Postdoc opportunity in clade definitions for the Tree of Life

October 12th, 2016
By Cellinese,Nico

We are seeking a second postdoctoral fellow to support the Phyloreferencing project. Our ideal candidate is a biologist by training, and has strong expertise in systematic biology. The focus of your work would be on working with select NSF GoLife projects to develop meaningful phyloreferences and to use these in proof-of-concept applications for aggregating trait and other domain-relevant data. In addition, you would work with the ARBOR project to research integrating phyloreferences into trait-based analysis and visualization workflows.

The Phyloreferencing project is a collaboration between Dr. Nico Cellinese (Florida Museum of Natural History, University of Florida) and Hilmar Lapp (Center for Genomic and Computational Biology, Duke University) newly funded by the National Science Foundation. The postdoc will be based in the lab of Dr. Cellinese, but will work closely with both PIs. Starting date is negotiable. Salary is $50,000.

Why phyloreferencing?

The ability to freely and precisely communicate organism-linked data suffers serious limitations from the traditionally used taxon names based in Linnaean nomenclature. The semantics of such names are too often ambiguous, subject to divergent interpretation, and unavailable to computation. And with the advent of next-generation sequencing, metagenomics, and other modern biological data collection technologies, many groups of organisms for which we have interesting data do not yet, and may never have a Linnaean name.

Our project aims to overcome these limitations by defining ontology-based references (phyloreferences) to elements on the Tree of Life that are unambiguous and the semantics of which are amenable to powerful machine reasoning. One of the foundations of phyloreferencing is formed by the decades of theoretical and applied work on phylogenetic taxonomy. Ongoing computational work involves researching and developing OWL models and ontologies, tools for converting existing data into OWL format, and online proof-of-concept applications for using machine reasoning to navigate biodiversity data by clade semantics.

You can read the full grant proposal here.

Postdoctoral project responsibilities

You will work closely with the project PIs, existing postdoc and graduate students to generate the major project deliverables, focus on extending proof-of-concept tools to data integration use-cases beyond the Open Tree of Life project as the main phylogeny provider. Specifically, you will work with other projects funded by NSF’s GoLife program to obtain large phylogenies, gather sources for meaningful phyloreferences, and develop phyloreferencing proof-of-concept applications for these. These applications will include aggregating trait and other domain-relevant data. You will also work with the ARBOR Evolutionary Workflows project to prototype ways for integrating phyloreferences into trait-based analysis and visualization workflows that can be executed within the ARBOR framework.

While working with us on this project, you will gain familiarity with ontology development and ontology-enabled applications, including generating phyloreferences at a Tree-of-Life scale. You will also have the opportunity to explore, develop and test alternative approaches to clade definitions at every taxonomic level and at the broadest possible scales. You will have opportunities to publish both empirical and theoretical work.

Qualifications:

  • PhD in Biology or a related field.
  • Strong background in Systematic Biology required. You should be well versed in all aspects of theoretical phylogenetics and related topics.
  • Programming experience in languages frequently used in scientific computing and for managing or converting scientific data (e.g., Python) is useful (and thus preferred) but not required.
  • Excellent communication and writing skills, and ability to interact productively with other projects’ PIs and personnel.
    How to apply:

Please submit a letter of interest and CV, together with the names and contact information of three academic references, to Dr. Nico Cellinese (ncellinese@flmnh.ufl.edu). All other inquiries should also be directed to Dr. Cellinese. The position will remain open until filled.

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