Senior Bioinformatics Engineer (Hybrid)

Quest Diagnostics

  • Lewisville, TX
  • Permanent
  • Full-time
  • 1 month ago
Job Category: ScientistJob 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.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.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 Lewisville, TX. 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 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 is intended to be near-site / hybrid with the intention of working on-site 2-3 days per week in our Lewisville, TX lab, and, if needed, provide rotating weekend coverage among a team of 5-6.Responsibilities:
  • Execute and improve sequence analysis workflows and automation
  • Track, troubleshoot and mitigate issues encountered in processing production samples
  • Develop new software applications or customize existing applications to meet specific scientific project needs.
  • Plan and develop solutions to recurring issues to be merged back into development branch maintained by the Engineering group
  • Develop and present web-based results and dashboards for clinical geneticists, medical directors and operations lab personnel staff, ensuring transparency and clarity in processes.
  • 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, testing, and production deployment in pursuit of systems to standardize processes across all Quest Diagnostics genetic testing labs
  • Support production day-to-day operations and on-call off hours
  • Maintain production documentation for compliance and supportability of all bioinformatics processes in production environment
  • Produce charts and visualization in dashboards, reporting and in support of data driven hypotheses
  • Perform validations, formal testing, and deployment schemes to production systems
  • Perform validations, formal testing, and deployment schemes to production systems
  • Perform LIS support duties (maintain database for user, tests, clients….)
  • Support interface integrating and testing projects
  • Be an active team player and support the group
  • Excellent analytical, troubleshooting and problem-solving abilities. Proficient in diagnosing and providing solutions for bugs and issues.
  • Support On-call rotations as needed.
Qualifications:
  • 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, JavaScript
  • Frameworks: Python Celery, Python Flask, React Native, Bootstrap
  • Environments: R Statistical Language, iPython, Jupyter
  • Visualization: Plotly, matplot lib, ggplot2/tidyverse, Tableau, d3.js
  • Database: SQL (e.g., PostgresSQL, MySQL), MongoDB
  • Cloud Computing: AWS EC2 and serverless, DNAnexus
  • Infrastructure management: Terraform
  • Pipeline Workflow Manager: Nextflow
  • Source Control: Git
  • CI/CD: Gitlab/GitHub
  • Containerizing: Docker
Education:
Bachelor's Degree Required
Master's Degree or PhD PreferredAbout the Team: Quest Diagnostics honors our service members and encourages veterans to apply.While we appreciate and value our staffing partners, we do not accept unsolicited resumes from agencies. Quest will not be responsible for paying agency fees for any individual as to whom an agency has sent an unsolicited resume.Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets or any other legally protected status.

Quest Diagnostics