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Staff Software Engineer

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 currently hiring a Staff Software Engineer at Nautilus Biotechnology. Your role will encapsulate the design, execution, and optimization of sophisticated algorithms driving our Protein Identification by Short-epitope Mapping technology (PrISM). These algorithms are central to translating observed binding data to confident protein quantities. You will be responsible for novel algorithm implementation, optimization (including on GPU), and driving and innovating best-practices around this ecosystem of software tools. 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.


  • Develop, maintain, and optimize our protein decoding algorithm (implemented in C++) in collaboration with members of the bioinformatics team.

  • Devise and implement novel ways to ensure the correctness of these protein decoding algorithms.

  • Generalize these solutions to solve other analytical problems that require high-speed computation or leverage GPU-based techniques.

  • 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 7+ 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.

  • 2-3 years experience working with bioinformatics

  • Proficiency in C++ is crucial.

  • Experience with Python – and particularly integrating Python with C++ is a huge plus.

  • 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