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Nautilus Biotechnology co-founders Sujal Patel (left) and Parag Mallick. (Nautilus Photo)

Parag Mallick spent more than 20 years studying the intersection of software engineering and life sciences to better understand predictive and personalized medicine. Then, one weekend, a light bulb went off. The Stanford professor and cancer researcher had a big idea. He needed to start a company.

Mallick called his longtime friend Sujal Patel, the veteran Seattle tech entrepreneur who co-founded and sold Isilon Systems to EMC for $2.5 billion in 2010.

“It didn’t take me very long to realize Parag was on to something,” Patel said in an interview with GeekWire this week.

Mallick and Patel teamed up to create Nautilus Biotechnology. They’ve operated under the radar for the past four years, quietly building the foundation of a next-generation platform to study the human proteome, the body’s full set of proteins. Now the startup is coming out of stealth mode, revealing an all-star group of investors and an ambitious plan to change the way therapeutics are developed, seeking to catalyze a new wave of medical treatment.

“We are creating a platform to enable a fundamental transformation in how people look at biology,” said Mallick, the company’s co-founder and chief scientist.

Nautilus on Thursday announced a $76 million Series B investment round led by Vulcan Capital, the multi-billion-dollar holding company created by the late Microsoft co-founder Paul Allen. Bezos Expeditions, the VC arm of Amazon founder Jeff Bezos, also invested, along with top biotech firm Perceptive Advisors and Defy Partners. Previous backers AME Cloud Ventures, Andreessen Horowitz, Bolt, and Madrona Venture Group invested more cash.

The unusually large Series B round brings total funding to more than $100 million and reflects investor confidence in the 50-person company, particularly amid a global pandemic that is expected to curb startup investing.

“They’ve done an incredibly good job of executing over the last four years,” said Madrona Managing Director Matt McIlwain, whose firm was an early Isilon investor. “Now it’s about putting all the pieces together and bringing it out commercially.”

Patel, the Nautilus CEO, declined to comment on the company’s valuation. McIlwain called the recent financing a “substantial up-round.”

Democratizing proteomics

GeekWire first uncovered the startup — then called Ignite Biosciences — almost a year ago, after digging up public records and patent filings that provided a glimpse into the company’s vision.

Mallick and Patel described their plan in more detail this week. The company, co-located in Seattle and Silicon Valley, is building a combination of hardware and software to more accurately and efficiently quantify the human proteome.

While it’s now relatively simple and cheap to analyze a genome with a drop of blood, Patel said the same progress hasn’t been made with the proteome — and that’s the opportunity Nautilus is looking to capture with what it describes as faster, cheaper, and more precise proteomic technologies.

“The reason why proteomic information is so important is that your genome is simply a map of what’s possible,” Patel explained. “A genome doesn’t describe the exact state of what’s going on inside a human today. That information is contained in the proteins, which is the cellular machinery that makes your body work.”

He added: “If you want to understand if you’re healthy, if you’re sick, if you respond to a drug — you’re much more likely to look at what’s going on at the protein level.”

In some ways, Nautilus wants to democratize proteomics, similar to how companies such as publicly-traded biotech giant Illumina have done with genomics.

“It will be a feat of technology in the world of bio that will be just as fundamental a leap forward, and with just as massive consequences, as sequencing the human genome,” a16z General Partner Vijay Pande wrote in a blog post.

It’s not clear how exactly Nautilus plans to measure proteins effectively. The company’s patent applications focus largely on blood tests, with one noting that the system could analyze blood samples “with the goal of monitoring individual health and early detection of health issues.”

“Ultimately this is a complete platform solution,” Patel said. “We have developed a piece of equipment — you put the sample in, and out comes the answer on the other side.”

There are several use cases for the company’s technology, including therapeutics development. A majority of FDA-approved drugs target a protein, and knowing more about the proteome can help make the drug development process more efficient, Mallick said. Only 20% of marketed drugs return revenues that match or exceed R&D costs, according to the company.

Other applications include diagnostics and health monitoring — knowing which drug a patient should take based on their proteome, for example, or predicting potential health problems.

“The potential of proteomics has not been fully realized because of the limitations of current analysis methods,” said Lee Hartwell, PhD, President and Director Emeritus of the Fred Hutchinson Cancer Research Center​, 2001 co-recipient ​of the Nobel Prize in ​Physiology and Medicine, and member of Nautilus’ Scientific Advisory Board.

He added, “A greater resolution of the proteome will make it possible for the entire scientific and pharma R&D communities to undertake a wider range of high-value scientific inquiries, thereby accelerating both their research and the benefits that can accrue to human health.”

Part of Nautilus’ secret sauce is the ability to crunch huge amounts of data required when reading a proteome and applying technology such as machine learning. That’s where Patel’s experience at data storage Isilon comes in handy. He and his co-founders at the Seattle startup that eventually went public correctly anticipated a massive increase in unstructured data in the world.

“Being able to read a meaningful amount of data and make sense of it requires computational technologies that are at the forefront of what’s available today,” Patel said.

Patel estimates the initial market size to be well north of $3 billion. He also believes the longer-term opportunity is bigger than the genomics market, estimated to be $31.1 billion by 2027.

“This company has an opportunity to have a much bigger impact than Isilon,” Patel added.

‘An opportunity that doesn’t come along, ever’

Nautilus plans to double the size of its team over the next 18 months as it continues to refine the platform and build out a business arm.

The co-founders first connected back in 2004 when Mallick started using Isilon’s storage software for his research data. They stayed in close contact over the years; Patel and his wife were so impressed with Mallick that they donated to his research lab at Stanford.

Patel left EMC in 2012 and was thinking about his next move when Mallick called.

“If anyone on the planet brought me an idea in biomedical research, therapeutics, or life sciences, I would hand it to Parag and ask him what he thought,” said Patel. “The fact that he was the one bringing me this idea … that meant a huge amount to me.”

Nautilus spent its early days inside the Madrona office in Seattle. Patel is a strategic director at the firm.

In a blog post, Madrona’s McIlwain wrote that the company “approaches the challenge of mapping the proteome differently at every stage of their automated and re-imagined process,” from preparing samples to analysis with cloud computing.

Mallick’s lab is pursuing research in areas including how and why cells malfunction, the underlying biology of biomarkers that target cancer, and creating technology to study proteins. He runs ProteoWizard, an open source platform for studying proteomics data, and his lab created ImmunoGlobe, an online map that shows how immune cells interact.

In his spare time, Mallick is a magician and performer who juggles giant knives and does card tricks. He also has Seattle roots. For his post-doctorate work at the Institute for Systems Biology in Seattle, he studied how proteins could be used to diagnose cancer. In addition, he was director of clinical proteomics at Cedars-Sinai Medical Center from 2006 to 2009.

“If you can fundamentally change the way that people do biological research, that is an opportunity that doesn’t come along, ever,” Mallick said. “And that’s what I see us doing here.”

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