Manager and Staff Scientist, Computational Proteomics Research

South San Francisco, CA
May 21, 2022
Biotech Bay
Required Education
Masters Degree/MBA
Position Type
Full time


About Freenome 

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.


As Manager, Computational Proteomics Research in the Computational Biology group at Freenome, you will play a key role in advancing the company’s mission to detect cancer early via cutting-edge, non-invasive multiomics tests. You are a strong individual contributor with an outstanding record of scientific achievement, who has recently moved — or is ready to move — into a formal scientific leadership role. You will apply both your scientific expertise and leadership skills to mentor and grow a team that will work closely with Molecular Research scientists to design, execute, and analyze experiments identifying new protein and peptide biomarkers of disease. 

Via regular literature review and conference attendance, you and your team will keep abreast of the state of the art in computational proteomics and identify novel research avenues and opportunities. Finally, you will collaborate with a multi-disciplinary, multi-analyte scientific and engineering team to help translate the results of your work into Freenome’s portfolio of diagnostic products.

How you’ll contribute:

  • Lead and support the growth of the Computational Proteomics team in contributing to the development of Freenome’s proteomics discovery platform. 
  • Contribute to the design of experiments at the forefront of protein characterization techniques requiring mass spectrometry data generation (including DDA, DIA, PTMs, AP-MS) and immunoassays (ELISA, Olink, Luminex, MSD, flow cytometry).
  • Design studies and execute analyses focused on discovering novel protein-based biomarkers.
  • Develop new bioinformatics pipelines and computational tools to extract actionable information from high-throughput proteomics datasets.
  • Partner cross-functionally with computational and wet-lab scientific leaders at Freenome to develop a multiomic scientific roadmap and research strategy.
  • Inspire a culture of scientific innovation, focused on translating discoveries into high-impact clinical applications.

What you’ll bring: 


  • Ph.D. in bioinformatics, cancer biology, or related field with a focus on computational proteomics.
  • 3+ years of industry experience, including experience leading scientific teams  
    • Experience in experimental design and analysis of high-throughput, quantitative technologies in proteomics.
    • Experience in the evaluation and application of appropriate statistical methods given a hypothesis and available data.
  • Expertise in effective data analysis and visualization using Python, R,  or equivalent. 
  • Experience with source code version control. Experience with cloud-based computing and containerized compute environments is a plus.
  • Excellent oral and written communication skills to communicate to scientific and broader audiences, with keen attention to detail.
  • Ability to work on a cross-functional team in our highly collaborative environment, working with both computational and experimental scientists.
  • Valuable supplementary qualifications include:
    • Industry experience applying computational techniques to biological discovery and product development.
    • Knowledge of cancer biology, and experience leveraging this knowledge for problems in cancer computational biology and diagnostics. 
    • Experience using quantitative proteomics and systems biology approaches (e.g., proteogenomics, network analysis, gene ontology) for biomarker discovery or related applications.


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 

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Applicants have rights under Federal Employment Laws.  


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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