May 172016

The Phenoscape project is recruiting a postdoc with training in bioinformatics and/or developmental biology who is interested in analyzing genomic and developmental data in relation to phenotypic data, with a focus on the vertebrate fin/limb.

The problem of how organismal phenotypes have evolved, are constrained, and acquire novelty, is one of the grand challenges in biology. The Phenoscape group has developed ontology-based methods for representing species phenotypes so that they can be integrated with model organism developmental and genetic data. The Phenoscape Knowledgebase (KB) contains over 500,000 vertebrate species phenotypes that are linked to ~16,000 genes associated with 320,000+ phenotypes and 37,000 genes with in situ expression data from model organisms (zebrafish, mouse, Xenopus, human). These data present a tremendous opportunity for integration with other data types to address questions about the evolution of phenotype.

We are seeking an individual with expertise in developmental biology and/or genomics, to (1) help evaluate results of bioinformatics methods being developed by Phenoscape and (2) leverage the Phenoscape Knowledgebase to study whole-organism phenotype and functional genomics in non-model organisms. The purpose of the methods is to improve prediction of the genetic basis of evolutionarily novel phenotypes by incorporating semantic similarity, homology, and phylogenetic propagation. Vertebrate fin and limb phenotypes and genes are enriched in the KB, and we are thus seeking candidates who ideally have knowledge of genes and networks involved fin/limb development. Further, this position presents a unique opportunity to leverage the linked developmental and genetic data in the Phenoscape KB for large-scale analysis of patterns of phenotypic evolution.

The postdoc will work under the direction of Paula Mabee (University of South Dakota) in association with Todd Vision (University of North Carolina), as part of a distributed, multidisciplinary team that includes evolutionary and model organism biologists, computer scientists, and bioinformaticists. Ideally the applicant will be based in South Dakota (with opportunities to travel to other sites), but we will consider qualified applicants who are available remotely and/or half-time. The position is available immediately for an initial appointment of one year, with potential to renew.

Required qualifications:

  • Ph.D. degree with strong background in bioinformatics; previous experience with ontologies preferred
  • Experience in functional genomics or developmental biology, with preference for candidates with a background in vertebrate fin and/or limb developmen
  • Demonstrated communication and writing skills in English
  • Demonstrated ability to work in a team setting

How to apply:

  • Please contact Dr. Mabee ( for inquiries.
  • Applications should be directed to Dr. Mabee and include a cover letter, CV, a brief statement detailing your research interests and career goals, and three letters of reference.

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 Posted by on May 17, 2016 at 5:17 pm

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