Explicitly model errors Account for paralogy & horizontal transfer Reduce ascertainment bias Unbiased taxon / gene discovery
  11. 11. Activity Goal Publication and/or software release Y1 Port existing tools Build framework Phylogenomics tools Runtime visualisation Taxonomic assignment Sitewise diversity Y2 I/O & GUI, review Develop framework Visualisation tools Review literature, develop theory Non-standard genetic codes Raft-aligned reads (RAR) demonstration Y3 RARs, phylo stress Anhomologous phylogenetics Asynchronous phylogenomics RARs MPI implementation Y4 Core method Integrate research Core method demonstration, including agent-based computation Core method released Y5 Alpha releases Deploy Stable releases ported to Geneious, CLC, Galaxy Final report

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