Bioinformatics Engineer

At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can affect change at a rate unheard of in many organizations of our size and scope. While we invest in and develop technology to drive our innovations, our ongoing success relies on our people.

Quest Diagnostics Specialty Genetics products provide specific answers that clinicians need to deliver the appropriate diagnostic and prognostic care to their patients. You will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing. 

Bioinformatics, US Operations – the role

As a Bioinformatics Engineer, you will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing.

This position is in our Bioinformatics Operations group, part of the Research and Development organization, in Advanced Diagnostics based in Marlborough, MA. The team supports genetic/genomic testing in a highly regulated CAP/CLIA laboratory environment primarily using short and long-read sequencing as the basis of evidence.  The right candidate will know how to balance innovation, standards, and quality with a practical understanding of when each is appropriate.  The Bioinformatics Operations group supports, hones, and executes the processes defined by our Engineering and Lab Operations groups with emphasis on compliance and continuous improvement.  While coupled tightly to regulation through standards in validation, documentation, and data retention, the group is an integral part of the development cycle of our analysis workflows and visualization.

This position is intended to be near-site / hybrid with the intention of working on-site 2-3 days per week in our Marlborough, MA lab, and, if needed, provide rotating weekend coverage among a team of 5-6.

• Execute and improve sequence analysis workflows and automation
• Track, troubleshoot and mitigate issues encountered in processing production samples
• Assist in planning and development of solutions to recurring issues to be merged back into development branch maintained by the Engineering group
• Develop web-based results display and dashboards for clinical geneticists, medical directors and operations lab personnel providing clarity in our process
• Generate, wrangle, merge and glean information from varied and complex data sets Design and implementation of RESTful APIs linked to various systems including LIMS, AWS job runners and other systems necessary for data processing and execution
• Design and perform validation, testing, and production deployment of systems and software to standardize processes across all Quest Diagnostics genetic testing labs
• Design and perform validation analysis for new genomic testing products.
• Support production day-to-day operations
• Write and maintain production documentation for compliance and supportability of all bioinformatics processes in production environment
• Work directly with medical/quality/compliance to identify, track, resolve and report on any relevant quality-related issues
• Produce charts and visualization for dashboards, reporting, and in support of data driven hypothesis testing
• Perform LIS support duties (maintain database for user, tests, clients….)
• Support interface, integration, and testing projects
• Utilize a Software Development Life Cycle documentation procedure
• Be an active team player and support the group
• Accept input on solutions from other colleagues and teams

• 5 years experience using formal programming and scripting languages
• 5 years experience working on a Linux command-line to process, parse, and merge varied data sets
• 2 years experience working with web services and implementing API communications (REST, SOAP, etc.)
• 3 years experience in a distributed HPC environment (cluster, cloud)
• Knowledge and understanding of genomics, next-generation sequencing, and bioinformatics
• Experience developing and testing software
• Experience with source control in a development, testing, and production environment
• Automated testing experience; CI/CD experience preferred
• Knowledge of CAP documentation requirements a plus
• Experience communicating technical results and data is desirable

Current tech stack experience is a plus

Examples:

• Programming Languages: Python, PERL, Groovy, javascript, terraform
• Web Frameworks: Python Flask, React Native, Bootstrap
• Environments: R Statistical Language, iPython, Jupyter
• Visualization: Plotly, matplot lib, ggplot2/tidyverse, Tableau, d3.js
• Database: SQL (e.g., postgress, MySQL), MongoDB
• Cloud Computing: AWS
• Infrastructure management: terraform
• Pipeline Workflow Manager: Nextflow
• Source Control: Git
• CI/CD: Gitlab, AWS CDK
• Containerizing: Docker
• Microsoft UI: Access, VBA, Macros

Education:
Bachelor’s Degree - Required
Master’s Degree or PhD - Preferred

Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets