(Senior) Research Scientist - Proteomics

South San Francisco, CA
Oct 08, 2021
Biotech Bay
Required Education
Position Type

About the Role

At Freenome, our goal is to improve patient outcomes by pioneering the next-generation of blood tests for early and accurate disease detection using our combined multi-omics and machine learning platform. As a (Senior) Research Scientist in Proteomics, you will contribute to the program’s technical base by creating and optimizing new assays and workflows for protein biomarker discovery (including mass spectrometry and immunoaffinity approaches), and to the program’s scientific base by elevating our understanding of the biological context of these assay signals. In this role, you will evaluate emergent technologies that have the potential to improve our diagnostic tests, collect and analyze proteomics data for biomarker discovery, and augment existing multi-omic models with novel signals you discover. You will also work closely with computational biologists and machine learning scientists to provide biological and technical insights, and to provide new data sources to enhance ongoing computational research projects.

How you’ll contribute:

  • Develop and employ novel assays to discover and quantify protein biomarkers in clinical samples by applying expert knowledge of analytical chemistry and protein biochemistry.
  • Identify and test new proteomics technologies at pilot scale, and evaluate opportunities to integrate them into Freenome’s multiomics platform and products.
  • Refine existing proteomics assays by characterizing assay performance and implementing workflow and protocol improvements (including biofluid sample collection, protein extraction and depletion, and quantitation on discovery or targeted platforms).
  • Investigate the biological origin of blood-based biomarkers by performing detailed characterization of cell-free material, tumor tissues, and the immune compartments. 
  • Drive biomarker discovery studies that leverage datasets generated in-house and published reference databases.
  • Collaborate with computational biologists and software engineers to build analysis pipelines that appropriately integrate new molecular technologies.

What you’ll bring:

  • PhD (or equivalent industry experience) in molecular biology, biochemistry, chemistry, or a related field, with specific domain knowledge in cancer biology, immunology, and/or epigenetics.
  • ~3+ years post-PhD experience for Senior-level Research Scientist (or ~0+ years for Research Scientist) in proteomics assay development or biomarker discovery, with working knowledge of complex biological samples (e.g., plasma and tissue) and associated proteomic sample treatment methods (e.g., depletion, enrichment, and fractionation).
  • Proven track record of establishing or evaluating proteomics techniques for biomarker discovery and protein quantitation, including mass spectrometry and immunoaffinity approaches at the global and targeted scales.
  • Ability to perform basic data analysis to enable experimental iteration independent of external support. More advanced skills working with proteomics datasets using a scientific programming language (e.g., Python or R) are useful but not required.
  • Clear communications skills and ability to work with team members in the same, adjacent, and even unrelated disciplines.
  • Ability to manage broad research projects with contract research organizations, and to mentor and train research associates and junior scientists.
  • Valuable supplementary skills include:
    • Hands-on experience with multiplexed and/or high-throughput analytical platforms, such as peptide arrays, protein arrays, mass spectrometry, Luminex, Olink, and MSD.
    • Experience with experimental techniques for expressing, purifying, modifying, and characterizing protein products.
    • Experience with isolation, characterization, and analysis of extracellular vesicles from various bodily fluids
    • Previous industry/start-up experience in the life sciences, preferably in a regulated laboratory environment (CLIA, GLP/GCLP, IVD development).


Freenome has adopted a COVID-19 vaccination policy to safeguard the health and well-being of our employees. As a condition of employment, our employees working on-site are required to be fully vaccinated for COVID-19, unless a reasonable accommodation is approved or as otherwise required by law.


About Freenome

Freenome is on a mission to empower everyone with the tools they need to detect, treat, and ultimately prevent cancer.

We have pioneered the most comprehensive multiomics platform for early cancer detection through a routine blood draw.  By combining deep expertise in molecular biology with advanced computational biology and machine learning techniques to recognize disease-associated patterns among billions of circulating, cell-free biomarkers, we are developing simple and accurate blood tests for early cancer detection and integrating the actionable insights into health systems to operationalize a machine learning feedback loop between care and science. 

Our recent $270 Million Series C brings our financing to over $500 million from investors, including;  Bain Capital, Perceptive Advisors, RA Capital, Polaris Partners, Andreessen Horowitz, funds and accounts advised by T. Rowe Price Associates, Inc., GV (formerly Google Ventures), Roche Venture Fund, Kaiser Permanente Ventures, American Cancer Society’s BrightEdge Ventures, Data Collective Venture Capital, Novartis and Verily Life Sciences. 

Our Science

Freenome is building technology to advance the understanding of cancer through multiple analytes derived from blood. These signals include cell-free DNA, methylation of cell-free DNA, cell-free RNA, circulating proteins, and immune profiling derived from thousands of prospective samples. By developing novel statistical learning methods and applying them to integrate various -omics datasets, Freenome is a leader in modeling specific biological mechanisms to capture disease-dependent signatures, including gene expression, immune response, tumor burden, the tissue of origin, and 3D chromatin structure. 

By building comprehensive discovery datasets and modeling critical biological systems, Freenome is learning what biological changes are present within the blood between a variety of different disease states, including cancer, autoimmune disorders, infections, drug response, and aging. The synthesis of Freenome’s datasets, cross-functional technical expertise, and audacious mission to discover biological truth, we seek to improve the lives of millions through early detection and early treatment of disease.  

Our Culture

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. 

We value empathy, integrity, and trust in one another, and we respect the diverse perspectives of our colleagues and those we serve.  We assume positive intent and give each other the benefit of the doubt with the firm belief that we are a team working toward the same objectives.  We believe in empowering and supporting each other in a collaborative and dynamic environment. 

What does a successful person look like at Freenome?

Those who thrive at Freenome prioritize, manage, and execute their own goals with ownership and alignment with those of the company. They embrace our values of empathy, integrity, striving for greatness, servant leadership, trust, and holding themselves and their team accountable to these values. They crave collaboration with brilliant minds from disparate fields of study and believe that hiring and mentorship are fundamental to our success. Above all, they welcome and provide constructive feedback and criticism, trusting in others’ good intentions, and being secure in knowing that embracing mistakes is the best way to learn and grow. For those who pursue challenges, understudied problems, and want the opportunity to see their work impact the lives of millions of people affected by cancer every year, there’s no better place to be than Freenome.

Freenome is proud to be an equal opportunity employer and we value diversity. Freenome does not discriminate on the basis of race, religion, color, sex, gender identity, sexual orientation, age, non-disqualifying physical or mental disability, national origin, veteran status, or any other basis covered by appropriate law.