Senior Bioinformatics Engineer, remote in Marlborough, MA at Quest Diagnostics

Date Posted: 7/17/2022

Job Snapshot

  • Employee Type:
    Full-Time
  • Location:
    200 Forest Street
    Marlborough, MA
  • Job Type:
  • Experience:
    Not Specified
  • Date Posted:
    7/17/2022
  • Job ID:
    req99029

Job Description



Look for more than answers.

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.

As a Senior 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 Operations group, part of the Research and Development organization, in Advanced Diagnostics based in Marlborough, MA.  The role is specific to genetic testing in a highly regulated CAP/CLIA laboratory environment using short and long-read sequencing as the basis of evidence.  The right candidate will know how to balance between innovation and standards with a practical understanding of when each is appropriate.  The Operations group supports, hones, and executes the processes defined by our Engineering group with emphasis in compliance and continuous improvement.  Though 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 can work 100% remote.



Job Responsibilities:

- Execute and improve sequence analysis workflows and automation

- Track, troubleshoot and mitigate issues encountered in processing production samples

- Plan and develop solutions to recurring issues to be merged back into development branch maintained by the Engineering group

- Produce data driven results and solutions for clinical geneticists, medical directors, operations lab personnel and other key stakeholders

- Generate, wrangle, merge and glean information from varied and complex data sets

- Implement RESTful APIs to various systems including LIMS, AWS job runners and other systems necessary for data processing and execution

- Perform validation, formal testing, and production deployments in pursuit of standardized processes across all Quest Diagnostics genetic testing labs

- Support production day-to-day operations

- Maintain production documentation for compliance and supportability of all bioinformatics processes in production environment

- Devise charts and visualization for use in dashboards, reports and in support of data driven hypotheses



Education, Experience preferred:

- B.S. plus 7 years applicable experience

- M.S. plus 5 years applicable experience

- Ph. D. plus 3 years applicable experience



Qualifications:

The ideal candidate will have the following skills and experience:

- 7 years experience using formal programming and scripting languages

- 7 years experience working on a Linux command-line to process, parse, and merge varied data sets

- 3 years experience working with web services and implementing API communications (REST, SOAP, etc)

- 3 years experience in a distributed HPC environment (cluster, cloud)

- Experience developing production grade software both supportable and extensible

- 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



Current tech stack experience is a plus:

- Programming Languages: Python, PERL, Groovy

- Web Frameworks: Python Flask, React Native, Bootstrap

- Environments: R Statistical Language

- Visualization: ggplot2/tidyverse, Tableau, d3.js

- Database: MySQL, MongoDB

- Cloud Computing: AWS, DNAnexus

- Pipeline Workflow Manager: Nextflow

- Source Control: Git

- CI/CD: Gitlab, AWS CDK

- Containerizing: Docker