ORISE Position, Enteric Disease Laboratory Branch at the CDC
Category : Alumni
Synopsis
Working on the bioinformatics of cgMLST and nanopore in the Enteric Diseases Laboratory Branch at CDC.
Project description
The mission of EDLB is to lead the preparedness and response to foodborne and diarrheal diseases in the United States and abroad by facilitating laboratory detection, identification, and characterization of foodborne bacterial pathogens. The selected participant will be trained in a team of expert bioinformaticians to help create and run workflows. These workflows include, but are not limited to, Oxford Nanopore Technologies (ONT) assembly and core genome multilocus sequence typing (cgMLST). In this role, the fellow will work as a part of a multidisciplinary team to develop, maintain, and support bioinformatics applications and systems used in CDC’s national foodborne illness surveillance program.
The fellow will apply their training to design and develop genome analysis tools. Successful workflows will be used in EDLB and the broader CDC scope but may also be deployed to public health labs for characterizing bacterial pathogens.
Learning objectives
• Developing and implementing bioinformatics tools for analysis of bacterial whole genome sequences
• Performing quality control, assembly, annotation, and analysis of genetic subtyping data
• Preparing data for submission to public repositories including NCBI
• Developing and documenting standard operating procedures for bioinformatics analysis pipelines and workflows
Preferred skills
• Excellent oral and written communication skills
• Team player
• Experience scripting in at least one language (Python, perl, R, or shell preferred)
• Comfortable working in a highly interdisciplinary environment
• Familiarity with the following is helpful but not required
– UNIX command line bioinformatics tools
– Medium to large code bases
– High Performance Computing (HPC) environments
– Docker, Singularity, and/or Conda platforms
– DSL languages (Nextflow, etc)
– Modern development operations (DevOps) tools such as git
Education
• Degree requirement: Bachelor’s Degree or Master’s Degree received within the last 3 years
• Suggested Discipline(s):
o Computer, Information, and Data Sciences
– Computer Science (general)
– Data Science
– Software Engineering
o Life Health and Medical Sciences
– Bioinformatics
– Biology (General)
– Computational Biology
– Epidemiology
– Evolutionary Biology
– Microbiology
– Population Medicine, Public Health and Epidemiology
Contact Lee Katz <gzu2 [at] cdc [dot] gov> for more details and/or for submiting a cover letter and CV for consideration.
