Biophysicist Stephen Quake has held many titles. He’s invented devices, developed diagnostics and launched companies. He’s won dozens of prizes and been elected to four National Academies — a feat achieved by fewer than a handful of scientists.
He spent 10 years as an Investigator of the Howard Hughes Medical Institute, and then gave a decade to Chan Zuckerberg philanthropy as founding president of the Biohub Network and then Head of Science.
When still driven by a desire to “do something big for science” by measuring and manipulating life’s smallest components, what does such a polymath do next?
Keep exploring.
He’s returned to running his Stanford laboratory full-time. He also joined the Board of Directors at the Institute for Protein Innovation (IPI).
“Science can move in trends and fads,” says Quake, the Lee Otterson Professor of Bioengineering and Applied Physics at Stanford University. The last two decades belonged to genomics and “proteins got pushed to the side, but it hasn’t become any less important.”
Physics plus biology equals innovation
Quake isn’t a protein scientist, but he’s made a career in scouting the next big idea. He spent his undergraduate days at Stanford University, studying physics in the laboratory of Steven Chu. He worked with optical tweezers, wielding lasers to trap and stretch molecules to measure forces on DNA.
Upon graduation, he won a Marshall Scholarship and joined statistical physicist Robin Stinchcombe at the University of Oxford. He delved into theory, working out what happens when polymers get tied into knots.
Wanting to test his ideas, he toggled between exploring theory with Stinchcombe in Oxfordshire while doing lab work with Chu in California. Doctorate in hand, he joined the Chu Lab as a postdoc, exploring polymer dynamics with more sophisticated experiments.
In 1997, Chu won the Nobel Prize in Physics. Ironically, Quake had left his lab a year earlier to join Caltech as an assistant professor in applied physics. There, he pivoted toward biology, a move inspired by Chu many years earlier.
“In Steve’s lab, I was thinking about DNA as a model polymer,” Quake says. “To physicists, it is a polymer that shares the same universal behavior of all polymers. But to biologists, it is a molecule of inheritance.”
Spurred to ask biological questions with new physical tools, Quake and his team created the first microfluidic valve that could be built at scale. With thousands of those valves in hand, Quake’s team forged a new field and spawned a company called Fluidigm. Its first product was a chip that enabled protein crystallization, solving many protein structures.
In 2005, Quake got an offer he couldn’t refuse. Stanford was hatching a newfound department, the brainchild of Jim Plummer, Stanford’s Dean of Engineering, and Phil Pizzo, Dean of Medicine. Quake, now firmly grounded at the biophysical intersection, fit perfectly as the first recruit to Stanford’s Bioengineering Department.
By collaborating closely with the Medical School, Quake began to think differently about how his basic-science ingenuity could make a more direct impact in the clinic.
After stumbling across an obscure finding of cell-free DNA in the blood, he recalled his experience as a new parent. He was struggling with his then-pregnant wife to decide if a needle biopsy result was worth risking the life of their unborn daughter. Driven by this dilemma, Quake found that blood-borne DNA, when combined with genomic sequencing, could yield a powerful noninvasive replacement for amniocentesis. That work opened the door to blood tests for transplant patients, deep infectious disease and cancer, which Quake also helped to develop.
“The patient stories of how lives have been saved because of these tests keep me going,” he says. “They’re like a drug.”
From lab-scale tools to ecosystem-scale infrastructure
The ambition grew as Quake reached his next career change. In 2016, Facebook founder Mark Zuckerberg and his wife, Priscilla Chan, came to Stanford shopping for big ideas to seed a new philanthropic institute. Their initial vision was audacious: curing, preventing or managing all diseases by the end of the century.
After much brainstorming and conversation, Zuckerberg appointed Quake as founding co-president of the resulting Chan Zuckerberg Biohub, a nonprofit aimed at nucleating scientific collaboration between Stanford, University of California (UC) San Francisco and UC Berkeley.
“There were big problems that I wanted to take on,” he says, “problems bigger than my lab.”
One was how to comprehensively map and understand the diversity of human cell types and their molecular programming across the whole body.
Quake envisioned building a comprehensive, single-cell, multi-organ transcriptomic atlas. Under his leadership, the CZ Biohub created the Tabula Sapiens, an open, shareable molecular reference atlas for more than 400 cell types in the human body. Along with humans came atlases of mice, flies and lemurs — all of which has led to many biological discoveries.
In 2022, Quake became CZI’s head of science, overseeing a budget of $450 million and the creation of Biohubs in Chicago and New York. In the role, he learned that philanthropic nonprofits could move with a speed and agility foreign to academia.
“That velocity was one of the secrets of our success,” he says.
And one of the reasons he left. In 2025, after launching the new Biohubs and pivoting the organization to make a big bet on artificial intelligence-aided science, Quake stepped down and returned to his passion: the lab and his students.
Why IPI, why now
Now stationed back at Stanford, Quake is still finding room for philanthropy-driven science, like that happening at IPI.
In early 2026, he received an invitation to join the Board from IPI co-founder Tim Springer, whom Quake had known for nearly 25 years. With his “unusual experience in how to start institutes,” Quake believes he can add to IPI’s list of assets.
He’s also harboring novel ideas about harnessing protein science for therapeutics. Many drugs are based on monoclonal antibodies, he points out, and the knowledge informing those therapeutics “has survived, kept alive by time.”
He imagines IPI as a modern-day Library of Alexandria, preserving and activating protein knowledge to influence how a whole new generation of therapies will be made.
“As a freestanding self-governed institute, IPI has an amazing role to play,” he says. “Taking on big problems that academia would not do by themselves. Having the wherewithal to have longer timescale. As academics, we think in terms of PhD or postdoc scales. IPI can take on bigger things.”
Sources:
Stephen Quake, quake@stanford.edu
Writer:
Trisha Gura, trisha.gura@proteininnovation.org
About IPI
The Institute for Protein Innovation is pioneering a new approach to scientific discovery and collaboration. As a nonprofit research institute, we provide the biomedical research community with synthetic antibodies and deep protein expertise, empowering scientists to explore fundamental biological processes and pinpoint new targets for therapeutic development. Our mission is to advance protein science to accelerate research and improve human health. For more information, visit proteininnovation.org or follow us on social media, @ipiproteins.