Bioinformatician/computer scientist fellowship

Centers for Disease Control and Prevention
Job Location
1600 Clifton Rd
Atlanta, GA 30329
Commensurate with degree and experience

Health insurance provided through ORISE fellowship program. Travel to conferences, workshops and training depending on funding availability.

Job Description


A fellowship opportunity is currently available with the Laboratory Branch of the Division of HIV/AIDS Prevention (DHAP) within the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (NCHHSTP) at the Centers for Disease Control and Prevention (CDC).

This fellowship offers the opportunity to join a high-priority, high-impact issue in domestic HIV, hepatitis, tuberculosis (TB) and sexually transmitted disease (STD) surveillance. This is an exciting opportunity for a skilled and experienced bioinformatician or computer scientist to lead and manage an innovative CDC project to develop a bioinformatics pipeline for the analysis and visualization of microbial transmission networks. The opportunity includes working with internationally renowned laboratory and epidemiology scientists at the CDC with expertise with a variety of pathogens in our center, including TB, HIV, hepatitis and STDs. Very large microbial datasets exist to both develop and be analyzed by using this new platform, the outcomes of which will have significant public health impact. The fellow will help develop a comprehensive software system that integrates multiple bioinformatics tools for the analysis and visualization of transmission networks, including development of methods to improve integration, analysis, and interpretation of phylogenetic, network, and epidemiologic, clinical and antimicrobial treatment data. When possible, this approach will utilize existing individual software programs and bioinformatics tools that are free and open source. The developed methods will use the rich metadata available from various studies and allow for searching and filtering sequences and metadata by specific characteristics, risk groups, and antimicrobial treatments. These new tools will help identify meaningful cluster characteristics and trends in subgroups at local and national levels. This work will provide CDC with a better understanding of pathogen transmission in communities and will better utilize resources to target specific prevention efforts. The new tools will also facilitate providing data and results back to state and local health departments for use in additional investigations and to guide local prevention efforts.

Specific opportunities during the fellowship may include: • Develop novel bioinformatics pipeline for characterizing and visualizing microbial transmission networks • Participating in multidisciplinary research projects involving molecular epidemiology, microbiome analysis and bioinformatics • Assisting in the training of scientists in the selection and use of bioinformatics tools • Collaborating with external and internal stakeholders • Lead and manage a high profile public health project • Analysis of large complex microbial datasets using the new pipeline • Preparing manuscripts describing new pipeline and/or analysis of dataset • Communicating research results through conference presentations, scientific publications or project reports

The Research Participation Program for CDC is administered by the Oak Ridge Institute for Science and Education (ORISE). The initial appointment is for one year, but may be renewed upon recommendation of CDC contingent on the availability of funds. The participant will receive a monthly stipend depending on educational level and experience. The participant must show proof of health insurance. The appointment is full-time at CDC in the Atlanta, Georgia, area. Participants do not become employees of CDC or the program administrator, and there are no fringe benefits paid.


Skills and Qualifications: • MS or PhD degree in an area of computational or life sciences with at least two years programming experience, including bioinformatics. • Familiarity with molecular and public health epidemiology and analysis of genetic sequence data, including phylogenetic and network analyses.
• Experience with data manipulation and development of software utilizing various programming languages, including Java, Linux, Perl/Python, C++, and be willing to learn additional programming languages as necessary. • Experience with relational databases (MySQL, Oracle or PostgreSQL). Experience manipulating, analyzing, and annotating very large biological sequence data sets, both in exploratory and pipelined fashions. • Highly capable of working collaboratively with an interdisciplinary team, including laboratory scientists, epidemiologists, bioinformaticians, statisticians, and data analysts, and have strong written and verbal communication skills.
• Must be self-motivated, work independently in a team environment, and be able to multi-task. • The fellow is expected to comply with DHAP, CDC, and DHHS policies and procedures for the handling of human subject’s data.

How to Apply

To be considered, please send a current CV/resume and a one-page cover letter addressing your relevant experience and your interest in this position to the attention of :

William M. Switzer, M.P.H. Diagnostics & Incidence Team Lead Laboratory Branch Division of HIV/AIDS Prevention Centers for Disease Control and Prevention 1600 Clifton Road, Mailstop G-45 Atlanta, GA 30329 Email:[email protected]

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