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Associate Director, Software Engineering

Nautilus Biotechnology

Nautilus Biotechnology

Software Engineering
San Diego, CA, USA
Posted on Tuesday, June 25, 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 looking for an Associate Director of Software Engineering to join our growing company. A candidate stepping into this highly visible role will provide both technical and people leadership for diverse software engineering teams, contribute their voice to the ongoing conversation around the Nautilus software architecture, scale, and long-term strategy, and be responsible for the design and implementation of the real-time control software that runs our instruments and the image processing software that extracts precise signal from acquired image data. Our novel proteomic technology is still in its formative stages, which means that anyone in this role will be able to have a meaningful & outsized impact on our technology and on the company’s path to future success.

This position will report to the Senior Director of Software Engineering and is preferentially located in San Carlos, CA, or in San Diego, CA or Seattle, WA.


  • You will provide direct, hands-on technical and people leadership for the Instrument Control software team as well as indirect leadership support for the Image Processing software team

  • You will manage, mentor, and grow several teams of software engineers across a wide range of experience levels, areas of expertise, and scopes of responsibility

  • You will be responsible for the successful delivery of all software components required for us to ship the Voyager instrument as part of the broader Nautilus proteomic platform

  • You will work cross-functionally with representatives of many other disciplines – such as Bioinformatics, Biology, and Hardware Engineering – to set your teams’ direction, strategy, and priorities

  • You will lead multi-disciplinary software engineering projects to successfully ship deliverables to external and internal customers

  • You will provide hands-on technical contributions for our Instrument Control software engineering efforts

  • As a member of our leadership team, you will be expected to contribute to corporate strategy & initiatives, be a positive cultural role model, and be one of Nautilus’s ambassadors to the world!


  • You have 15+ years of relevant experience in a high performing software engineering organization, including 7+ years of experience in a leadership role

  • You have a Bachelor’s degree in Computer Science or a similar related field

  • You have a proven track record of leading many software teams to success on very complex projects throughout all stages of the development life cycle, culminating in multiple products that have been successfully shipped to customers

  • You know how to create and nurture high performing software teams through a combination of coaching, hiring, performance reviews, technical mentorship, and other leadership techniques

  • You are fluent in a wide variety of programming concepts, disciplines, tools, environments (such as FreeRTOS, Linux, Windows, and cloud), languages (most notably C/C++ and Python), and have the ability to quickly acquire expertise in new topics on the fly as needed

  • You have worked on multiple real-time or instrument control systems that have been successfully deployed to external customers

  • You have strong organization, communication, problem solving, and project management skills, along with a willingness to jump in to help wherever it is needed

  • You are a leader who is trusted by everyone within the organization; you are able to lead directly as well as through collaboration & influence

  • You have fun when building complex systems that solve large, novel problems while working side-by-side with experts from a variety of disciplines

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