CDC Public Health Bioinformatics Fellowship
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A complete application consists of:
- An application
- Transcripts – Click here for detailed information about acceptable transcripts
- A current resume/CV, including academic history, employment history, relevant experiences, and publication list
- One educational or professional recommendation
All documents must be in English or include an official English translation.
If you have questions, send an email to ORISE.CDC.NCEZID@orau.org. Please include the reference code for this opportunity in your email.
*Applications will be reviewed on a rolling-basis.
A research opportunity is currently available in the Enteric Diseases Laboratory Branch (EDLB) at the Division of Foodborne, Waterborne, and Environmental Diseases (DFWED), in the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), at the Centers for Disease Control and Prevention (CDC) located in Atlanta, Georgia.
To maintain long-term viability, foodborne enteric pathogen outbreak surveillance systems must transition from culture-based methods, which require extensive laboratory work to isolate pathogens from other microbes in a patient stool sample, to molecular techniques compatible with complex metagenomic samples. CDC Information Management Services (CIMS) is working closely with PulseNet, the National Antimicrobial Resistance Surveillance Team in EDLB, and other partners to develop complete workflows covering specimen collection to final pathogen report. As a part of this work, CIMS is offering a fellowship to support the development of bioinformatic pipelines to aid in the development of laboratory assays and analysis of laboratory assay data.
Under the guidance of a mentor, the fellow will collaborate with a team of bioinformaticians on multiple pipelines and assist in:
- The writing of new pipeline modules
- The testing of modules written by others
- The writing of documentation for modules
Pipelines under active development include those for linking host genomes with important antimicrobial resistance genes found on plasmids using Hi-C techniques, designing core genome multilocus sequence typing schemes and primers from selected reference genomes, and analyzing and interpreting data generated from large targeted sequencing panels.
Anticipated Appointment Start Date: October 2020
This program, administered by ORAU through its contract with the U.S. Department of Energy to manage the Oak Ridge Institute for Science and Education, was established through an interagency agreement between DOE and CDC. The initial appointment can be up to one year, but may be renewed upon recommendation of CDC contingent on the availability of funds. The participant will receive a monthly stipend commensurate with educational level and experience. Proof of health insurance is required for participation in this program. The appointment is full-time at CDC in the Atlanta, Georgia, area. Participants do not become employees of CDC, DOE or the program administrator, and there are no employment-related benefits.
The qualified candidate should have received a master's or doctoral degree in one of the relevant fields. Degree must have been received within five years of the appointment start date.
Preferred skills:
- Excellent oral and written communication skills
- Comfortable working in a highly interdisciplinary environment
- Experience scripting in at least one language (e.g. Python, R, Perl)
- Familiarity with the following is helpful, but not required:
- UNIX command line bioinformatics tools
- Analysis of next generation sequencing data, including QC, alignment, quantification, or phylogeny tools
- Metagenomics, comparative genomics, targeted sequencing, or AMR-related analysis tools
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