Lead Bioinformatics Engineer

Job Description

Pay Range: $ - $ / year

Salary offers are based on a wide range of factors including relevant skills, training, experience, education, and, where applicable, certifications obtained. Market and organizational factors are also considered. Successful candidates may be eligible to receive annual performance bonus compensation.

• Day 1 Medical, supplemental health, dental & vision for FT employees who work 30+ hours
• Best-in-class well-being programs
• Annual, no-cost health assessment program Blueprint for Wellness®
• healthy MINDS mental health program
• Vacation and Health/Flex Time
• 6 Holidays plus 1 'MyDay' off
• Fin Fit financial coaching and services
• 401(k) pre-tax and/or Roth IRA with company match up to 5% after 12 months of service
• Employee stock purchase plan
• Life and disability insurance, plus buy-up option
• Flexible Spending Accounts
• Annual incentive plans
• Matching gifts program
• Education assistance through MyQuest for Education
• Career advancement opportunities
• and so much more!

We are a leading oncology diagnostics company dedicated to advancing precision medicine through cutting edge ultra-sensitive genomic technologies. As we expand our portfolio of minimal residual disease (MRD) testing solutions, we are seeking a highly skilled and motivated Senior Bioinformatics Engineer to join our team. This role offers the opportunity to contribute to the development and implementation of bioinformatics methods that directly impact cancer patient care, enabling improved monitoring, and more informed treatment decisions.

The Senior Bioinformatics Pipeline Engineer will design, architect, optimize, and scale our clinical-grade Next-Generation Sequencing Bioinformatics workflows.

As a senior technical contributor, you will bridge the gap between assay development, assay validation, and clinical informatics systems. You will lead the implementation of automated computational workflows that process massive genomic datasets, ensuring the rapid, accurate, and secure delivery of diagnostic insights. Operating within a regulated clinical laboratory environment, you will champion modern software engineering practices, Infrastructure as Code (IaC), containerization, and advanced cloud orchestration to ensure high reproducibility, robust security, and absolute compliance with CAP, CLIA, NYSDOH, and FDA regulations.

This professional will work in a hybrid capacity out of one of the following offices:

Baltimore, MD
Secaucus, NJ
Marlborough, MA
Lewisville, TX

• Architect, implement, and maintain highly scalable genomic pipelines for processing high-throughput clinical NGS data (including Whole Genome, Whole Exome, Targeted Panels, RNA-Seq, Liquid Biopsy, and Somatic Variant Calling assays).
• Develop, modularize, and optimize complex workflow code using Nextflow or Snakemake to orchestrate data processing from raw sequencer output to final clinical variant interpretation.
• Design and implement containerization strategies (Docker, Singularity) to guarantee strict environment isolation, portability, and reproducibility across local HPC and cloud environments.
• Lead the migration, deployment, and monitoring of pipelines on cloud platforms (AWS), utilizing services such as AWS Batch, ECS, S3, Step Functions, Lambda, and Cloud Watch.
• Drive the adoption of modern software development life cycle (SDLC) best practices, including Git branch strategies, continuous integration/continuous deployment (CI/CD) workflows, comprehensive automated unit/integration testing (pytest, linting), and structural code documentation.
• Profile, benchmark, and optimize cloud compute resources to systematically reduce runtime, improve data throughput, and control operational cloud spend.
• Collaborate closely with Molecular Pathologists, R&D Scientists, and Software Engineers to integrate genomic pipelines with Laboratory Information Management Systems (LIMS), local/cloud clinical databases (SQL/No
  
  SQL), and electronic medical records via HL7/FHIR protocols.
• Author and execute formal Software Validation Plans, Software Design Specifications, Test Cases, and Validation Summary Reports in accordance with Quest's internal Quality System and regulatory frameworks (CAP/CLIA, FDA, NYSDOH).
• Establish automated regression testing frameworks, synthetic validation datasets, and benchmark controls to monitor pipeline precision, sensitivity, and clinical-grade accuracy.
• Provide technical guidance, conduct rigorous peer code reviews, and mentor mid-level and junior bioinformatics engineers on the team.

• Required
  
  Work Experience:
  
  
  • Python & Shell:
    Advanced proficiency in Python (including pandas, numpy, and testing libraries like pytest) and robust Bash/Shell scripting.
  • Workflow Management:
    Extensive hands-on experience designing and maintaining production-grade workflows using Nextflow (DSL2 preferred) or Snakemake in high-throughput environments.
  • Genomic Tools:
    Deep, working knowledge of NGS alignment, variant calling, and annotation suites (e.g., BWA, GATK,…