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Senior Director, Research Engineering

Remote, CA, USA | Freenome

  • Industry:
    Pharmaceutical / Biotech
  • Position Type:
  • Functions:
    General Management
    Scientific Research
  • Experience:
    3-5 years
    5-7 years
    7-10 years
Job Description:
61 people have viewed this job

Freenome is a high-growth biotech company on a mission since 2014 to create tools that empower everyone to prevent, detect, and treat their disease.

To achieve this mission, Freenome is developing next-generation blood tests to detect cancer in its earliest, most treatable stages using our multiomics platform and machine learning techniques. Our first blood test will detect early-stage colorectal cancer and advanced adenomas.

About the Role

As a Senior Director of Research Engineering at Freenome, you will be a leader contributing to the development of noninvasive tests for early cancer detection. 

In this role, you will lead a team of talented bioinformatics software engineers, machine learning (ML) software engineers, and informaticians. Through high-quality engineering and close collaboration with scientists, your team will implement best-in-class cloud-based infrastructure, guarantee data and results integrity, accelerate discovery, and provide the bridge from bespoke scientific analyses to mature software applications.

You will leverage a deep understanding of machine learning model development and/or computational approaches for molecular biology data types. You will provide scientific inspiration and technical guidance to team members, helping them to grow and develop, and empowering them to do their best work. Finally, you will be a key member of Freenome’s scientific and engineering leadership teams, contributing to decision making and prioritization.

Your contribution: 

  • Lead a team that implements best-in-class cloud-based data and computing infrastructure. Team responsibilities include:

    • ML Research Engineering: Developing robust and efficient computational infrastructure for ML model training, evaluation and application. Working closely with ML scientists to optimize infrastructure and support the evaluation and development of new ML architectures.

    • Bioinformatics Research Engineering: Developing robust and efficient computational infrastructure for molecular assay data. Working closely with computational and wet-lab scientists to optimize infrastructure and support exploration of new assay types and analysis approaches.

    • R&D Informatics: Accessioning and curating scientific data, and guaranteeing data integrity. Working closely with Freenome’s Real World Data Informatics group to share techniques and apply consistent approaches to research & development (R&D) data. 

    • Making R&D digital assets findable, accessible, interoperable and reusable (FAIR).

    • Collaborating with computational biologists and machine learning scientists to advance proof-of-concept approaches and deploy them as high-throughput reproducible workflows.

  • Serve as a key thought leader on scientific leadership teams.

  • Partner with other engineering and scientific staff at Freenome to develop roadmaps and strategies.

  • Nurture and grow a high-functioning Research Engineering team, by mentoring existing staff and recruiting new staff with skill sets and development goals aligned with Freenome’s mission.

  • Create opportunities for team members to undertake independent work and shape their own professional directions.

  • Interact effectively with teams and leadership in Freenome’s Software Engineering department, which implements the regulated, product-grade software used by our commercial blood tests.

  • Inspire a culture of innovation, translating discoveries into high-impact R&D pipelines and clinical applications. 

  • Exemplify Freenome’s commitment to “servant leadership” by maximizing the full team’s potential for impactful contribution. 

Your background, perspective and experience: 

  • PhD or equivalent experience in computer science, bioinformatics or another relevant computational analysis discipline.

    • Alternatively, a PhD in molecular or cancer biology (or similar) with extensive experience applying computational biology, bioinformatics and/or machine learning techniques.

  • 7+ years post-PhD (or PhD-equivalent) experience applying computational techniques to biological discovery and/or product development, managing large-scale molecular data repositories, or supporting machine learning model development.

  • Outstanding command of modern software engineering and data architecture practices, including several of the following:

    • Distributed high-performance computing.

    • Semantic modeling and graph database techniques.

    • Source code management.

    • Automated testing; continuous integration and deployment.

    • Containerization or other mechanisms for compute environment management.

    • User- and developer-facing documentation.

  • 3+ years managing scientific software engineers and/or computational scientists. Experience managing sub-team leads as well, helping them to grow as managers.

  • Track record of selflessly supporting highly effective cross-functional teams, and of collaborating closely with subject matter experts in other disciplines.

Nice to haves: 

  • Industry experience working in a diagnostics, pharmaceutical, or other biotechnology environment.

  • Experience managing and/or computing on genomics, epigenomics, proteomics, or transcriptomics data.

  • Experience with cloud-based high-performance computing.

COVID safety:

As a condition of employment, you agree to know and comply with our COVID-19 vaccination policy requiring all employees who work on-site and/or attend work-related events to be fully vaccinated and to receive a COVID-19 booster once eligible. Company employees working on-site are required to be fully vaccinated for COVID-19 and to receive a COVID-19 booster once eligible, unless a reasonable accommodation is approved or as otherwise required by law. Absent a reasonable accommodation or legal exception, you agree to provide proof of your vaccination status and to be fully vaccinated by your first day on-site, in accordance with our policy.If you are currently eligible for a COVID-19 booster, you also agree to provide proof of having received a booster.If you are not yet eligible for a COVID-19 booster, you must provide proof of receiving a booster within two weeks of becoming eligible.

Freenome is proud to be an equal opportunity employer and we value diversity. Freenome does not discriminate on the basis of race, color, religion, marital status, age, national origin, ancestry, physical or mental disability, medical condition, pregnancy, genetic information, gender, sexual orientation, gender identity or expression, veteran status, or any other status protected under federal, state, or local law.


We have raised more than $1.1B from leading investors including Perceptive Advisors, RA Capital Management, Roche Venture Fund, Kaiser Permanente, Novartis and the American Cancer Society’s BrightEdge Ventures. 


A ‘Freenomer’ is a mission-driven employee who is fueled by the opportunity to make a positive impact on patients' lives, who thrives in a culture of respect and cross collaboration, and whose work makes a significant impact on the company and their career. 

Freenomers are technical, creative, visionary, grounded, empathetic and passionate. We build teams around divergent expertise, allowing us to solve problems and ascertain opportunities in unique ways. Freenomers are some of the most talented experts in their fields, joining together to advance healthcare, one breakthrough at a time. 

Benefits include but are not limited to:

  • Competitive compensation 

  • Pre-IPO equity

  • Flexible PTO (exempt) and generous PTO (non-exempt) 

  • Comprehensive health coverage, including medical, dental, and vision 

  • Wellness and mental health resources, including Employee Assistance Programs (EAPs), Paid maternity and paternity leave

  • 401(k) plan 

  • $250.00 new hire stipend to enhance your home office experience

  • Plus, a variety of other perks, including pre-tax commuter benefits, two paid volunteer days per year, pet insurance, and additional discounts 

Notice to agencies:

Our in-house Talent Acquisition Team manages all employment opportunities at Freenome.Agencies and independent recruiters must be approved as a vendor by Freenome’s Talent Acquisition team before submitting candidates to any Freenome employee. 

We do not accept unsolicited resumes or biographies from agencies under any circumstances. Any unsolicited resumes sent to Freenome, including those sent to a Freenome email address or directly to Freenome employees, will be considered Freenome property. Freenome will NOT pay a fee for any placement resulting from the receipt of an unsolicited resume. Freenome will consider any candidate for whom an Agency has submitted an unsolicited resume to have been referred by the Agency free of any charges or fees. 

Please do not contact Freenome employees directly. Compliance with this request will impact our decision to work with you.

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