Bioinformatics Scientist I/II/Senior

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 platformDevelop and apply machine learning techniques tailored to the platform’s unique data characteristicsAnalyze 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-makingEvaluate and recommend software tools for epigenomic data analysisWrite clean, maintainable code following software engineering best practicesPresent findings clearly, concisely, and quantitatively to cross-functional stakeholdersCommunicate hypotheses, data insights, and experimental designs to colleagues, collaborators, and advisorsEmbody 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 focusExperience working with genomics technologies, preferably with cell free DNAAbility to interpret biological data quantitatively using principles of molecular biology and biochemistryProficiency 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 plusUnderstanding of common parametric and non-parametric statistical testsStrong programming skills in Python and/or RExperience 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 teamsExperience with relational databases and SQL is a plusExperience with AWS services, particularly EC2 and Batch, is a plusThe 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.