Lead Bioinformatics Engineer

Pay Range: $130000.00 - $160000.00 / 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.

Benefits Information:

We are proud to offer best-in-class benefits and programs to support employees and their families in living healthy happy lives. Our pay and benefit plans have been designed to promote employee health in all respects physical financial and developmental. Depending on whether it is a part-time or full-time position some of the benefits offered may include:

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

healthyMINDS mental health program

Vacation and Health/Flex Time

6 Holidays plus 1 MyDay off

FinFit 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 CloudWatch.
• 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/NoSQL) 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 Quests 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 DeepVariant Mutect2 VarDict Ensembl VEP SnpEff) and biological file formats (FASTQ BAM VCF BED).
• Cloud & DevOps: Demonstrated experience configuring and managing AWS cloud infrastructure (AWS Batch EC2 S3 IAM CloudWatch) using Infrastructure-as-Code (Terraform or CloudFormation).
• CI/CD & Git: Strong expertise in git version control collaboration (branching patterns pull requests) and automation via GitHub Actions or Jenkins.
• Containerization: Proficiency with Docker and Singularity including multi-stage builds and optimization.

Preferred Work Experience:

• Regulated Environments: 2 years of experience working in a clinical genomics space adhering to CAP CLIA GxP or FDA Title 21 CFR Part 11 requirements.
• LIMS & Integration: Experience integrating pipeline outputs into clinical reporting engines relational databases (PostgreSQL MySQL) or NoSQL databases.
• Databases: Working knowledge of clinical genomics databases (e.g. ClinVar gnomAD COSMIC ClinGen).

Work Environment:

• Hybrid work schedule

Travel required

Education

• Required: Bachelors in bioinformatics Computational Biology Computer Science Software Engineering or a closely related quantitative field with 7 years of professional industry experience.
• Preferred: Masters in bioinformatics Computational Biology Computer Science Software Engineering or a closely related quantitative field with 5 years of professional industry experience with a strong track record of production-level pipeline development.