Postdoc opportunity to advance computable clade definitions at Tree of Life scale

We are seeking a postdoctoral fellow to support the Phyloreferencing project by developing and advocating driving biological research use cases, and to coordinate these with large research projects in comparative biodiversity. Our ideal candidate is a biologist by training with strong expertise in systematic biology, and a deep interest in research questions that benefit from enabling a phylogenetic (as opposed to a taxonomic) perspective for integrating biodiversity data at a level that depends on computation.

The Phyloreferencing project aims to create the data standards and computational resources to render phylogenetic clade definitions, specifically their semantics, fully computable. A major part of our effort is to build an ontology of published and peer-reviewed phylogenetic clade definitions expressed in the Web Ontology Language (OWL), as well as the machine reasoning capabilities to resolve such definitions to clades in a given phylogenetic tree, including at the scale of the synthetic Open Tree of Life.

One role of the postdoc is to provide critical guidance and inform prioritization of software development efforts by developing, advocating, and ideally pursuing compelling research questions as use cases. As part of being compelling, such use cases should demonstrate how the phylogenetic view that phyloreferencing enables for linking data is different from traditional solutions to this problem (such as identifying clades manually, or using taxonomic checklists and synthetic taxonomy backbones).

The other major role of the postdoc is to serve as an ambassador of the project both to the comparative biodiversity research community at large, as well as in particular to select research projects (such as NSF GoLife-funded projects, or the ARBOR project) that could benefit from our technologies for integrating or communicating trait data with other biodiversity data resources at a large-scale. We expect that as a result at least some of our driving research use cases would be informed by or even actively coordinated with such projects, and the postdoc initiating and leading deeper collaborations would be welcome.

By rendering the semantics of phylogenetic clade definitions fully computable, phyloreferencing also enables computationally reproducing, disambiguating, and evaluating the effect of changing such clade definitions, features lacking in or made very difficult for taxonomic name-based approaches. Candidates with research ideas that take particular advantage of these features are equally encouraged to apply. More generally speaking, we are particularly interested in how you might incorporate phyloreferencing into your own research projects, current or future.

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) 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.


  • 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 popular in scientific computing (e.g., Python, JavaScript) is useful (and thus preferred) but not required.
  • Similarly, prior exposure to or familiarity with ontologies and ontology languages (in particular, OWL) is useful 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 ( All other inquiries should also be directed to Dr. Cellinese. The position will remain open until filled.

The University of Florida is an Equal Opportunity Employer.