Bioinformatician

Position Summary:

We are seeking an experienced bioinformatician to join our global Augmented Diagnostics team. This team is dedicated to solving critical customer quality and safety challenges through data in the Global Food and Pharmaceutical Business spaces. The bioinformatician, who will be working out of the Invisible Sentinel’s offices in Philadelphia, will support a dynamic team  by understanding specific needs in terms of  bioinformatics data analysis of high throughput sequencing data. Next to the bioinformatics team, the candidate will work with software development and data science teams with the ultimate goal of creating novel tools for in vitro diagnostics assay design from high-throughput sequencing data.

This will be an exciting opportunity to bring state-of-the-art bioinformatics data analysis and data modeling techniques to the food and pharmaceutical manufacturing and assay development space. The Bioinformatician will be responsible for developing data analysis pipelines for microbial (bacterial, viral , yeast and molds) whole genome sequencing and metagenomics analysis: identification, assembly, target finding, annotation and phylogenetic inference, metataxonomics (amplicon-based) and shotgun metagenomics. He/she will work collaboratively with the Augmented Diagnostics and Invisible Sentinel teams to create state-of-the-art bioinformatics solutions that deliver actionable results to the final costumers.

Objectives of this Role:

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• Passion for discovering novel solutions for the analysis of sequencing data and work with stakeholders to improve business outcomes.
• Creative mindset—ability and willingness to try new out of the box approaches that might better fit the problem at hand
• Strong focus on value-creation for the customer and the team, in terms of short-term, day-to-day benefits and longer-term problem-solving
• Collaborative mindset as you will work with globally distributed bioinformatics, data science and development teams
• Learning together—adept at contributing to a growing pool of bioinformatics solutions and sharing knowledge within the international team
• Focus on communication—strong team interactions, and the ability to communicate analytic solutions to stakeholders and provide suggestions to implement improvements as needed to operational systems
• Capacity for self-development, independent work and flexibility to adapt to novel situations

Technical Skills

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• Proven experience in installing, using and maintaining bioinformatics tools for the genomic analysis for datasets originating from  bacterial, viral ,yeast or mold samples, with focus on high throughput sequencing data
• Proven experience in software and/or pipeline development for bioinformatics needs
• Experience in installing, using and maintaining bioinformatics tools for metataxonomics and/or shotgun metagenomicsCapacity to work in High Performance or Cloud Computing environments
• Ability to extract specific information and datasets from publicly available repositories
• Devise and utilize novel algorithms as needed to mine the available datasets , perform data and error analysis to improve models, and clean and validate resulting data for uniformity and accuracy
• Develop reporting templates for the bioinformatics pipelines developed with easy to interpret data visualization strategies
• Keep current with technical and industry developments
• Implement analytical pipelines into production environment by collaborating with software developers and engineers.

Required Education and Experience:

• 5-year degree (or equivalent) in Bioinformatics, Biology, Computer Science or related field
• 5 years of experience in microbial Bioinformatics (bacterial, viral and/or yeast) with focus in analyzing genomic data
• 5 Years of experience of programming experience in at least one of the most employed programming languages in bioinformatics: Python, R, or similar high level languages
• Demonstrated Python proficiency and knowledge of Javascript, CSS and other programming languages for the web and data visualization are preferential.
• Experience in using container based technologies such as Docker or Singularity
• Experience with High Performance Computing environments, using job scheduling software (SLURM, SGE, UGE) and workflow managers (Nextflow, SnakeMake, Apache AirFlow)
• Experience with common productivity software such as Word, Excel, PowerPoint
• Proficiency with data mining, mathematics, and statistical analysis
• Comfort working in a dynamic, research-oriented group with several ongoing concurrent projects
• Excellent written and verbal communication skills for coordinating across teams with multidisciplinary skill-sets.