Lead Bioinformatics Engineer
Quest Diagnostics7 days ago
Baltimore, MD, USAStaff+
Base Salary
$130k - $160k/yr
Responsibilities
- Architect, implement, maintain, and scale clinical genomic pipelines for high-throughput NGS data across whole genome, whole exome, targeted panel, RNA-Seq, liquid biopsy, and somatic variant calling assays.
- Develop and optimize production workflows using Nextflow or Snakemake from raw sequencer output through clinical variant interpretation.
- Design containerization strategies with Docker and Singularity for reproducibility across HPC and cloud environments.
- Deploy and monitor pipelines on AWS using AWS Batch, ECS, S3, Step Functions, Lambda, and CloudWatch.
- Implement software development, Git, CI/CD, automated testing, documentation, and peer review practices.
- Benchmark cloud resources to improve runtime and throughput while controlling cloud costs.
- Integrate genomic pipelines with LIMS, clinical databases, reporting engines, and electronic medical records through HL7/FHIR.
- Author and execute software validation plans, design specifications, test cases, and validation summary reports under applicable quality and regulatory frameworks.
- Establish regression testing, synthetic validation datasets, and benchmark controls for pipeline precision, sensitivity, and clinical accuracy.
- Provide technical guidance and mentor junior and mid-level bioinformatics engineers.
Requirements
- Bachelor's degree in bioinformatics, computational biology, computer science, software engineering, or a closely related quantitative field plus 7+ years of professional industry experience, or a master's degree plus 5+ years of professional industry experience.
- Advanced Python proficiency, including pandas, NumPy, pytest, and robust Bash or shell scripting.
- Extensive hands-on experience designing and maintaining production workflows with Nextflow or Snakemake, preferably Nextflow DSL2.
- Deep knowledge of NGS alignment, variant calling, annotation tools, and biological file formats including FASTQ, BAM, VCF, and BED.
- Demonstrated AWS infrastructure experience with AWS Batch, EC2, S3, IAM, and CloudWatch using Terraform or CloudFormation.
- Strong Git, branching, pull request, CI/CD, GitHub Actions, or Jenkins experience.
- Proficiency with Docker and Singularity, including multi-stage builds and optimization.
- Preferred: 2+ years in clinical genomics or regulated environments using CAP, CLIA, GxP, or FDA Title 21 CFR Part 11 requirements.
- Preferred: experience integrating pipelines with clinical reporting engines, PostgreSQL, MySQL, or NoSQL databases.
- Preferred: working knowledge of ClinVar, gnomAD, COSMIC, and ClinGen.
Benefits
- Day 1 medical, supplemental health, dental, and vision coverage for eligible full-time employees.
- Well-being, mental health, health assessment, vacation, health/flex time, holiday, financial coaching, life and disability insurance, flexible spending, and 401(k) programs.
- Employee stock purchase plan, annual incentive plans, matching gifts, education assistance, and career advancement opportunities.
- Hybrid work schedule in Baltimore, MD; Secaucus, NJ; Marlborough, MA; or Lewisville, TX.
- Travel is required.
Categories
Data Engineering