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Postdoc position: HIV phylogenetics in the Dunn Lab at Yale University

Postdoc position: HIV phylogenetics at Yale University

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Advisor: Casey Dunn

Location: Department of Ecology and Evolutionary Biology, Yale University, in New Haven, Connecticut, USA

Application due date: June 1, 2018 (or until filled)

Start date: September 1, 2018

I have a one year computational phylogenetic postdoc position available in my lab. The postdoc will apply phylogenetic methods to identify potential transmission clusters on HIV phylogenies. These methods will include existing "phylodynamic" approaches, as well as new methods to be developed and implemented. Activities will include the use of model-based approaches to identify transmission clusters based on HIV phylogeny structure, and longitudinal analysis of clusters through time as sequence data from new patients are added to the trees.

This position is supported by the newly funded NIH R01 award "Real Time Phylogeny and Contact Tracing to Disrupt HIV Transmission". This exciting collaboration, led by Dr Rami Kantor and including colleagues from the Rhode Island Department of Health and other institutions, seeks to integrate real time phylogenetic and phylodynamic analyses of HIV sequence data into public health interventions to disrupt HIV transmission. Collaborators will acquire sequence data and generate phylogenetic trees that will serve as the starting point for the postdoc’s work. All patient data will be fully anonymized, and the postdoc will not work with any materials that are identifiable to patients.

Research skills sought

The successful candidate will have expertise and experience in the following areas:

  • Phylogenetic methods, including a solid grounding in phylogenetic models and phylogenetic comparative methods
  • Computational biology, including R and/or python, git, and common statistical methods

The following areas of expertise are desirable but not required:

  • Virus evolution
  • HIV biology
  • Epidemiology

Your application

Interested candidates should e-mail me at with the following items and information:

  • CV
  • A brief description of why you are a good fit for the position
  • If available, a link to your GitHub profile, or other relevant accounts, with examples of code and analyses you have worked on in the past.

I will then request follow-up materials, including references, from the most suitable candidates. Applications will be considered until the position is filled, but please submit your application by the due date above to receive full consideration.

The candidate must have completed all requirements for a doctorate degree by the start date.

Workplace and lab environment

In the Dunn Lab, we place a strong emphasis on open reproducible science and industry-standard tools (like Slack, Docker, and GitHub) for computational biology. See our publications list for links to preprints and git repositories associated with our papers. This builds on our work training biologists in general-purpose computational tools, including the book Practical Computing for Biologists that I co-authored. The postdoc who works on this computational project will benefit intellectually from interactions with others in the lab who are working on a variety of other phylogenetic projects, both theoretical and empirical. Many other labs in the Yale Department of Ecology and Evolutionary Biology also work on phylogenetic biology, providing a strong broader community.

Yale University is an Equal Opportunity/Affirmative Action Employer. Yale values diversity among its students, staff, and faculty and strongly welcomes applications from women, persons with disabilities, protected veterans and under-represented groups.

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