The Cobey Lab in the Department of Ecology and Evolution at the University of Chicago investigates how the dynamics of adaptive immunity shape the evolution and epidemiology of influenza and SARS-CoV-2. We use diverse computational modeling approaches in close collaboration with experimental collaborators in immunology, virology, and epidemiology, including as part of NIH-funded consortia. A current focus is to understand how immune memory evolves after repeated antigen exposures.

The postdoctoral fellow would work with Dr. Cobey’s lab and external collaborators to model immune responses to repeat influenza vaccination. Repeated vaccination sometimes appears to blunt the immune response, but the impact of vaccination appears sensitive to the strains involved, childhood infections, recent infections, and other factors. The primary source of data will come from a randomized clinical trial, the DRIVE Study, that Dr. Cobey leads with Dr. Benjamin Cowling at the University of Hong Kong. The DRIVE Study is now in its fourth year, and extensive longitudinal data are becoming available. Additional data come from other randomized trials and observational cohorts that PIs Dr. Cobey, Dr. Benjamin Cowling, and Dr. John Tsang (Yale University) are analyzing in a separate R01 to understand variability in responses to influenza infection and vaccination.

This research will fill a valuable gap by developing and testing mechanistic hypotheses to explain vaccine responses. Another goal will be prediction. This work will directly support other projects in the lab that aim to understand variability in vaccine effectiveness, develop new methods to estimate vaccine effectiveness, infer correlates of protection through dynamical models, and measure immunity in the population.

The fellow will lead model development, implementation, and testing and have extensive opportunities to share their findings with our large network of collaborators as well as at conferences. If productive, there are many possible follow-up projects and opportunities for leadership.

Responsibilities:
• Develop, implement, and validate mathematical and computational models of the immune response to influenza vaccination and infection over time. Follow good programming practices and plan multiple approaches to enhance rigor and reproducibility.
• Oversee integration and appropriate storage of DRIVE Study data needed for modeling from the Hong Kong clinical site and collaborators at other sites who are performing serological and cellular assays.
• Develop visualizations and perform ad hoc analyses to investigate data sets and related hypotheses.
• Maintain intellectual ownership of the project by keeping up to date with the multidisciplinary literature, identifying research priorities in consultation with collaborators, and staying involved in other relevant networks (e.g., the NIH CEIRR and CIVIC consortia).
• Help manage the project with the PI through team communications, establishing meeting agendas, mentoring other researchers, and managing deadlines.
• Prepare manuscripts, data, and software for publication.
• Meet with collaborators at off-site (including international) meetings and present findings at domestic and international conferences.
• Assist with progress reports and IRB protocols.
• Engage constructively with other lab members on their projects.

Qualifications
• PhD in a quantitative field such as mathematics, statistics, epidemiology, ecology and evolution, physics, computer science, engineering, and related disciplines.
• Strong background in mechanistic modeling and Bayesian or frequentist inference.
• Ability to quickly learn new biological, statistical, and programming concepts and skills.
• Proficiency in programming languages, such as R, Python, and C(++).
• Excellent oral and written communication skills in English.
• Ability to work independently and collaboratively in a rigorous and fast-paced academic environment.
• Ability to travel domestically and ideally internationally.

Please see our lab handbook (on our website) for information on lab culture and expectations.

We pay a competitive salary and especially welcome members of underrepresented groups.

Please email Dr. Cobey at cobey@uchicago.edu with any questions. To apply, please email Dr. Cobey a cover letter explaining interests and suitability for the position, CV, one or two representative publications (or manuscripts), a link to sample code, and names and contact details of 2-3 references and their relation to the candidate.