Bioinformatics DevOps Engineer/Developer

Summary

Join WiredPeople as a Bioinformatics DevOps Engineer/Developer - Advanced Molecular Detection to contribute to genomic surveillance and outbreak investigations. You will work with the Bioinformatics Team, developing and implementing a cloud computing architecture to enhance our computational infrastructure. This remote role requires a Doctorate degree, 5+ years of post-degree experience, and AWS/Cloud experience. Responsibilities include planning and executing genomic analyses, developing bioinformatics pipelines, managing databases, providing technical assistance, and disseminating research results. The ideal candidate will have extensive experience in microbial bioinformatics, cloud computing, and scientific communication.

Requirements

• A PhD in bioinformatics, genomic epidemiology, microbiology, virology, parasitology, evolutionary biology, microbial genetics, molecular biology, computer science, or related field
• Must have 5 years+ experience following your degree
• At least five years of practical and technical experience in microbial and/or public health bioinformatics
• At least five years of experience with bioinformatic development of pipelines for the phylogenetic and comparative genomic analysis of microbial organisms
• At least two 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 (i.e., assembly, annotation, variant detection, multiple sequence alignment, phylogenetic tree building, pairwise SNP matrices, etc.)
• 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 with experience presenting complex, technical data to multidisciplinary teams
• Excellent written communication and experience publishing in the relevant scientific literature

Responsibilities

• Plan and execute whole-genome sequencing analysis, comparative genomic analysis, and other analytic research projects, establishing new standard operating procedures (SOPs) by developing custom bioinformatics pipelines/workflows
• 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 telephonic and web based 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
• Attend approved training workshops and complete a corresponding report on the training received

Preferred Qualifications

• Strong background in phylogenetics of bacterial and/or viral pathogens
• Must have 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

Benefits

Remote work