CDC Bioinformatics Fellowship
*Applications will be reviewed on a rolling-basis.
CDC Office and Location: A bioinformatics fellowship is available in the Culture Independent and Metagenomic Subtyping group (CIMS) in the Enteric Diseases Laboratory Branch (EDLB) in the 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: 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. CIMS is working closely with PulseNet, the National Antimicrobial Resistance Surveillance Team in EDLB, and other partners to develop complete workflows spanning specimen collection to final pathogen report.
As a part of this work, CIMS is evaluating highly multiplexed amplicon sequencing (HMAS) assays for the subtyping of enteric pathogens directly from clinical patient stool sample DNA. A significant challenge for the use of this methodology is that analytical methods currently in use cannot sort amplicon sequencing data obtained from closely related strains of pathogen or species (e.g. Shiga toxin-producing E. coli and commensal E. coli) occurring in the same sample. Without the ability to sort data from multiple strains or closely related species, HMAS assays cannot be deployed for broad use in enteric pathogen surveillance. CIMS is offering a fellowship to support the evaluation and adaptation of bioinformatics pipelines for use sorting HMAS sequence data. The selected participant will collaborate closely with CIMS’ collaborators at neighboring academic institutions with expertise in relevant analysis methods as well as a team of bioinformaticians in EDLB with frequent input from laboratory scientists generating the data. Activities will include:
- Frequent consultation with CIMS and academic partners to evaluate potential solutions to the analytical challenge
- Adaptation of selected methods to meet the analysis need, including writing new code
- Testing code performance against relevant data sets
- Consulting with laboratory scientists to design relevant experiments to assist in pipeline development and testing
- Adapting pipelines on CDC computing systems
- Documentation for code and pipelines
- Preparation of final pipelines for publication and deployment to partner public health laboratories
Learning Objectives:
- Skills in collaborating with laboratory scientists on joint projects. For example, the fellow will learn to effective methods for providing feedback on laboratory data and interpretation of analytical findings.
- Bioinformatic troubleshooting skills.
- Introduction to (or additional experience in, depending on candidate's background) functional programming approaches and how to apply them to public health problems.
- Effective strategies for oral and written presentation of scientific work to other scientists.
Mentor(s): The mentors for this opportunity are Andrew Huang (wwm8@cdc.gov), A. Jo Williams-Newkirk (igy7@cdc.gov) and Sherricka Stephens (gii8@cdc.gov). If you have questions about the nature of the research please contact the mentor(s).
Anticipated Appointment Start Date: August 2021. Start date is flexible and will depend on a variety of factors.
Appointment Length: The 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 Participation: The appointment is full-time.
Participant Stipend: The participant will receive a monthly stipend commensurate with educational level and experience.
Citizenship Requirements: This 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 Information: This 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 for this opportunity.