Lead/Staff Bioinformatics Scientist - (Algo Dev for cfDNA pipelines)

Natera is seeking a highly skilled and innovative Lead or Staff Bioinformatics Scientist to join our Bioinformatics team as an individual contributor focused on algorithm development within production-scale pipelines. This role is critical to advancing our genomic technologies in Women’s Health and Organ Health, with a focus on cell-free DNA (cfDNA) applications.

You will be responsible for developing, optimizing, and validating novel algorithms and analysis modules for variant calling (SNVs, CNVs, SVs), methylation and fragment based biomarker development, custom quality control metrics, and tailored solutions using both short- and long-read sequencing data. The ideal candidate will have deep experience in algorithmic genomics, strong programming skills, and a passion for developing scalable, clinically impactful computational tools.

Primary Responsibilities:

Algorithm Development: Design, implement, and optimize novel algorithms for detecting SNVs, CNVs, and structural variants from cfDNA data. Develop customized biomarkers from SNPs, methylation, fragmentomics, multiomics. Establish QC metric frameworks to assess data integrity, coverage, noise, and assay-specific performance. Tailor algorithmic approaches to unique challenges in Women’s Health and Organ Health applications, including non-invasive prenatal testing (NIPT), organ transplant monitoring, and other cfDNA-based assays.

Integration into Production Pipelines: Collaborate closely with pipeline developers to integrate new algorithms into modular, scalable bioinformatics workflows. Ensure algorithms meet performance, reliability, and runtime benchmarks for clinical production environments. Contribute to pipeline architecture decisions to support extensibility and reproducibility.

Data Analysis Validation:Conduct in-depth performance benchmarking using synthetic, retrospective, and clinical datasets. Partner with assay development and clinical teams to define truth sets and evaluation criteria.

Cross-functional Collaboration: Work closely with RD, Data Science, Pipeline Engineering, and QA to align development with clinical requirements and operational standards. Participate in cross-functional initiatives to improve the interpretability, sensitivity, and specificity of Natera’s genomic products.

Innovation and Technical Leadership: Evaluate emerging tools and methods in variant detection, structural variation, and cfDNA data analysis. Propose and prototype novel statistical or machine learning approaches where appropriate. Contribute to the scientific direction of algorithmic innovation in Natera’s pipeline stack.

Qualifications:

• Ph.D. or M.S. in Bioinformatics, Computational Biology, Computer Science, or a related quantitative discipline.

• 4+ years (Lead) or 7+ years (Staff) of hands-on experience in NGS algorithm development post degree, preferably in clinical or production environments.

• Proven expertise in designing and validating biomarkers, variant calling and QC algorithms.

Knowledge, Skills, and Abilities:

• Strong knowledge of NGS variant calling for SNVs, CNVs, and structural variants, with emphasis on cfDNA analysis.

• Experience developing algorithms for both short-read and long-read sequencing platforms (e.g., Illumina, ONT, PacBio).

• Solid understanding of QC strategies for clinical sequencing, including noise modeling, coverage normalization, and contamination detection.

• Proficient in Python with strong background in performance optimization and numerical methods.

• Familiarity with statistical modeling, signal processing, or machine learning techniques for genomic data analysis.

• Experience working with pipeline orchestration tools (e.g., Nextflow, WDL, Snakemake) and version control (Git).

• Strong problem-solving and communication skills, with a demonstrated ability to work across interdisciplinary teams.