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Senior Software Engineer II, Bioinformatics

Nautilus Biotechnology

Nautilus Biotechnology

Software Engineering
San Carlos, CA, USA · San Diego, CA, USA · Seattle, WA, USA · Seattle, WA, USA · San Carlos, CA, USA · San Diego, CA, USA
Posted on Wednesday, May 22, 2024

At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the proteome to accelerate drug development and enable a new world of precision and personalized medicine. We are developing a single-molecule protein analysis platform of unprecedented sensitivity, scale, and ease of use that we believe will democratize access to the proteome – one of the most dynamic and valuable sources of biological insight. To accomplish this, we are pursuing hard scientific problems with an entrepreneurial mindset and creating a world-class team of builders, innovators, and dreamers across a wide range of disciplines.

We are hiring a Senior Software Engineer II, Bioinformatics at Nautilus Biotechnology. Your role will encapsulate the design, execution, deployment, and evolution of systems to drive critical analyses supporting research and development. These systems will gather, store, collate, and expose via API the raw data that drives key research insights. Moreover, you will play a key role in fortifying our data engineering processes to accelerate development of research tools supporting our internal R&D efforts. The individual in this role has a significant opportunity to make a profound, lasting impact on our technology and the company's trajectory.

This position will report to the Associate Director of Software Engineering.


  • Implement best practices in data warehousing, transformation, and modeling to support internal research efforts.

  • Work with the bioinformatics and experimental teams to put powerful data visualizations and analyses into the hands of our experimentalists.

  • Coordinate with other software teams to deploy decoding algorithm updates to our customer-facing portal.

  • Maintain comprehensive documentation for algorithms, data engineering processes, and code to facilitate knowledge sharing and future research.

  • Remain current on new technologies and available vendor packages; evaluate them and make recommendations as necessary.


  • A minimum of 5+ years of relevant experience in a high performing software engineering organization(s) is required.

  • Bachelor’s degree in Computer Science or related field is required.

  • Proficiency in C++ and python is crucial.

  • Fluency in a wide array of programming concepts, languages, and tools.

  • Experience with data storage and processing technologies like SQL, NoSQL, Hadoop, Spark, and cloud-based solutions (e.g., AWS, Azure, or GCP).

  • Excellent problem-solving skills and the ability to collaborate effectively in a multidisciplinary environment.

  • Strong communication skills and the ability to translate technical concepts for non-technical stakeholders.

  • Enthusiasm for science and a strong commitment to advancing scientific research through software engineering.

  • Proven experience in developing algorithms and data engineering solutions in the biotech or proteomics space preferred.

  • Familiarity with PySpark, or other distributed computation framework preferred.

Nautilus Team Culture

  • We are curious go-getters: this is a team of life-long learners who aren’t afraid to tackle the big challenges and we embrace the journey

  • We are detail-oriented: we do great science by working smart & with diligence where we learn from our trials and mistakes

  • We are easy to work with: we want our workplace to be one where everyone can share their perspective and be treated with respect and kindness