Bioinformatics Engineer I/II
FLSA: Exempt
Location: San Mateo, San Diego or Remote
Description
ClearNote Health is seeking a motivated and detail-oriented Bioinformatics Engineer to join our team. In this role, you will support internal research initiatives and help drive successful external collaborations through the development, maintenance, and execution of bioinformatics workflows. You will work closely with other research and development personnel in the Company to understand scientific requirements and to identify bioinformatics solutions. You will incorporate a range of existing and custom software to develop robust, scalable, and reproducible bioinformatic workflows in a timely manner. The ideal candidate should have a strong working knowledge of bioinformatics tools and pipelines, excellent organization skills, and good understanding of software engineering best-practices.
Responsibilities
- Develop and maintain cloud-based bioinformatics pipelines for next-generation sequencing (NGS) data in support of the research & development team
- Collaborate with the R&D team to identify and evaluate bioinformatics tools
- Collaborate with the R&D team to develop new machine learning features suitable for machine learning models trained to detect cancer and monitor treatment response
- Document requirements including expected input and output data types and example use cases
- Develop unit tests to ensure reproducible workflows
- Track development plans and progress of sprints
- Work with the rest of the engineering team to transition computational pipelines in the research environment to use in the clinical environment
- Survey current industry practices to identify opportunities for improving our code base
- Assist with servicing of customers, including the timely execution of in-house data processing and analysis pipelines and the transfer of these data to customers
Requirements
- Experience with developing scientific workflow system (e.g. Nextflow, Snakemake) for bioinformatics analysis
- Familiarity with best practices in software engineering and strong organizational skills
- Proficiency in Unix, SQL, Python and R
- Experience with working in a cloud computing environment (e.g. AWS, Azure)
- Working knowledge of molecular biology concepts and the principles of genomics technology
- Team player with excellent communication skills
- Ability to meet deadlines
- Attentive to detail with the ability to independently investigate/troubleshoot complex computational workflows
- Strong knowledge of file formats and tools commonly used in NGS bioinformatics workflows such as fastq, BAM, vcf, bed, bedtools, reference genome, annotations, bwa, WGS, samtools,
- Familiarity with containerization technology (e.g. Docker, Singularity)
- Familiarity with Git and best practices in software version control
Preferred
- Exposure to JIRA
- Experience creating visualizations for bioinformatics analysis
- Experience with differential gene expression analysis
What We Value
At ClearNote Health, we are driven by our mission and guided by our values:
- Put Patients First - Focused on serving patients and their support system, we direct all our efforts toward the area of greatest impact by discovering and building with speed, excellence, and purpose.
- Redefine the Possible - We are daring, imaginative, and focused in our pursuit of the next big idea. We take calculated risks to grow our business and improve patients’ lives.
- Together We Win - We encourage and challenge each other to achieve the greatest positive impact on those we serve: our customers, patients, colleagues, and stakeholders.
Compensation
Compensation is based on skills, experience, and qualifications. The estimated base salary range for this position is $121,667 - $187,833. with potential variation based on depth of experience and location. This role includes stock options and generous benefits.
Why ClearNote Health
ClearNote Health is a pioneering life sciences company applying next-generation epigenomic technologies to transform cancer diagnostics. Our tests are used by the National Cancer Institute and physicians around the world to detect cancer early, when it is most treatable. Founded on research from the Stanford lab of Dr. Stephen Quake and guided by world-class advisors, we are building products that provide actionable insights into human health and disease. With a passionate, experienced team and multiple commercially available tests, we are poised to make a lasting impact in precision medicine.
We are based in San Diego, CA and San Mateo, CA and backed by leading investors. Join us in redefining what’s possible in early cancer detection.Our Commitment to Diversity, Equity, Inclusion, and Belonging
We believe that innovation thrives in a culture of diverse perspectives and inclusive collaboration. We are committed to building a team that reflects the patients we serve and the world we want to live in. We celebrate individuality, equity, and integrity as foundational to our mission and success.
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.