Anticipated Manuscripts

Jamie expects the following manuscripts to result from this work:

Anticipated Manuscripts from TR work:

Tree Reconciliation Ontology
1. Scope: Describe the tree reconciliation ontology and its application to communicating reconciled trees in NeXML
2. Journal: Frontiers in Genetics - Special Issue on Biological Ontologies
3. Anticipated Submission Date: April 27th, 2012
4. Audience: People interested in co-phylogeny analyses (gene/species trees and well as host/pathogen), phylogenetic ontologies, reconciliation methods and interoperable communication of phylogenetic analysis results. This will include both bio and comp-bio crowds.
5. More: This will include NeXML work done by Daniel Packer.
6. Title:
  The tree reconciliation ontology for the mapping of guest trees to host trees allows for interoperable exchange of cophylogenetic analyses
7. Abstract:
  Cophylogenetic analyses allow for the description of the co-evolution between pathogens and their hosts as well as provide the framework for phylogenomic studies of gene trees reconciled to their host genomes. We have defined an ontology for tree reconciliation which describes: 1) the topological mapping between guest tree nodes and host trees, 2) the algorithms and software used to infer reconciliations and 3) the biological processes producing the inferred topological mappings. The tree reconciliation ontology (TRON) has been implemented in the OWL web ontology language in order to be compatible with the evolutionary comparative data analysis ontology (CDAO) and the NeXML standard for the exchange of rich phyloinformatic data. We provide an example of how TRON can be used with these existing standards to provide an XML based description of the results from cophylogenetic analyses. TRON is released under the Simplified BSD License, with both stable and development versions available from GitHub (https://github.com/jestill/tron_ontology).
8. Status:
  Abstract accepted by journal with extension accepted by journal.
9. Needs:
  - finish remaining work on ontology
  - send outline out to collaborators for feedback
  - writing manuscript
  - identify example reconciled trees to illustrate as NeXML encoded representations
    - Gene Tree/Species trees:
      - Major Histocompatibility Complex class I for three primates as used in PrimeGSR paper
        (http://prime.sbc.su.se/primetv/MHC.pdf)
    - Example host-pathogen dataset(s):
      - Anther Smut http://www.biomedcentral.com/1471-2148/8/100
        Includes host shifts
      - also see http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2004.tb00479.x/abstract for plant pathogen with host shifts
      - Pocket gophers and chewing lice ( Hafner MS, Nadler SA: Phylogenetic trees support the coevolution of parasites and their hosts. Nature 1988, 332:258-259.) This tree includes 8 host nodes and 10 guest nodes.Hafner MS, Nadler SA: Phylogenetic trees support the coevolution of parasites and their hosts.
        Nature 1988, 332:258-259. PubMed Abstract | Publisher Full Text
        Return to text
      - gypsy transposable elements in Drosophilids (http://mbe.oxfordjournals.org/content/21/10/1831.abstract) if easy to get trees available
Tree Reconciliation Database and Viewer
1. Scope: Focus on informatic tools produced: Discuss the tree reconciliation database schema as an extension of Ensemble Compara schema and the standalone TR viewer as a visualization environment for exploring TR results.
2. Anticipated Journal: BMC Bioinformatics?
3. Anticipated Submission Date: May 31, 2012
4. Audience: Audience will be end users interested in using the TR GUI interface as well as DB maintainers interested in implementing TR database.
5. More:
  This will be similar in scope to the talk given in iEvoBio in summer of 2011 and the poster Sheldon presented with a focus on the informatics tools.
6. Status: Jamie, Naim and Ray will be finishing up coding by April 23rd. Public repository already exist and will be updated with final publication quality release and documentation
7. Needs:
  - finish support for multiple reconciliation methods in viewer and services
  - stress test viewer for very large species tree and gene trees
  - documentation needed on
  - updated pdf of schema for archive
Comparing tree reconciliation methods
1. Scope: Application of the tree reconciliation database and associated analysis pipelines to compare methods for gene tree to species tree reconciliation. An overview of existing methodological approaches, a 'consumer report' for existing TR analysis pipelines, an excellent example showing off the power of the TR database we have made, and a place to discuss future needs in TR reconstruction analysis by pointing out global weaknesses in existing tools.
2. Anticipated Journal: __________
3. Anticipated Submission Date: July 8, 2012
4. Audience: Biologists interested in picking methods and software for TR analysis as well as reconciliation software producers.
5. More:
  Using Bowers synteny informed reconstructions (perhaps curated Bowers ) as a 'gold-standard' this will demonstrate how the database schema itself allows for queries within an among co-phylogenetic analyses.
6. Status: Pipelines exist for PrimGSR and treebest.
7. Needs:
  1. Make decision regarding how to to treat species trees regarding location of Populus.
  2. Jamie will need some feedback from PIs regarding the methods used for comparing co-phylogenetic results, but first Jamie will need to write up a general comparison methods with equations and SQL implementations.
  3. Decide on list of TR software to include in analyses. At minimum should be
  4. Extend Sheldon's pipeline as needed to additional software
  5. Install Phyldog on TACC resources.