Description:
A bioinformatics fellowship is currently available in the Enteric Diseases Laboratory Branch (EDLB) in the Division of Foodborne, Waterborne, and Environmental Diseases (DFWED) within the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) at the Centers for Disease Control and Prevention (CDC).
The fellow will work in the interdisciplinary Culture-Independent and Metagenomic Subtyping (CIMS) group within EDLB. The main focus is to complete the design and implementation of a pipeline that leverages the branch’s extensive pathogen genome collection to produce highly multiplexed primer panels for the subtyping of foodborne bacteria in routine public health surveillance. Each primer panel will consist of hundreds to thousands of primer pairs. Some pipeline development has been performed already; the fellow will be responsible for refining and expanding the existing pipeline with support from both microbiology and bioinformatics subject matter experts in the branch. The primers will be used to amplify short (~200 bp), informative regions from the genomes of target pathogens in DNA extracted from stool samples. The resulting amplicons will then be sequenced on a short read sequencing platform like Illumina or Ion Torrent. The fellow may also coordinate with companies to refine primer designs for compatibility with different methods that generate amplicons for next generation sequencing platforms, e.g. Ion Torrent AmpliSeq, Fluidigm Juno.
The fellow will also be engaged in evaluating existing tools for analyzing the data produced by the subtyping primer panels and, if necessary, developing alternative solutions.
Activities will include:
Qualifications:
Stipend is based on degree attained and other experience. This is a one year fellowship appointment through the Oak Ridge Institute for Science and Education program administered through the Department of Energy. Interested applicants should send their CV and letter of interest to Jo Williams-Newkirk at [email protected].
A bioinformatics fellowship is currently available in the Enteric Diseases Laboratory Branch (EDLB) in the Division of Foodborne, Waterborne, and Environmental Diseases (DFWED) within the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) at the Centers for Disease Control and Prevention (CDC).
The fellow will work in the interdisciplinary Culture-Independent and Metagenomic Subtyping (CIMS) group within EDLB. The main focus is to complete the design and implementation of a pipeline that leverages the branch’s extensive pathogen genome collection to produce highly multiplexed primer panels for the subtyping of foodborne bacteria in routine public health surveillance. Each primer panel will consist of hundreds to thousands of primer pairs. Some pipeline development has been performed already; the fellow will be responsible for refining and expanding the existing pipeline with support from both microbiology and bioinformatics subject matter experts in the branch. The primers will be used to amplify short (~200 bp), informative regions from the genomes of target pathogens in DNA extracted from stool samples. The resulting amplicons will then be sequenced on a short read sequencing platform like Illumina or Ion Torrent. The fellow may also coordinate with companies to refine primer designs for compatibility with different methods that generate amplicons for next generation sequencing platforms, e.g. Ion Torrent AmpliSeq, Fluidigm Juno.
The fellow will also be engaged in evaluating existing tools for analyzing the data produced by the subtyping primer panels and, if necessary, developing alternative solutions.
Activities will include:
- Evaluating and choosing command line software for a variety of comparative genomic and phylogenetic tasks, including but not limited to: ortholog identification; multiple sequence alignment; generation, visualization, and comparison of phylogenies; genome annotation
- Evaluating and choosing command line software to design PCR primers and assess their performance in a multiplexed PCR against complex metagenomic backgrounds
- Writing scripts to manipulate the output files from command line software
- Creating an automated pipeline from the selected software for each task involved in primer design and evaluation
- Evaluating existing command line tools for calling alleles from data generated by primer panels down to the level of detail required for bacterial foodborne pathogen subtyping
- Choosing or creating an automated pipeline for primer panel data analysis and working with others to integrate the pipeline into our existing analysis platform
Qualifications:
- Master’s degree in bioinformatics or computer science preferred; biological sciences or related fields will be considered with demonstrated programming experience (graduation within the last three years required)
- Two or more years of experience programming (Python and R experience preferred)
- Experience designing and implementing bioinformatics pipelines in a high performance cluster computing environment
- Strong UNIX command line skills
- Good written and oral communication skills
- Comfortable working in a highly interdisciplinary team environment
- Experience and willingness to multitask
Stipend is based on degree attained and other experience. This is a one year fellowship appointment through the Oak Ridge Institute for Science and Education program administered through the Department of Energy. Interested applicants should send their CV and letter of interest to Jo Williams-Newkirk at [email protected].