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Nautilus: Driving a revolution in proteomic analysis (Part 2)

Chris Blessington

Chris Blessington

September 30, 2022

Nautilus was conceived with the goal of revolutionizing proteomics and making comprehensive, high throughput assessment of the proteome accessible to all researchers and clinicians. While many successful companies have come from incremental thinking and advancement, to accomplish our audacious goal we needed start with a blank sheet of paper. The leaps in proteomic technology and innovation that have and will continue to come from Nautilus are powered by cross-disciplinary thinking and collaboration – two characteristics vital to true breakthroughs. Indeed, these have become core values at Nautilus. In this series of blog posts (find the first one here), we’ll give you an inside view on how cross-disciplinary thinking and collaboration have and will continue to propel us into a proteomics-powered future.

A cross-functional partnership leveraging business acumen, computational skills, and biochemical knowledge gets Nautilus off the ground 

After Parag Mallick devised the technology that would become the basis for Nautilus, he needed a partner who could help his nascent proteomics start-up get off the ground. Parag recognized that he needed someone with a complementary skill set. He needed someone who had both the computational know-how to build the algorithms required for his technology and the business acumen required to start a company. Thankfully, Parag was already good friends with Sujal Patel.

Sujal was the perfect match for Parag. He had previously built a highly successful data storage company called Isilon Systems. At Isilon, Sujal developed ways to store and access huge amounts of data, something that would be essential for a proteomics platform generating binding information for billions of proteins in a single run. Sujal even had the computational knowledge required to develop the original algorithms Nautilus would use to identify proteins. Building Isilon, he additionally had a good understanding of the business structures that would be required to build a successful start-up and, to top it all off, he knew investors who could provide the necessary funding.

Sujal was quickly convinced of the worth of Parag’s nascent proteomics platform when Parag explained how comprehensive proteome measurements could potentially ascertain the molecular mechanisms of disease, revolutionize drug development, and make novel treatments available to people all over the world. Parag’s excitement alone went a long way to convincing Sujal who says:

Headshot and quote from Nautilus Co-Founder and CEO, Sujal Patel

Their collaboration came at a serendipitous time. Even just a couple of years ago it would have been difficult if not impossible to cost-effectively create and store the amount of data that the Nautilus platform generates. Advances in nanofabrication, imaging, machine learning, data storage, and more have only recently made this novel technology possible. As leaders in these fields, Sujal and Parag were well-positioned to pull in the cutting-edge knowledge required to make the Nautilus platform a reality.

Critically, Sujal and Parag’s relationship was truly collaborative. Rather than silo themselves away and build the computational and biochemical components of the Nautilus platform in isolation, Sujal and Parag taught, learned, and applied their joint-knowledge to its development. Sujal, then a self-described ‘biology novice’, watched YouTube videos of college biology lectures and peppered Parag with “Dumb Questions of the Day.” The answers to these questions helped Sujal understand how the platform could theoretically interact with proteins. This established the informational constraints under which his software would have to identify proteins and helped him build the computational core of the platform.

For his part, Parag tapped Sujal’s understanding of machine learning to determine just how many and what kinds of affinity probes they needed to generate to make the platform work. He used this information to guide his experiments in the lab and figure out the most accommodating ways to isolate proteins for analysis. All the while, Parag and Sujal worked with experts in nanofabrication and imaging to determine how they could isolate billions of proteins at once while maintaining the ability to optically analyze them. In essence, they crossed disciplines to determine how to craft a device that could identify billions of proteins in a reasonable amount of time – a daunting task for one but doable when the work was spread amongst expert collaborators united toward a common goal.

In these initial stages of Nautilus’ development, Parag and Sujal’s interactions forced Parag to fundamentally rethink the scale of what Nautilus could become. While Parag originally wanted a few hundred thousand dollars to develop his technology, Sujal saw its potential and pushed Parag to think much bigger. Sujal brought in far more funding both from independent investors and ultimately, by going public (NASDAQ: NAUT). With initial experimental and computational evidence that their platform could work and the funding to drive its growth, Sujal, Parag, and the team they have built are well on their way to leading a proteomics revolution.

Join us to drive the proteomics revolution

Cross-disciplinary innovation has been at the core of Nautilus since its inception and will continue to make the company thrive as its technologies grow, are applied, and evolve. We look forward to working with more scientists, engineers, magicians, entrepreneurs, and more who are excited to push the boundaries of a variety of disciplines.

If this sounds like you, we encourage you to apply for one of our many open positions!

Check out the Translating Proteomics podcast to learn more about why we’re poised for a proteomics revolution

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