CDC’s National Center for Immunization and Respiratory Diseases (NCIRD) Public Health Internship Program – Bioinformatics Fellowship

*Applications will be reviewed on a rolling-basis.

CDC Office and Location: A fellowship opportunity is available with the Influenza Division (ID) in the National Center for Immunization and Respiratory Diseases (NCIRD) at the Centers for Disease Control and Prevention (CDC) in ) in Atlanta, Georgia. This opportunity can be part-time or full-time and is eligible for 100% telework from Atlanta, GA or San Juan, PR.

The Centers for Disease Control and Prevention (CDC) is one of the major operation components of the Department of Health and Human Services. CDC works to protect America from health, safety, and security threats, both foreign and in the U.S. Whether diseases start at home or abroad, are chronic or acute, curable or preventable, human error or deliberate attack, CDC fights disease and supports communities and citizens to do the same.

The mission of the Infectious Division (ID) is to improve global prevention and control of seasonal and novel influenza and improve influenza pandemic preparedness and response.

NCIRD - Immunization and Respiratory Diseases (NCIRD) Home | CDC

ID - About Influenza Division | CDC

Research Project: The Influenza Division uses Next Generation Sequencing (NGS) internally and through national and international partners to monitor for genetic changes in viruses, develop risk assessments, and recommend vaccine components to the World Health Organization.

The Informatics Team in ID is seeking a qualified and motivated candidate to contribute to the development of user-friendly software for local and cloud deployment of viral NGS assembly, annotation, quality control and public database submission. Project goals include enhancing NGS analysis applications, improving graphical interface using NextFlow and Python, deploying applications to the cloud using AWS products, and delivering automated phylogenetic and variant-based analysis reporting tool for laboratory scientists that will help to prioritize downstream experiments.

Learning Objectives: The activities listed below represent the minimum training opportunities that the fellow will complete:

• Learn principles of viral genomics, including NGS-based consensus assembly, minor variant analysis, and phylogenetics
• Learn how to maintain, test, and develop automated production-scale NGS bioinformatics pipelines
• Participate in developing solutions for integration and analyses of sequencing, phenotypic, and epidemiological data
• Learn practical bioinformatics skills desired in high throughput settings like government and industry (i.e., deployable application development, reproducible pipeline development, cluster computing, and distributed database architecture)
• Collaborate with diverse groups of bioinformatics and laboratory scientists and result in practical solutions.
• Demonstrate proficiency in querying and retrieving data using SQL through multiple data projects
• Demonstrate proficiency in manipulating and managing data using Python with multiple completed operational data flows, including source code and runtime elements
• Collaborate on data visualizations and analyses with division laboratory and epidemiology teams to support public health decision making

Mentor(s): The mentor for this opportunity is Brian Lee (fya1@cdc.gov). If you have questions about the nature of the research please contact the mentor.

Anticipated Appointment Start Date: February 5, 2024.  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, or part-time, and is negotiable.

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.

The successful applicant(s) will be required to comply with Environmental, Safety and Health (ES&H) requirements of the hosting facility, including but not limited to, COVID-19 requirements (e.g. facial covering, physical distancing, testing, vaccination).

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

Qualifications

The qualified candidate should be a current University of Puerto Rico School of Medicine and Biomedical Sciences student pursuing a master's, doctoral, or medical degree in Biomedical Sciences, Health Sciences, Medicine, Public Health, or other related disciplines. Recent graduates from UPR will also be considered, and a degree must have been received within the past five years.

Preferred skills:

• Experiences in bioinformatics and scripting (i.e. Linux/command line, R, Python), graphical interface frameworks (i.e. Rshiny, Python Dash) bioinformatic pipeline development (i.e. Nextflow/Snakemake/WDL), and cloud computing
• Analytical/assessment skills
• Communications skills (oral/written)
• Leadership and systems thinking skills