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Principal Bioinformatics Scientist, Protein Decoding

Nautilus Biotechnology

Nautilus Biotechnology

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 actively seeking a talented Principal Bioinformatics Scientist in Protein Decoding. To democratize proteomic analysis, we rely on our ability to convert data from our instrument into actionable proteomic conclusions using our Protein Identification by Short-epitope Mapping (PrISM) approach. Your role will involve developing the protein decoding algorithms underlying PrISM which transform raw data into accurate protein identities and quantities for users.

We seek a leader whose communication, strategic thinking, and leadership abilities are as strong as their technical abilities. Your responsibilities will extend beyond the scientific. You'll cultivate a respectful environment, promoting open dialogue and nurturing team growth through individualized development plans. You will anticipate, define, and prioritize future technical directions for the protein decoding algorithms and workflows based on a holistic understanding of our product and customer needs. Research of these approaches is highly inter-dependent on many active research efforts across Nautilus including sample preparation, design of short-epitope recognition molecules, and instrument engineering. With so many moving parts and interactions, change is the expectation. As a people manager, this role requires an ability to maintain focus on key objectives and core principles while managing change effectively. You'll also manage recruitment initiatives for team expansion and set and monitor quarterly objectives.

This position will report to the Associate Director of Bioinformatics. This position is based in either San Carlos, CA, San Diego, CA, or Seattle, WA. A minimum of three days in office, preferred.


  • Independently devise and execute analyses on primary protein data, then communicate the results of said analyses in a clear and actionable manner to all members of the company regardless of their scientific background.

  • Set the direction for future evolution of our protein decoding approaches, including hands-on work to research, prototype, and test the accuracy & performance of any modifications to the decoding algorithms.

  • Work closely and cross-functionally with representatives of other disciplines across the company to provide them with an understanding of our current protein decoding capabilities and to guide experimental & instrument improvements to optimize our decoding performance.

  • Collaborate with the software engineering team to implement, validate, deploy, and monitor the identification & quantification algorithms in production at scale.

  • Build and drive execution of a quarterly development plan for all aspects of the decode work, including management of key cross-functional dependencies.

  • Lead bioinformatics efforts required to develop our protein identification and quantification algorithms.

  • Foster an environment where everyone can share their perspective and be treated with respect and kindness.

  • Grow the members of your team by working with them to develop and execute on their growth plan.

  • Drive the hiring process to expand your team as needed.

  • Set quarterly goals with your team and regularly report out on the status of those goals.

  • Provide thoughtful and actionable feedback on how to improve the effectiveness of the Decode Bioinformatics team.


  • PhD in Bioinformatics, Computational Biology, or related field with a minimum of 14 years of relevant industry experience.

  • 5+ years of experience in managing a team of bioinformatic scientists.

  • Demonstrated history of effectively leading an organized and dynamic team in a fast-paced, deadline driven environment, including determining team research direction and priorities.

  • Demonstrated ability to computationally model biological processes, then conceive and implement novel algorithmic approaches that extract insight from real-world data based on these models.

  • Familiar with combinatorics, probability, information theory, and supervised and unsupervised classification approaches.

  • Proficient with model evaluation and inference approaches, e.g., least squares regression, maximum likelihood estimation, expectation maximization, Gibbs & Metropolis-Hastings sampling.

  • Highly organized, motivated, know how to communicate clearly & effectively, and possess strong analytical and technical skills.

  • You can inspire positive change and foster a cooperative environment, all while operating effectively without direct oversight

  • You have a track record of driving organizational alignment with cross-functional and senior-level stakeholders, both within the company and outside it.

  • Comfortable working with complex algorithms and data sets in Python.


  • Experience in working with C++ is strongly preferred.

  • Experience managing a team of direct reports is preferred.

  • Experience working with AWS data storage and processing services (e.g. Athena, EC2, Batch, Glue).

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.