Bioinformatics Scientist I/II/Senior

ClearNote Health; San Mateo, San Diego (CA, CA); Hybrid; USD 125,000 - 180,000; Full time

Benefits offered by this job

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Job summary

ClearNote Health seeks a Bioinformatics Scientist I/II/Senior to design algorithms identifying early-stage cancer from cell free DNA in plasma. You will work with a collaborative team across data analysis, model development, and production-ready code, delivering clinically relevant predictions from epigenomic data.

The role involves experimental design, data interpretation, and presenting results to diverse stakeholders while upholding ClearNote’s values of vision, integrity, and diversity.

Qualifications

• PhD or equivalent experience in Biophysics, Genetics, Genomics, Biochemistry, Molecular Biology, or related field with a strong computational focus.

Responsibilities

• Design and analyze experiments using ClearNote’s epigenomics platform.
• Develop and apply machine learning techniques tailored to the platform’s data.
• Analyze clinical genomics data to train models for cancer detection.
• Apply statistical methods to support rigorous decision-making.
• Evaluate and recommend software tools for epigenomic data analysis.
• Write clean, maintainable code following software engineering best practices.
• Present findings clearly to cross-functional stakeholders.
• Communicate hypotheses, data insights, and experimental designs to colleagues and advisors.
• Uphold ClearNote’s values with transparency and integrity.

Skills

Machine learning

Statistical methods

Python

R

Communication

Education

PhD or equivalent (Biophysics, Genetics, Genomics, Biochemistry, Molecular Biology)

Tools

Git

SQL

Python

R

AWS (EC2, Batch)

Job description

ClearNote Health is an early cancer detection company focused on the development and commercialization of non-invasive epigenomic tests to detect cancer through a standard blood draw, earlier than existing methods and when the disease is still treatable. Leveraging its novel liquid biopsy technology, ClearNote Health is initially focused on high-mortality cancers with the greatest need for early detection, starting with pancreatic and ovarian cancers.

Position Summary

We are seeking a Bioinformatics Scientist I/II/Senior to play a pivotal role in designing algorithms to identify early-stage cancer in cell free DNA from plasma.

In this high-impact position, you will work as part of a collaborative team to analyze epigenomic and genomic features from cell free DNA and develop classification algorithms for early cancer detection. You’ll contribute across the full lifecycle—from experimental design and data analysis to production-ready code and results presentation to cross-functional teams.

Key Responsibilities

• Design and analyze experiments using ClearNote’s epigenomics platform
• Develop and apply machine learning techniques tailored to the platform’s unique data characteristics
• Analyze clinical genomics data to train models that make clinically relevant predictions (e.g., cancer detection from epigenomic profiles)
• Apply appropriate statistical methods to support rigorous, scientifically sound decision-making
• Evaluate and recommend software tools for epigenomic data analysis
• Write clean, maintainable code following software engineering best practices
• Present findings clearly, concisely, and quantitatively to cross-functional stakeholders
• Communicate hypotheses, data insights, and experimental designs to colleagues, collaborators, and advisors
• Embody and uphold ClearNote’s core values—visionary, pioneering, truth-seeking, driven, honest and considerate communication, and a commitment to diversity—while operating with transparency and integrity

Qualifications

• PhD or equivalent experience in Biophysics, Genetics, Genomics, Biochemistry, Molecular Biology, or a related field with a strong computational focus
• Experience working with genomics technologies, preferably with cell free DNA
• Ability to interpret biological data quantitatively using principles of molecular biology and biochemistry
• Proficiency in statistical methods for supervised machine learning including logistic regression, random forest, and XGBoostExperience developing neural network models, particularly multi-layer perceptrons (MLPs)
• Familiarity with deep learning approaches for genomic/epigenomic data (e.g., DNA sequence models or foundation models) is a plus
• Understanding of common parametric and non-parametric statistical tests
• Strong programming skills in Python and/or R
• Experience using Git for version control in a collaborative environment (branching, merging, pull requests)
• Strong communication skills — both written and verbal — with the ability to explain complex concepts to cross-functional teams
• Experience with relational databases and SQL is a plus
• Experience with AWS services, particularly EC2 and Batch, is a plus

The anticipated salary range for this position is $125,000 to $180,000. The actual salary will be dependent on various factors that may include experience level, knowledge, skills, and abilities.

Come join us in addressing large healthcare needs through precision epigenomic medicine!

ClearNote Health is an exciting life science company that is reinventing non-invasive molecular diagnostic testing using next generation epigenomic technologies. We are passionate and dedicated to discovering and developing medicines that will make a significant difference in cancer and other epigenomic-driven diseases. Our technologies provide novel insight and quantitation of human health and disease, with our focus on precision medicine applications improving both clinical and health system outcomes. Our company was founded based on pioneering work in the Stanford laboratory of Stephen Quake, with advisors from Stanford and UCSF.

We look for extraordinary lifelong learners with a passion and growth mindset for these areas, and for combining biological ingenuity with AI and data analysis. Led by a team with decades of experience bringing products from concept to market, we are an equal opportunity employer and value diversity at our company.

We provide generous benefits to all employees including stock options. We are building a world-class company, based in San Diego and San Mateo.

Our commitment to Diversity, Equity, Inclusion, and Belonging:

We celebrate diversity in perspectives and backgrounds, and this is reflected in our innovation, our mission, and values. Our differences make us unique, help us innovate, and allow us to persevere. We strive to achieve representation and inclusion and redefine the possible in patients living longer lives.