Bioinformatics Pipeline Engineer – NGS & Validation

Mount Sinai Medical Center; New York, Northern (NY, KY); Hybrid; USD 65,000 - 91,000; Full time

Job summary

Mount Sinai Health System is seeking a Bioinformatician to implement, validate, optimize, and maintain robust bioinformatics workflows in a Linux environment. The role emphasizes reproducible, scalable pipelines and adherence to scientific and regulatory standards.

The ideal candidate combines software development with hands-on NGS experience and collaboration with cross-functional teams to align delivery with research and clinical needs.

Qualifications

• BS in Biological Sciences, Bioinformatics, CS, Statistics or related; MS preferred.
• 3 years of experience; 2+ years in Linux software development preferred.
• Programming experience in Python, R, or Bash.
• Solid understanding of NGS technologies and QC metrics.
• Proficiency with workflow systems Nextflow, Snakemake, or WDL/Cromwell.
• Strong Linux system administration knowledge.
• Experience implementing tools in regulated environments.

Responsibilities

• Implement NGS bioinformatics pipelines, including annotation, QC workflows, and downstream analytical components.
• Own end-to-end validation of implemented pipelines, ensuring they meet scientific and regulatory requirements.
• Execute software verification and validation (SV&V) protocols and maintain thorough documentation of results.
• Evaluate new tools, algorithms, and software for integration into analytical workflows.
• Troubleshoot pipeline failures and drive root-cause analyses.
• Ensure reproducibility, scalability, and robustness of computational workflows.
• Partner with wet-lab teams, quality assurance, clinical operations, and product management to align implementation and validation objectives with project timelines and business needs.
• Maintain detailed records of implementation, validation activities, version control, and release notes.
• Prepare documentation in support of internal quality audits.
• Other related duties as assigned.

Skills

Python

R

Bash

Education

Bachelor's degree in Biological Sciences / Bioinformatics / CS / Statistics

MS preferred

Tools

Nextflow

Snakemake

WDL/Cromwell

Job description

Mount Sinai Health System is seeking a Bioinformatician to implement, validate, optimize, and maintain robust bioinformatics workflows in a Linux environment. The role emphasizes reproducible, scalable pipelines and adherence to scientific and regulatory standards.

The ideal candidate combines software development with hands-on NGS experience and collaboration with cross-functional teams to align delivery with research and clinical needs.