Senior Computational Biologist, Assay Research

South San Francisco, CA
Nov 20, 2021
Biotech Bay
Required Education
Position Type
Full time


 About the Role

As a Senior Computational Biologist  on the Assay Research team at Freenome, you will help build novel NGS assays for early, noninvasive tests for cancer detection. You will bring a strong foundation in molecular biology to perform computational analyses enabling us to understand and identify cancer’s unique molecular signatures. You will work in close collaboration with wet lab scientists and other computational scientists to both iterate upon and build new assays  with the goal of developing clinical products that save lives.

How you’ll contribute:

  • Drive computational analysis in collaboration with wet-lab scientists to rapidly characterize and iterate on experimental methods by providing real-time assessments of assay performance.
  • Remain at the forefront of molecular techniques in NGS data generation and analysis (including genomics, epigenomics, and transcriptomics), and develop hypotheses regarding these techniques to assess computationally and in the lab.
  • Develop new bioinformatics pipelines and use computational tools to extract actionable information from high-throughput sequencing datasets, appropriately integrating new molecular technologies.
  • Develop classification models using novel molecular signatures and evaluate feasibility of entering the development phase.
  • Overcome analytical challenges inherent in the study of cell-free circulating

What you’ll bring:

  • PhD or equivalent experience in a relevant field such as molecular biology, computational biology, bioinformatics, or equivalent.
  • 3+ years post-PhD experience, including industry experience in molecular diagnostics.
  • Expertise in computational analysis of NGS datasets to derive technical and biological insights. Experience in liquid biopsy and transcriptomics is highly preferred.
  • Experience building and maintaining bioinformatics pipelines, with proficiency in common bioinformatics tools, such as FastQC, Atropos, Picard, Bowtie, BWA, Samtools, and IGV.
  • Fundamental understanding of the central dogma, including background in molecular biology, cancer biology, and familiarity with regulation of molecular processes.
  • Strong quantitative reasoning and statistical analysis skills, with a demonstrated ability to apply them effectively to relevant scientific problems.
  • Strong computational and programming skills, including experience with Python statistical packages (Numpy, Matplotlib, Pandas). Equivalents in other languages like R or C/C++ are also suitable.
  • Familiarity working in a Linux server-based environment.
  • Excellent oral and written communication skills to communicate to both scientific and broader audiences.
  • Ability to work on a cross-functional team in our highly collaborative environment, working with both computational and experimental scientists.

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.