UCSF Establishes Quantitative Biosciences Institute

New Research Unit will Identify Opportunities for Disease Treatments Using Computation, Mathematics and Statistics

By Jennifer O'Brien

Nevan Krogan, PhD
Nevan Krogan, PhD, is the founding director of UCSF’s new Quantitative Biosciences Institute. Photo by Susan Merrell

UC San Francisco today announced the establishment of the Quantitative Biosciences Institute (QBI). The mission of QBI, located on the UCSF Mission Bay health sciences campus, is to drive forward the application of computation, mathematics, and statistics toward a deeper understanding of complex problems in biology, with the ultimate goal of developing new treatments for disease.

The founding director of QBI is Nevan Krogan, PhD, who in this role reports to B. Joseph Guglielmo, PharmD, dean of the UCSF School of Pharmacy. Krogan, a UCSF professor of cellular and molecular pharmacology and a senior investigator at the Gladstone Institutes, is known for his research into developing and using systems biology approaches to help understand complex biological phenomena at a mechanistic level.

“Our goal at QBI is to help make precision medicine a reality by using quantitative research tools to understand the underlying biology behind different disease states, and then to use that knowledge to develop novel diagnostics and therapies and put them into the hands of clinicians,” said Krogan.

The institute initially will focus on such conditions as breast cancer, head and neck cancer, psychiatric disorders, including autism, bipolar disorder and schizophrenia, as well as the relationships between infectious diseases and their hosts.

Collaboration for the Work at the Institute

QBI scientists will work in collaboration with researchers from across the University of California and beyond.

At QBI, [Nevan Krogan] will be in an even better position to facilitate productive new cross-disciplinary collaborations between researchers, clinicians and industry.

UCSF Chancellor Sam Hawgood


Krogan also directs the UCSF site of the California Institute for Quantitative Biosciences (QB3), a state institute spanning three UC campuses – San Francisco, Santa Cruz and Berkeley – with a mission of supporting scientists at the intersection between the biological and quantitative sciences, and supporting entrepreneurial efforts stemming from that science to grow the California economy. QBI will be located in Byers Hall, which is the QB3 headquarters at UCSF. In his role leading QB3-UCSF, Krogan reports to UCSF neuroscientist Regis Kelly, PhD, former executive vice chancellor at UCSF and chair of the Department of Biochemistry and Biophysics, who leads QB3.

“As director of QB3-UCSF, Nevan is already helping to revolutionize biological research at UCSF,” said UCSF Chancellor Sam Hawgood, MBBS. “At QBI, he will be in an even better positioned to facilitate productive new cross-disciplinary collaborations between researchers, clinicians and industry.”

“We now have an immense amount of gene sequencing information for a number of different diseases,” said Krogan. “But there is now a realization that there is only so much we can do with purely genomic information. UCSF faculty affiliates of QBI are in a perfect position to take the next step, which is to extract insight from the genomic data by developing and using computational and experimental tools to study how genes and proteins function together. We also aim to gain a deeper biochemical and biophysical understanding of how the machines of the cell – the protein complexes – are perturbed in different disease states, as well as exploit novel approaches for intervention using chemical biology tools.”

To tackle breast cancer and head and neck cancer, Krogan is co-directing the Cancer Cell Map Initiative (CCMI) with Trey Ideker, PhD, chief of medical genetics in the UC San Diego Department of Medicine. Krogan described the CCMI as a “cross-UC program focused on using quantitative systems tools to help understand the underlying biology behind the genomic data derived from breast, head and neck, and other cancers.” Alan Ashworth, PhD, FRS, director of UCSF Helen Diller Family Comprehensive Cancer Center; Jennifer Grandis, MD, associate vice chancellor of Clinical and Translational Research (AVC-CTR); and Scott M. Lippman, MD, director of the UC San Diego Moores Cancer Center, are also key participants of the CCMI and will provide access to tissue samples donated by cancer patients.  

QBI is collaborating with Jeff Cox, PhD, faculty director of the Henry Wheeler Center for Emerging and Neglected Diseases at UC Berkeley, on the Host-Pathogen Mapping Initiative (HPMI). The aim of HPMI, said Krogan, is to bring UCSF and UC Berkeley investigators together in an effort to use quantitative approaches to study the host-pathogen interface, focusing on both bacteria and viruses.

Research Into Psychiatric Disorders

Work is also under way to study the underlying biology behind psychiatric disorders, including autism, bipolar disorder and schizophrenia, in collaboration with the UCSF Department of Psychiatry under the direction of department chair Matthew W. State, MD, PhD.  

“I am extremely pleased that Nevan has accepted the challenge of directing QBI,” said Guglielmo. “A major focus of many UCSF scientists is to apply techniques of quantitative biology to better understand disease and develop effective treatments. With the establishment of QBI, our researchers across campus will be able to carry out that strategy more comprehensively. We have the expertise; now we have the framework for increased success."

Guglielmo noted that as an official University of California Organized Research Unit, QBI will be in a position to apply for large collaborative cross-disciplinary grants from the National Institutes of Health, which, he said, will ultimately benefit the work of QBI faculty affiliates, as well as faculty affiliates of QB3-UCSF. “Because of the success of its entrepreneurial efforts involving startup incubators and venture funds, the QB3 name is associated strongly with commercialization,” said Kelly. “By launching QBI, with its emphasis on the science, Nevan is reaffirming that the quantitative sciences are central to our mission at UCSF. It is the powerful link between our academic scientists and our entrepreneurs that makes QB3 so special.”

Work to Make QBI Possible

QBI was formerly known as the Molecular Design Institute (MDI), founded in 1993 by Irwin “Tack” Kuntz, PhD, today a professor emeritus in the School of Pharmacy’s Department of Pharmaceutical Chemistry. The goal of MDI was to promote the discovery, design and delivery of novel pharmaceutical agents.

“Tack Kuntz did much of the fundamental work to make QBI possible,” said Krogan. “Of course, when MDI was established, many of the experimental and computational tools were simply not there to do drug design based on quantitative biology. Now, thanks to revolutions in detection, analysis and computation over the last 20 years, we will be able to use quantitative approaches to identify compounds that could have an effect on different proteins and pathways, and therefore different disease states.”

Today, said Krogan, “two different patients with the same disease are usually prescribed the same treatment. Ideally, with the new quantitative tools being developed at QBI, we will be able to differentiate different disease states into different subcategories as well as determine that patient A should get treatment X, while patient B should get treatment Y. That will truly be precision medicine.”

UCSF is a leading university dedicated to transforming health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. Founded in 1864 as a medical college, UCSF now includes top-ranked graduate schools of dentistry, medicine, nursing and pharmacy; a graduate division with world-renowned programs in the biological sciences, a preeminent biomedical research enterprise and top-tier hospitals, UCSF Medical Center and UCSF Benioff Children's Hospitals.