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. PrimaryResponsibilities: 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 R&D, 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. The pay range is listed and actual compensation packages are based on a wide array of factors unique to each candidate, including but not limited to skill set, years & depth of experience, certifications and specific office location.This may differ in other locations due to cost of labor considerations. Remote USA $156,200 - $195,300 USD OUR OPPORTUNITY Natera™ is a global leader in cell-free DNA (cfDNA) testing, dedicated to oncology, women’s health, and organ health. Our aim is to make personalized genetic testing and diagnostics part of the standard of care to protect health and enable earlier and more targeted interventions that lead to longer, healthier lives. The Natera team consists of highly dedicated statisticians, geneticists, doctors, laboratory scientists, business professionals, software engineers and many other professionals from world-class institutions, who care deeply for our work and each other.When you join Natera, you’ll work hard and grow quickly. Working alongside the elite of the industry, you’ll be stretched and challenged, and take pride in being part of a company that is changing the landscape of genetic disease management. WHAT WE OFFER Competitive Benefits - Employee benefits include comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents. Additionally, Natera employees and their immediate families receive free testing in addition to fertility care benefits.Other benefits include pregnancy and baby bonding leave, 401k benefits, commuter benefits and much more. We also offer a generous employee referral program! For more information, visit www.natera.com. Natera is proud to be an Equal Opportunity Employer. We are committed to ensuring a diverse and inclusive workplace environment, and welcome people of different backgrounds, experiences, abilities and perspectives. Inclusive collaboration benefits our employees, our community and our patients, and is critical to our mission of changing the management of disease worldwide.All qualified applicants are encouraged to apply, and will be considered without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, age, veteran status, disability or any other legally protected status. We also consider qualified applicants regardless of criminal histories, consistent with applicable laws. If you are based in California, we encourage you to read this important information for California residents. Link: Please be advised that Natera will reach out to candidates with a @natera.com email domain ONLY.Email communications from all other domain names are not from Natera or its employees and are fraudulent. Natera does not request interviews via text messages and does not ask for personal information until a candidate has engaged with the company and has spoken to a recruiter and the hiring team. Natera takes cyber crimes seriously, and will collaborate with law enforcement authorities to prosecute any related cyber crimes. For more information:- BBB announcement on job scams - FBI Cyber Crime resource page Apply tot his job