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Senior Bioinformatics Scientist

Nautilus Biotechnology

Nautilus Biotechnology

San Carlos, CA, USA
Posted on Saturday, November 4, 2023
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 Senior Bioinformatics Scientist to join our growing team. Our vision of a world in which proteomic results are democratized hinges on our ability to convert data generated by our instrument and into actionable proteomic conclusions using our Protein Identification by Short-epitope Mapping (PrISM) approach. Your work will focus on fundamental research and development of the protein decoding algorithms that underpin this approach – algorithms that transform raw data into accurate protein identities and quantities presented to the user. We are looking for someone with strong communication and strategic thinking skills as well as technical abilities. 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 development. With so many moving parts and interactions, change is the expectation. Success in this role requires an ability to maintain focus on key objectives and core principles, while managing change effectively.
This position will report to the Associate Director of Bioinformatics. This position is based in San Carlos, CA. A minimum of three days in the 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 execute on a quarterly plan for your work including management of key cross-functional dependencies and prioritization of efforts.
  • Efficiently prioritize your time on a weekly basis to ensure the successful execution of the quarterly plan, while maintaining adaptability to unforeseen requirements, all while delivering timely status updates to key stakeholders whenever adjustments to the plan are necessary.


  • A PhD in Computational Biology, Bioinformatics, or a related field.
  • A minimum of 2-4 years of experience in industry
  • 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.
  • Familiarity with any of molecular biology, biophysics, analytical chemistry, systems biology.
  • Familiar with combinatorics, probability, information theory, and supervised and unsupervised classification approaches.
  • Ability to contribute on an organized and dynamic team in a fast-pace, deadline driven environment.
  • 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.
  • Comfortable working with complex algorithms and data sets in Python.
  • Experience in working with C++ is strongly preferred.
  • Experience working with AWS data storage and processing services (e.g. Athena, EC2, Batch, Glue) preferred.
  • Strong data visualization and communication skills.
  • Proven problem-solving skills and collaborative nature in fast-paced environment.

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.