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CDC Bioinformatics and Data Science Internship

*Applications will be reviewed on a rolling-basis.

CDC Office and Location: Two fellowship opportunities are currently available with the Bacterial Special Pathogens Branch (BSPB), in the Division of High Consequence Pathogens and Pathology (DHCPP) within the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) at the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia.

BSPB serves as a national reference laboratory for several high consequence bacterial pathogens, including Bacillus anthracis, Burkholderia mallei and pseudomallei, Brucella spp., as well as over 500 rare and unusual bacterial pathogens. A major component of the work done within BSPB is developing and maintaining bioinformatic tools to assist BSPB and its partners (both national and international) to investigate outbreaks, conduct surveillance, and identify novel species of bacterial pathogens.

Research Project: BSPB is looking for a candidate to participate in data management, bioinformatic pipeline development, analysis and visualization projects related to genomic and metagenomic data for bacterial pathogens. The fellow will contribute to efforts on containerizing specialized bioinformatic pipelines, currently in use within the branch, so that standardized bioinformatic tools may be deployed to partner labs unable to perform their own genomic analysis. This will increase both national and international capacity and ensure that genomic analysis is being performed in a consistent and reproducible manner between multiple laboratories.

This project will also involve efforts with MicrobeNet, a free online virtual reference laboratory run
within BSPB, to create an organized state and national surveillance network of diseases which are not currently captured by active systems.

Learning Objectives:
  • knowledge and awareness of the basic principles and concepts of biology, computer science, IT engineering, and mathematics
  • using software effectively to extract information from large databases and to use this information in computer modeling
  • problem-solving skills, including the ability to develop new algorithms and analysis methods
  • an understanding of the intersection of life and information sciences, the core of shared concepts, language and skills the ability to speak the language of structure-function relationships, information theory, gene expression, and database queries 

Mentor(s): The mentor for this opportunity is Zachary Weiner ( If you have questions about the nature of the research please contact the mentor(s).

Anticipated Appointment Start Date: September 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 and include the reference code for this opportunity.