Chan Zuckerberg Biohub funds new research efforts, microbiome initiative

Stanford faculty are helping to lead collaborative research teams funded by the Chan Zuckerberg Biohub.

Stephen Quake

Thirteen Stanford faculty are among the leaders of six research teams that received funding from the Chan Zuckerberg Biohub. Combined with the new microbiome initiative, which includes four Stanford faculty, the CZ Biohub is committing $13.7 million over three years to new collaborative research to enhance human health.

The intercampus research awards were given to teams of investigators that include faculty from Stanford, UCSF and UC-Berkeley with the goal of fostering scientific research collaboration across the Bay Area.

“This new collaborative, team-based funding allows investigators across the three campuses to tackle demanding problems to enhance health,” said Stephen Quake, PhD, co-president of CZ Biohub and professor of bioengineering and of applied physics at Stanford. “These research teams will shed new light on a diverse and challenging set of questions that will advance our understanding while developing technologies that open fresh avenues of research.”

Steven Palumbi, PhD, professor of biology, is one of five leaders on a team that received funding to investigate genome evolution and cell biology in organisms that aren’t traditional laboratory animals. “Mice can’t regenerate limbs, but we study worms that can, and corals can live thousands of years,” he said. “There are amazing things that these organisms do regularly that reveal the limits of our own cell biology.”

The CZ Biohub also announced funding to expand on the microbiome initiative that launched as a pilot program earlier this year. That initiative will carry out research on the community of microbes within the human body that influence many aspects of health, from nutrition and immune function to drug metabolism.

Of the eight investigators leading the initiative, four are Stanford faculty: Michael Fischbach, PhD, associate professor of bioengineering; KC Huang, PhD, associate professor of bioengineering and of microbiology and immunology; David Relman, MD, professor of medicine and of microbiology and immunology; and Justin Sonnenburg, PhD, associate professor of microbiology and immunology.

“The human microbiome is incredibly complex, individual and dynamic,” Sonnenberg said. “Hundreds of microbial species are a fundamental part of human biology, contributing to health and in some cases causing disease, so this is an important but difficult set of biomedical problems to address.”

As part of the microbiome initiative, CZ Biohub will establish a mass spectrometry facility for metabolomics at Stanford. The Biohub plans to make unused instrument time available to other members of the research community. It’s also exploring the idea of making software tools, mentoring and training accessible to biologists and engineers who are not specialists in metabolomics.

The CZ Biohub encourages collaboration between Bay Area institutions with regular meetings and chances for their investigators to exchange ideas. Team leaders of the intercampus research awards will be expected to participate in at least half of the biweekly meetings and to upload manuscripts reporting work supported by these awards to preprint servers such as or to accelerate the pace of scientific discovery.

The six awards and team leaders are:

  • Beyond model systems: Insights into genome evolution and cellular innovations — Christopher Lowe, Stephen Palumbi and Irving Weissman, Stanford; Daniel Rokhsar, UC-Berkeley; Wallace Marshall, UCSF.
  • Social network analysis of neuroimmune interactions in the developing human brain — James Zou and Alice Ting, Stanford; Tomasz Nowakowski, Jimmie Ye and Alex Pollen, UCSF; David Schaffer, UC-Berkeley.
  • Multi-scale deep learning and single-cell models of cardiovascular health — Euan Ashley and James Priest, Stanford; Rima Arnaout and Atul Butte, UCSF; Ben Brown and Bin Yu, UC-Berkeley.
  • Machine learning for interpreting rare genetic variation in comprehensive newborn screening and pharmacogenetics — Russ Altman and Carlos Bustamante, Stanford; Steven Brenner and Michael Jordan, UC-Berkeley; Renata Gallagher and Kathleen Giacomini, UCSF.
  • Defining host responses of virus-infected and uninfected neighbor cells — Karla Kirkegaard and Peter Sarnow, Stanford; Laurent Coscoy, UC-Berkeley; Melanie Ott, UCSF, Gladstone Institutes.
  • Imaging complex biological machines in action — Wah Chiu and John Boothroyd, Stanford; Carolyn Larabell, UCSF; James Sethian, UC-Berkeley.

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