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Associate Director, Bioinformatics Upstream R&D

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 hiring for an Associate Director to lead our Upstream R&D Bioinformatics Team. Being successful in our goal of delivering novel proteomic results to the world is dependent on our ability to perform targeted discovery and characterization of a large set of affinity reagents (probes) which, in turn, will provide differential information via their binding behaviors about the proteins and proteoforms under analysis on the Nautilus platform. This individual will work closely with experimentalists and scientists on the probe development and qualification, assay development, and biochemistry teams, as well as other senior bioinformatics leaders within the company, to guide our probe discovery approaches, generate quantitative metrics for probe performance, and assist with the characterization efforts required to make these probes effective for all platform applications.

This position will report to the Associate Director, Bioinformatics and can be in San Carlos, CA; Seattle, WA; and we are open to consider San Diego, CA.


  • Lead the bioinformatics team responsible for supporting all our upstream R&D efforts, such as probe development and qualification, including determining research priorities and approaches for the team.

  • Assess in silico approaches to affinity reagent design and optimization, both internally and externally.

  • Contribute to company-wide strategic planning by leveraging existing data and assumptions grounded in biology to forecast and predict outcomes in hypothetical scenarios.

  • Assist wet-lab scientists with experimental design, data analysis, and interpretation of results in the domains of assay development, selection of antibodies and other affinity reagents, and evaluation of binding kinetics.

  • Implement custom machine learning approaches to improve throughput and success rate of the overall probe development pipeline.

  • Develop and apply statistical learning approaches to generate clear, actionable statements and visuals from biologically relevant datasets.

  • Serve as the technical representative for the Upstream Bioinformatics team company wide.

  • Maintain existing and establish new external collaborations.


  • A PhD degree in Bioinformatics, Computational Biology, or similar field.

  • 10+ years of experience in developing and applying bioinformatic analyses in the fields of proteomics, genomics.

  • 5+ years of experience in a bioinformatics leadership role.

  • Excellent track record of leading complex bioinformatics projects throughout all stages, from inception to deployment.

  • Proven ability to guide experimental design, model protein interactions in silico, and generate inferences from data using customized modeling approaches.

  • Comfort applying statistical analysis and visualization approaches to surface insights within various types of data.

  • Experience building automated end-to-end data processing pipelines that deliver actionable conclusions to scientists.

  • Fluency in a variety of programming languages, frameworks, and tools, especially Python.

  • Must have experience with building novel tools and working with raw data.

  • Experience with modeling software such as Rosetta or Schrodinger preferred.

  • Competency with SQL and AWS.

  • Strong organization and communication skills, with the ability to lead others both directly and through collaboration.

  • Preferred experience in deep learning, especially for application to the field of proteomics.

  • Ability to have fun when building complex systems while working side-by-side with experts from a variety of disciplines.

  • Self-motivated, driving projects forward to meet deadlines.

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 while continuously pushing ourselves forward.

  • We are detail oriented: we do great science by working smart and with diligence, and by learning from our 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.