Cooper Laboratory

The Cooper laboratory is growing and is seeking researchers who share our goal of using evolutionary biology to advance medicine. This is part of a broader effort at the University of Pittsburgh to build in evolutionary biology. We are currently seeking applicants for the following positions:

  1. Postdoctoral Researcher, Experimental Evolution of Antimicrobial Resistance in vitro and in vivo. This position is now filled, but we would welcome opportunities to work with fellowship applicants on this project. The aim of this project is to identify antibiotic-specific evolutionary pathways that lead to resistance under distinctive growth and immune-system pressures. This project focuses on how S. pneumoniae, A. baumanii, and P. aeruginosa evolve under various antibiotic and host immune constraints, using genomics, transcriptomics, and state-of-the-immune-system profiling to identify selective forces on genetic and physiological targets. This NIH U01 project is described here and involves PI’s Tim van Opijnen, Ralph Isberg, Jason Rosch, and Jose Bento. We’re looking for candidates with expertise in microbiology, genomics, and/or evolutionary biology.
  2. Postdoctoral researcher, Mechanisms of Adaptation in Biofilms. The overall goal of this project is to disentangle eco-evolutionary dynamics in experimental biofilms and to define the precise targets of selection, which ultimately produce synergistic mixed communities. This project is focused in particular on how quorum-sensing and cyclic diguanylate signaling are coordinated to enable cells to produce the optimal stick-or-swim decision, and how variation in this decision associates with evolved diversity in biofilms. This work is supported by NIH and NASA and builds upon research reported in Traverse et al PNAS 2013, Ellis et al Evolution 2015, and Cooper et al Genomics 2014. Co-investigators on this project include Chris Waters and Matt Neiditch.
  3. Bioinformatics Research Staff. This position, listed here, is as follows: The Cooper lab generates and analyzes a wide range of genomic and transcriptomic data related to bacterial evolution during infections and in experimental laboratory and animal systems. Applicants must be proficient in one or more scripting languages (e.g. Python, Ruby, Perl) and familiar with Unix environments. This position provides an outstanding opportunity to gain expertise in high-throughput genomics and make intellectual contributions to projects supported by NIH, NSF, and NASA. Minimum requirements include a bachelors’s degree in computational biology, bioinformatics, biological science, or equivalent work experience.
  4. Evolution Curriculum Outreach Coordinator. Our most significant project is a curriculum, EvolvingSTEM, that enables 9th-grade students to learn principles of evolution and heredity with a weeklong evolution experiment in biofilms. We seek a student or staff member to help us refine and distribute this curriculum in greater Pittsburgh and beyond. This position will require both hands-on teaching and contribution to fundraising.
  5. Ph.D. positions are available for projects 1 and 2 and for students interested in bacterial population genetics or evolution during infections. Please apply through the graduate program that best suits you: a. Biology b. Carnegie Mellon-Pitt Computational Biology c. Molecular Virology and Microbiology

Please direct inquiries about all positions to Vaughn.