Senior Bioinformatics Engineer

BillionToOne is a next-generation molecular diagnostics company dedicated to developing powerful and accurate diagnostic tests that are accessible to all. Our innovative QCT molecular counting technology significantly enhances the resolution of disease detection using cell-free DNA by over a thousandfold. This groundbreaking technology is integral to our product offerings, including one of our flagship products, Unity Complete™, the only non-invasive prenatal screen capable of assessing fetal risk for both common recessive conditions and aneuploidies from a single maternal blood sample. Leveraging the same molecular counting technology, we've expanded our impact into oncology in 2023 with a pioneering liquid biopsy test, Northstar, that combines treatment selection with monitoring. To date, over 500,000 patients have benefited from our innovative and precise diagnostic tests, and our Annual Recurring Revenue (ARR) has grown from $0 to $125 million in the last ~4 years.

BillionToOne has successfully raised close to $400 million in funding, with a notable $130 million Series D round completed in June 2024, resulting in a company valuation of over $1 billion. This funding has come from prestigious global institutional investors, including Hummingbird, Adams Street Partners, Neuberger Berman, Baillie Gifford, and Premji Invest. BillionToOne has recently been recognized by Forbes as one of America's Best Startup Employers for 2024, highlighting the company's exceptional work environment and commitment to innovation.

Our team has grown significantly and we now proudly employ over 400 highly skilled individuals. Despite substantial growth, we have successfully maintained the unique culture that has defined BillionToOne from inception, continuing to cultivate a team that is not only diverse and passionate but also innovative. Headquartered in Menlo Park, California, with an additional facility in Union City, California, BillionToOne remains at the forefront of significant advances in molecular diagnostics, evidenced by the recent announcement of clinical outcomes data for its Unity Fetal Risk Screen and new advancements in cancer diagnostics. For more detailed information about BillionToOne and its groundbreaking work, please visit our website at www.billiontoone.com.

We are looking for a Senior Bioinformatics Engineer to create computational tools that enable the analysis, interpretation, and reporting of ground-breaking molecular diagnostics data. This person will be responsible for building the bioinformatics pipelines, data analytics, interpretation tools, and automation needed to manage the generation, analysis, QC, and interpretation of clinical next-generation DNA sequencing data for the prenatal Unity Complete™ product. Our sample volume is growing extremely quickly, and this role will own the further development and scaling of our analysis pipelines to analyze tens of thousands of samples, as well as being a key engineer managing the infrastructure for everything related to our bioinformatics analyses. The Senior Bioinformatics Engineer role is a full-time onsite position in our Menlo Park office. 

Responsibilities:

• Analyze and troubleshoot day-to-day operations for clinical NGS data analysis
• Build and maintain infrastructure and tools to support the collection and analysis of  assay performance metrics, and contribute to publications that demonstrate the clinical validity and utility of our tests
• Design and build new tools to scale and automate variant filtering, interpretation, and classification processes 
• Collaborate and build microservice solutions with 10+ other clinically-oriented teams at BillionToOne
• Support the development of sophisticated and robust NGS analysis pipelines capable of processing tens of thousands of samples
• Design and build new visualization tools to support clinical decisions made by genetic counselors and lab directors. 
• Utilize SDLC and design control processes for building software used in regulated environments
• Conduct software design reviews; communicates plans and outcomes through architecture diagrams, presentations, and other project reports

Requirements:

• PhD in Bioinformatics, Biostatistics, Computational Biology, Computer Science, Bioengineering, or 5 years of direct experience performing the above-mentioned responsibilities
• 3-5 years of biology or bioinformatics research experience (during PhD or afterwards)
• 2-3 years of experience analyzing NGS data (during PhD or afterwards)
• Expertise in Python 
• Experience with R, or other programming languages used for data visualization
• Experience using data structures and industry tools, (GitHub, AWS, Heroku, PostgreSQL)
• Expertise with command-line tools and shell scripting within UNIX environments
• Experience with building and maintaining front-end tools for interacting with and visualizing analytical data
• Excellent communication and presentation skills, ability to work across functional teams and with non-experts.

Nice-To-Haves:

• Experience working with cross-functional teams
• Experience in leading and managing projects involving external team stakeholders
• Experience in mentoring or managing direct reports
• Biophysics, Molecular biology (DNA purification, PCR, electrophoresis), DNA synthesis, or next-generation DNA sequencing laboratory experience
• IT troubleshooting experience

Benefits And Perks:

• Working with a team of ‘rockstars’ who bring out the best in everyone
• Open, transparent culture that includes weekly Town Hall meetings
• The ability to indirectly or directly change the lives of hundreds of thousands patients
• Multiple medical benefit options; employee premiums paid 100% of select plans, dependents covered at 80%
• Extremely generous Family Bonding Leave for new parents (16 weeks, paid at 100%)
• Retirement savings program including a 4% Company match
• Free daily on-site lunches provided from top eateries
• Latest and greatest hardware (laptop, lab equipment, facilities)
• A variety of perks on campus (state of the art gym, restaurant)
• Free on-site EV charging (compatible with all EVs, including Tesla)

At BillionToOne, we are proud to offer a combination of a (1) base pay range (actual amount offered is based on experience and salary/equity options split that the candidate chooses), (2) generous equity options offering, (3) corporate bonus program, on top of (4) industry leading company benefits (free healthcare options, 401k match, very generous fully paid parental leave, etc.).

For this position, the base pay range is: $153,000 - $173,400 per year.

BillionToOne is an equal opportunity employer. We do not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status.