A Pandemic Story: QI Helps Startup Seize Opportunity

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It was March 2020, and Shane Bowen '00, '05 was trying to figure out how to get home to San Diego from Australia, as the pandemic surged and regular travel routes and familiar routines began shutting down. Then Bowen’s cell phone rang.

“It was a friend of mine who is a professor at MIT,” Bowen said. “Both my friend and the PI [principal investigator] he had worked with at Caltech were locked off campus. They couldn’t go into their labs anymore, and their students couldn’t either. Between the two of them, they said, ‘You know, I think now’s the time to start a company. Would you be interested in chatting with us? Maybe participating?’”

Bowen responded that he was indeed interested, but first he had to get home.

Filling a Need

Bowen did manage to catch a flight back to San Diego, where frequent evening calls among the trio evolved into an idea for a company.

“The pandemic highlighted an underserved area—rapid detection of various different pathogens such as COVID, the flu, and other viruses,” said Bowen. “It would be very valuable if we could develop technology to do rapid and sensitive detection.”

The team decided their new firm, which they named Palamedrix, would develop biosensors based on DNA. The goal was to offer a complete view of a patient’s proteome—the entire complement of proteins expressed—with a single sample.

“There are tremendously successful companies making tools to interrogate the genome, but that data lacks actionability,” Bowen explained. “We wanted to address this deficiency. The proteome is something that can be acted upon immediately, as almost all therapeutics target interactions with specific proteins. A comprehensive view of an individual’s proteome provides an opportunity to have more accurate diagnoses and more effective treatments.”

The venture was well matched to the expertise of its co-founders.

Bowen’s friend, Ashwin Gopinath, Ph.D., was an assistant professor at MIT and former research scientist at Google [X] who ran a lab working at the intersection of complementary metal-oxide semiconductor nanofabrication, molecular self-assembly, biology and machine learning.

Gopinath’s mentor at Caltech, Paul W.K. Rothemund, Ph.D., a former MacArthur Fellow, ran a lab that used DNA and RNA as engineering materials so they could perform biochemical computations or serve as scaffolds for arranging functional nanodevices; he was the inventor of “DNA origami,” a method for folding arbitrary shapes from a long single strand of DNA.

Bowen himself, who earned an M.S. in applied physics and Ph.D. in physical chemistry (with Professor Robert Continetti) from UC San Diego, had spent more than a dozen years at Illumina. While there, Bowen had used UC San Diego’s Qualcomm Institute facilities — namely, Nano3 — to develop DNA sequencing and genotyping chips in the historic effort to bring down the cost of sequencing the human genome to under $1,000.

“After about a year of working by myself or maybe with one other scientist from Illumina in Nano3, we got a hit,” Bowen recalled. “All of a sudden, I was tasked with providing large numbers of chips to the company. I ended up building up a team of 10 scientists and engineers, all working in Nano3. We ended up developing a technology that went to Asia for mass manufacturing and ushering in the era of the $1,000 genome in 2014. It was an extremely big success for Illumina.”

Return to QI

Fascinated by the prospect of being on the ground floor of a startup, Bowen left Illumina in January 2020 to join Truvian. But when Palamedrix started to come together, Bowen left that job to concentrate on the startup he was co-founding. After a business plan came together, Palamedrix was incorporated in July 2020, and the founders soon raised $6 million in funding. 

To take the next step, Palamedrix needed facilities.

“We didn’t have lab space, and we wanted to build stuff—we had to build stuff, hardware and chemistry assays,” Bowen said. “Despite the pandemic, we found wet bench space at Biolabs to do the chemistry. But we also needed fabrication capabilities.”

Since Bowen had previous experience with QI and UC San Diego (where he still serves on the Department of Nanoengineering’s Industrial Advisory Board), he arrived quickly at the idea of using the QI Innovation Space as a base for Palamedrix’s work on a physical chip.

“The people at QI were very supportive,” Bowen said. “Together, we implemented facility upgrades and upgraded office space to meet our application’s requirements. The QI team was excited to help us realize our vision. They were asking the types of questions one could only hope for, ‘How do we implement the upgrades you need to give you a space that you can work in?’ In the end, we put in a high-end atomic-foce microscope, which we would use to examine what we made in the cleanroom downstairs.”

Things moved quickly for the company. After about eight months, another round of funding came in, and Palamedrix moved to a 10,000-square-foot facility down the street from UC San Diego. There, the team began some collaborative projects with biotech firm Somalogic. A few months later, in July 2022, a deal was struck for Somalogic to buy out Palamedrix for up to $52.5 million.

“The opportunity to join forces with Somalogic basically removed fundraising concerns and allowed us to focus on the technology development,” said Bowen, now general manager of the San Diego site and a vice president of technology development for Somalogic.  

With the future looking bright, Bowen is grateful for the opportunities that QI in particular and UC San Diego in general provided during crucial stages of Palamedrix’s journey.

“Location was critical—right in the heart of the biotech boom in San Diego—as was proximity to complementary resources, such as Nano3,” he said. “I also appreciated QI’s ability to flex to meet our needs.”

Read more about the QI Innovation Space, Palamedrix and Somalogic.