Summer 2023 internship for MPH student
The Grubaugh Lab at the Yale School of Public Health (YSPH) is seeking a 1st year MPH student in the Epidemiology of Microbial Diseases program to join the Yale SARS-CoV-2 Variant Surveillance Initiative. The position is to join the Grubaugh Lab’s experienced genomic epidemiology team to process routine SARS-CoV-2 sequencing, update public reports (https://covidtrackerct.com/), directly interact with public health agencies (including the CDC and Connecticut Department of Public Health), and assist with research investigating new lineages and variants (including opportunities for authorship on papers).
While specific training will be provided, the applicant should have previous experience in bioinformatics, including working in command line and R. Additional experience in website design and/or python is preferred. The applicant should also be currently taking Dr. Grubaugh’s EMD 531 Genomic Epidemiology of Infectious Diseases course. The technical tasks include:
- Performing QC and generating consensus genomes from raw sequencing data
- Assigning lineages to consensus genomes (https://cov-lineages.org/resources/pangolin.html)
- Maintaining/updating an internal database
- Submitting data to online repositories (https://gisaid.org/)
- Generating Nextstrain builds (https://nextstrain.org/community/grubaughlab/CT-SARS-CoV-2/connecticut)
- Executing custom R scripts
- Updating the shinyapp report (https://kphamyale.shinyapps.io/covidtrackerct/)
The student can start during the 2023 Spring semester for training and continue their work during the summer to count as their Applied Practice Experience (APE) and the Internship requirements. The student may also continue working with the Grubaugh Lab during their second year (depending on summer performance) and work with Dr. Grubaugh to develop a thesis project. The student will be paid hourly based on the current Yale rates for work during the school year and summer (except for thesis research which is for credit).
If you would like to apply, please email Nathan Grubaugh ([email protected]) with a copy of your CV and a cover letter indicating how your experience and interests would make you a good fit for the position.