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CDC Bioinformatics and Data Science Fellowship

*Applications will be reviewed on a rolling-basis.

CDC Office and LocationA research opportunity is currently available with the Mycotic Diseases Branch (MDB), Division of Foodborne, Waterborne, and Environmental Diseases (DFWED), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) at the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia. 

Research Project: The Mycotic Diseases Branch (MDB) is looking for a candidate to participate in data management, analysis and visualization projects related to genomic and metagenomic data for fungal pathogens such as the multidrug-resistant pathogenic yeast Candida auris. Using a newly developed NCBI tool, MDB aims to establish a sequence-based monitoring system that will prospectively scan Sequence Read Archive (SRA) metagenomic data for C. auris. This project will benefit public health by 1) identifying reservoirs and new routes of C. auris exposure, 2) elucidating the origin of C. auris and 3) providing the foundation for using this tool for other emerging pathogens.

This training experience will involve use of MDB’s main data system - the Data Collation and Integration for Public Health Event Response (DCIPHER) platform, the current data platform for the COVID-19 response. Under the guidance of a mentor, the participant will help establish the monitoring system involving implementation of cloud computing for analyzing genomic and metagenomic data in real time. The participant will train closely with CDC and state epidemiologists, laboratorians, data scientists, and bioinformaticians, as well as, develop program management skills.

Learning Objectives

  • Implement cloud computing for real-time molecular surveillance of the multidrug-resistant pathogen C. auris and other fungal pathogens. This will involve activities with CDC’s scientific computing team to run bioinformatics analyses via cloud.
  • Gain experience setting up and maintaining data management systems for a novel surveillance effort that require integrating information from epidemiologic, laboratory, and metagenomic data.
  • Prepare maps, charts, and data visualization to aid in efforts to interpret result metrics from molecular search program to communicate the metadata and sequence data findings to multiple stakeholders across various disciplines.
  • Perform outreach by contacting data submitters and supplying them with requests for metadata and forms for addition information. Update forms and compile responses into existing data management system.
  • Perform sequence assembly and annotation on informative sequence reads to facilitate molecular surveillance program.

Mentor(s)The mentor for this opportunity is Juliann Hudak (vpt0@cdc.gov). If you have questions about the nature of the research please contact the mentor(s).

Anticipated Appointment Start Date: September 7, 2021.  Start date is flexible and will depend on a variety of factors.

Appointment LengthThe appointment will initially be for one year, but may be renewed upon recommendation of CDC and is contingent on the availability of funds.

Level of ParticipationThe appointment is full-time.

Participant StipendThe participant will receive a monthly stipend commensurate with educational level and experience.

Citizenship RequirementsThis opportunity is available to U.S. citizens, Lawful Permanent Residents (LPR), and foreign nationals. Non-U.S. citizen applicants should refer to the Guidelines for Non-U.S. Citizens Details page of the program website for information about the valid immigration statuses that are acceptable for program participation.

ORISE InformationThis program, administered by ORAU through its contract with the U.S. Department of Energy (DOE) to manage the Oak Ridge Institute for Science and Education (ORISE), was established through an interagency agreement between DOE and CDC. Participants do not become employees of CDC, DOE or the program administrator, and there are no employment-related benefits. Proof of health insurance is required for participation in this program. Health insurance can be obtained through ORISE.

Questions: Please visit our Program Website. After reading, if you have additional questions about the application process please email ORISE.CDC.NCEZID@orau.org and include the reference code (CDC-DFWED-2021-0191) for this opportunity.