Staff Scientist, Machine Learning (Genomics)

Natera; United States; Remote; USD 167,000 - 209,000; Full time

Benefits offered by this job

Comprehensive medical

Dental

Vision

Life and disability plans

401k benefits

Commuter benefits

Job summary

Natera is seeking a Staff Machine Learning Scientist to join our Data Science research team. You will design and prototype cutting-edge algorithms for genetic and clinical data analysis, perform data analysis, and interact with R&D and product teams to define requirements and improve products.

You will lead ML/DL research, develop models using NGS data, and work with bioinformatics pipelines. The role involves collaboration with molecular biology teams, ensuring rigorous validation and

Qualifications

• MS or PhD in a quantitative field such as Computer Science, Applied Mathematics, Statistics, Bioinformatics, Computational Biology, Engineering, or similar. Equivalent depth built through work counts fully.
• 6+ years of hands-on experience in machine learning and data analysis on biological or genomic data after your degree.
• A demonstrated track record of models or algorithms you led that reached real use (a product, a production pipeline, or a decision someone relied on).
• We are hiring for depth in NGS, bioinformatics, and machine learning, and we will provide the domain ramp.

Responsibilities

• Lead ML/DL research on models using NGS data and set technical direction.
• Design, build, and benchmark models behind Women Health and Organ Health products.
• Work with sequencing pipelines and troubleshoot results across processing steps.
• Collaborate with biology scientists to design experiments and data requirements.
• Contribute to high-quality technical and design documentation.

Skills

Python

ML/DL

NGS data

Statistics

SQL

Cloud platforms

Model validation

Education

MS/PhD in quantitative field

Tools

PyTorch

TensorFlow

scikit-learn

Nextflow

Docker

AWS

Job description

Natera is seeking a highly motivated Staff Machine Learning Scientist to join our rapidly growing company. As a member of the Data Science research team you will participate in the design and prototyping of cutting edge algorithms for analysis of genetic and clinical data. You will perform data analysis, algorithm design, contribute to our intellectual property portfolio, and interact closely with R&D and product teams to define the requirements and improve the products and processes.

Primary Responsibilities

• ML/DL Research Leadership: Lead research on machine learning and deep learning models using NGS data. Frame the problem, choose the approach, and decide when a model has earned the next round of investment. This is an individual contributor role with Staff-level scope. You will set the technical direction of the work, not just carry out a plan someone else wrote.
• Algorithm and Model Development: Design, build, and benchmark the models and features behind the next generation of Women Health and Organ Health products. Apply statistical learning and deep learning to high-dimensional, noisy, often small-sample sequencing data. Know when a simpler method is the right answer.
• Working with Bioinformatics Pipelines: Work directly with the existing sequencing pipelines and their outputs without needing a bioinformatician to run, change, or interpret them for you. When results look wrong, trace the problem back through each processing step and work out whether it comes from the pipeline, the data, or the biology. Build or extend pipeline components when a project needs it.
• Study Design and Experimental Partnership: Work with molecular biology and assay development scientists to design experiments. Help decide what data to generate, how much of it, and with what controls so the analysis can answer the question. Troubleshoot experiments alongside the lab, and tell a biology problem from a data or analysis problem.
• Rigor and Documentation: Set the standard for careful analysis on the team: sound validation design, honest performance estimates, no leakage between training and evaluation data, and documentation. Support the group in producing high-quality technical and design documentation.
• Intellectual Property and Scientific Contribution: Contribute to Natera's IP portfolio through invention disclosures and patent work, and to its scientific reputation through publications and presentations where appropriate.
• Technical Leadership and Mentorship: Mentor data scientists and bioinformaticians, review their work, and be the person others bring hard modeling questions to. Make decisions about your own methods with minimal direction, including when the problem is ambiguous, and know when the problem is ambiguous, and know when to escalation.
• Ways of Working: AI is a routine part of the work here, including coding agents for implementation, analysis, and review. You own what you ship, whatever produced it. We do not screen for prior experience with these tools, and we provide the tooling and the ramp time.

Qualifications

• M.S. or Ph.D. in a quantitative field such as Computer Science, Applied Mathematics, Statistics, Bioinformatics, Computational Biology, Engineering, or similar. Equivalent depth built through work counts fully.
• 6+ years of hands‑on experience in machine learning and data analysis on biological or genomic data after your degree. We count relevant experience from the point your work became substantially independent, however you got there.
• A demonstrated track record of models or algorithms you led that reached real use (a product, a production pipeline, or a decision someone relied on), not only a result.
• We are hiring for depth in NGS, bioinformatics, and machine learning, and we will provide the domain ramp.

Knowledge, Skills, And Abilities

• Depth in next‑generation sequencing data analysis: sequencing QC, alignment and quantification, normalization, and the artifacts that come with them. You should have the judgment to spot a wrong result before someone else does.
• Working fluency with NGS bioinformatics pipelines. You can run them on your own, read their code and logs, follow a result back through each processing step, and diagnose failures or unexpected outputs. You can also build or modify pipeline components when needed.
• Extensive practical experience with machine learning, deep learning, and statistics, including model validation and performance estimation on limited or imbalanced data.
• Advanced Python, including open‑source ML libraries (e.g., scikit‑learn, PyTorch, TensorFlow, XGBoost) in a cloud environment.
• Experience processing large datasets and working with a query language such as SQL.
• A proven ability to apply mathematical and statistical principles to real estimation problems and turn them into practical solutions.
• Familiarity with assay development and analysis pipelines for molecular or clinical biomarkers.
• Clear communication of technical results to people who do not share your background, and a record of delivering complex projects with cross‑functional teams.

Preffered Skills

• Experience with RNA‑seq, small RNA/miRNA.
• Experience building probabilistic models for NGS and omics data.
• Experience with diagnostic product development in a regulated or CLIA/CAP setting.
• Experience with workflow orchestration (Nextflow, WDL, Snakemake) and containerization (Docker), enough to read, debug, and extend existing workflows.
• AWS or GCP for large‑scale ML training and inference.
• Patents, peer‑reviewed publications, or conference presentations.
• A desire to work in a fast‑paced environment where a small team has high impact.

Remote USA

$167,400—$209,200 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.

Competitive Benefits

• comprehensive medical
• dental
• vision
• life and disability plans
• free testing
• fertility care benefits
• pregnancy and baby bonding leave
• 401k benefits
• commuter benefits
• generous employee referral program!

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: https://www.natera.com/notice-of-data-collection-california-residents/

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.