Bioinformatics DevOps Engineer/Developer

4 weeks ago

Jacksonville, Florida, United States WiredPeople, Inc. Full time
Job Description

WiredPeople, Inc. is seeking a highly skilled Bioinformatics DevOps Engineer/Developer to support genomic surveillance and outbreak investigations for pathogens of public health concern in Florida.

The ideal candidate will work directly with the Bioinformatics Team, serving as a bioinformatics developer and primarily support the development and implementation of a cloud computing architecture to improve and expand our current computational infrastructure.

Key Responsibilities:

  • Plan and execute whole-genome sequencing analysis, comparative genomic analysis, and other analytic research projects.
  • Select and develop appropriate analysis techniques and measures, and identify and implement the necessary software and databases to complete defined analytical tasks.
  • Develop, manage, and curate databases for analysis.
  • Identify, implement, and maintain data quality control, data submissions, and management programs.
  • Lead the development and implementation of a cloud computing architecture to improve and expand our current computational infrastructure.
  • Provide technical assistance to other bioinformaticians, laboratory staff, and epidemiologists on the use of complex data analysis techniques and methods.
  • Provide approved updates with analytical results from developed bioinformatic pipelines to be disseminated to laboratory and epidemiological staff.
  • Lead and coordinate with other bioinformaticians involved in analysis projects, including data sharing and engagement across multidisciplinary project teams.
  • Disseminate approved results of research projects in a wide range of venues, including publications, peer-reviewed journals, summaries, manuscripts, special reports, and oral/poster presentations.

Qualifications and Experience:

Required:

  • A PhD in bioinformatics, genomic epidemiology, microbiology, virology, parasitology, evolutionary biology, microbial genetics, molecular biology, computer science, or a related field.
  • At least 5 years of experience following your degree.
  • At least 5 years of practical and technical experience in microbial and/or public health bioinformatics.
  • At least 5 years of experience with bioinformatic development of pipelines for the phylogenetic and comparative genomic analysis of microbial organisms.
  • At least 2 years of experience with cloud computing.
  • Bioinformatics experience with microbiology and/or public health applications.
  • Experience working in a UNIX/LINUX environment and writing shell scripts.
  • Proficiency in at least one scripting/programming language (e.g., Python, Perl, R, C++, Java) and willingness to learn new languages, if necessary.
  • Experience developing custom scripts and executing command-line bioinformatics tools for microbial genomics comparative analysis.
  • Experience in phylogenetics and interpreting comparative genomic data from microbial organisms.
  • Experience using git/github.
  • Experience querying and submitting genomic data from/to NCBI databases.
  • Excellent verbal communication and experience presenting complex, technical data to multidisciplinary teams.
  • Excellent written communication and experience publishing in the relevant scientific literature.

Preferred:

  • Strong background in phylogenetics of bacterial and/or viral pathogens.
  • Experience with AWS and/or Cloud.
  • Proficiency in Python and R.
  • Experience analyzing NGS data generated from Illumina, Oxford Nanopore, and PacBio platforms.
  • Experience with high-performance computing (HPC) and/or cloud computing.
  • Experience with Singularity and/or Docker.
  • Experience with Conda.
  • Experience developing and/or executing workflows using a workflow language (such as Snakemake, Nextflow, WDL).
  • Experience with pathogen genomics, especially of public health concern.

Equal Employment Opportunity:

WiredPeople, Inc. provides equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, national origin, age, disability, or genetics.

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