Staff Bioinformatician

Staff Bioinformatician

Role Summary

We are seeking a Staff Bioinformatician to lead the design, implementation, and optimization of computational methods supporting Germline, Prenatal, and Oncology next-generation sequencing (NGS) assays. You will drive analytical innovation across assay development, validation, and clinical deployment, collaborating closely with laboratory scientists, software engineers, and clinicians.

This is a senior technical individual contributor role—ideal for a scientist-engineer hybrid with deep NGS expertise and strong instincts for rigorous validation, robust pipeline design, and clinical performance.

Responsibilities

• Design, develop, and maintain analysis pipelines for germline variant calling, somatic variant detection, and cell-free DNA analysis.

• Lead bioinformatics strategy for assay development across multiple product lines (germline, oncology, and prenatal).

• Evaluate and integrate variant callers, CNV detection algorithms, phasing and haplotyping approaches, and artifact suppression models.

• Perform analytical validation and establish key performance metrics (sensitivity, specificity, LoD, LoQ, reproducibility, etc.) under CLIA/CAP and FDA frameworks.

• Collaborate with wet-lab scientists to guide assay design, capture performance, and sequencing strategy.

• Partner with software and data engineering teams to scale pipelines in production (e.g., AWS Batch, Kubernetes, Argo, Nextflow).

• Perform deep-dive analyses on challenging clinical cases, discordant results, and edge-case failure modes.

• Author technical documentation, validation reports, and regulatory submission materials.

• Mentor junior scientists and drive best practices in computational reproducibility and data governance.

Minimum Qualifications

• Ph.D. or equivalent experience in Bioinformatics, Computational Biology, or related field.

• 7+ years of experience in NGS data analysis, with at least 3 years in a clinical or regulated environment.

• Strong proficiency in Python, R, and Linux-based data processing.

• Expertise in one or more of:

  Germline variant calling (e.g., GATK, DeepVariant)

  Somatic variant calling (e.g., Mutect2, Strelka2, VarDict)

  CNV and SV detection (e.g., CNVkit, Manta, GATK-SV)

  Cell-free DNA or low-VAF variant detection

• Deep understanding of sequencing technologies (Illumina, hybrid capture, amplicon, cfDNA).

• Experience in analytical validation and regulatory submission (CAP/CLIA, NYS, or FDA).

• Strong collaborative communication skills across cross-functional teams.

Preferred Qualifications

• Experience with multi-analyte or liquid biopsy assays (ctDNA, cfDNA, fragmentomics).

• Familiarity with WES/WGS, exome panels, and hybrid capture performance modeling.

• Familiarity with containerized workflow execution (Docker, Kubernetes, Argo, Nextflow, WDL).

• Experience with cloud environments (AWS preferred) and distributed computing.

• Statistical modeling and ML experience for noise suppression, artifact modeling, or QC analytics.