Research Expertise and Interest
biological programming, LLMs for biology, genome mining and editing, functional genomics
Research Description
Patrick Hsu is Co-Founder and a Core Investigator of the Arc Institute and Assistant Professor of Bioengineering and Deb Faculty Fellow at the University of California, Berkeley. A pioneer in the field of CRISPR gene editing, Patrick’s work aims to accelerate scientific progress through innovation in biotechnology development, science funding, and research organizations. His research group works at the intersection of biology and AI to invent new biotechnologies, develop biological foundation models, and improve human health. Patrick received A.M. and Ph.D. degrees from Harvard University and his research has been recognized by the NIH Early Independence Award, the MIT Technology Review’s Innovators Under 35, the Rainwater Prize for Innovative Early Career Scientists, and the Amgen Young Investigator Award.
Current Hsu Lab areas of interest:
Molecular Technologies: We invent molecular tools for biological programming by leveraging microbial bioinformatics, functional biochemical and molecular assays, and protein engineering. Recent work from the lab include programmable transcriptome engineering (Cas13) and targeted genomic integration of large payloads (DNA integrases).
Merging Biology and AI: We work at the intersection of biology and AI by developing biological foundation models for generative DNA and protein design, as well as virtual cell models that can predict cellular response to chemical and genetic perturbations.
Human Synthetic Biology: We aim to push the boundaries of synthetic biology in human cells via genome, epigenome, transcriptome, and protein engineering. First, we think backwards from major unmet therapeutic needs and then develop platform solutions that enable new kinds of genetic manipulations. Current areas of interest include cell type-specific control of biological perturbations, turning the dial on epigenetic memory, and manipulation of RNA splicing.
In the News
Berkeley-Led Study Identifies Human Lung Proteins That Can Advance or Thwart SARS-CoV-2 Infections
Researchers have taken an important step toward understanding the microscopic battle that plays out between our lung cells and the SARS-CoV-2 virus that causes COVID-19. A UC Berkeley-led study has identified specific proteins within our bodies that can promote or protect us from SARS-CoV-2 infections, potentially opening the door to new antiviral therapies.
UC Berkeley Partners With New Arc Institute to Tackle Complex Diseases
UC Berkeley is partnering with UC San Francisco and Stanford University as founding scientific members of a new institute that aims to accelerate breakthroughs in complex diseases. The Arc Institute launched Dec. 15, 2021, with the goal of developing a new model for collaborative research that brings together world-class research with unconstrained funding to enable new discoveries that improve human health.
Using two CRISPR enzymes, a COVID diagnostic in only 20 minutes
Frequent, rapid testing for COVID-19 is critical to controlling the spread of outbreaks, especially as new, more transmissible variants emerge. A research team at the UC, Berkeley is aiming to develop a diagnostic test that is much faster and easier to deploy than the gold standard qRT-PCR diagnostic test. The team has now combined two different types of CRISPR enzymes to create an assay that can detect small amounts of viral RNA in less than an hour.
Scientists pivot to COVID-19 research, hoping for quick results to deal with pandemic
Thanks to a rapid funding program thrown together by wealthy entrepreneurs barely six weeks ago, seven COVID-19 research projects at the University of California, Berkeley, are getting an infusion of cash — $2.2 million in all — that could turn up new diagnostics and potential treatments for the infection within months.
What COVID-19 antibody tests can tell us, and what they can’t
As the United States and much of the world move toward relaxing shelter-in-place restrictions to let people move about more freely, public health experts hope to rely on antibody tests to determine who has been infected with the COVID-19 virus and may be immune — at least temporarily — and who is still susceptible.
Featured in the Media
Please note: The views and opinions expressed in these articles are those of the authors and do not necessarily reflect the official policy or positions of UC Berkeley.
June 29, 2020
A 60 Minutes investigation revealed that federal officials knew many of the antibody tests suddenly flooding the market were seriously flawed, but continued to allow them to be sold anyway. In early March, Dr. Alex Marson of UC San Francisco, and Dr. Patrick Hsu, an assistant professor of bioengineering at UC Berkeley, assembled a team of 50 scientists to do what the FDA had not: test the antibody tests. All but one test delivered so-called false-positives, meaning they mistakenly signaled antibodies in people who did not have them.
June 16, 2020
Coronavirus antibody testing is suddenly everywhere, but results are often incorrect or inconclusive. Patrick Hsu, an assistant professor of bioengineering at the University of California, Berkeley, was a senior author on a recent study on the accuracy of antibody tests. His group analyzed 14 tests and found only three produced consistently reliable results. "People want answers: Am I immune? Can I go back to work? Can I play soccer in the park?" Hsu says. "But the story's not quite so simple." He says that even for tests that can accurately detect the virus, many questions remain. For more on this, see our press release at Berkeley News
May 13, 2020
It's been pretty well publicized that an intensive study of proliferating COVID-19 antibody tests, co-led by assistant bioengineering professor Patrick Hsu of the Berkeley-UCSF Innovative Genomics Institute, has found that very few are effective and all have flaws, but that has not discouraged many eager buyers. "There are over 200 different antibody tests out there right at this point, more than we have for any other infectious disease," Professor Hsu says. "One of the things that we're able to do in our study is to test on individual blood samples both positive and negative, all of these tests against each other, head to head, right, in this bake-off, systematically." The tests returned too many false positives, and only one, called Sure Biotech, was found to be 100% accurate. "Some were over 10 percent, and some were even over 15 percent false positive, right? So that would really not be acceptable performance," he says. Link to video. For more on this study, see our press release at Berkeley News.
May 6, 2020
As the list of available antibody tests for the COVID-19 virus soars, scientists and the FDA are investigating their accuracy and effectiveness. Only 12 have received FDA authorization for emergency use. Assistant bioengineering professor Patrick Hsu and UCSF microbiology and immunology professor Alex Marson are both working on the Berkeley-UCSF Innovative Genomics Institute's effort to study more than 100 antibody test kits for their effectiveness. According to this reporter: "To assess their ability to identify antibodies against SARS-CoV-2, the team used plasma or serum samples from three groups: 80 people who had shown symptoms of COVID-19 and had tested positive using a PCR-based screen, 52 who had a respiratory infection but were found to be infected with another virus or had tested negative on a PCR test for SARS-CoV-2, and 108 blood donors whose samples were drawn in 2018 or earlier, before the pandemic began. ... Their assessment found that the ability to detect antibodies in people who had tested positive for the virus increased over time, rising to 81100 percent when more than 20 days had elapsed since symptoms began, depending on the product. One of the members of the team, Patrick Hsu ... notes that this finding highlights why longitudinal antibody testing is important, given that a negative result may mean a person had been exposed to the virus but hadn't yet developed a detectable level of antibodies. On the specificity side, the proportion of false positives found in the preCOVID-19 samples ranged from 016 percent. The agreement between the findings of LFAs and ELISAs ranged from 7594 percent. The team posted its results as a preprint on the project website on April 24. Alex Marson ... cautions that some numbers, especially for tests' ability to detect antibodies in positive cases, may be revised as his team continues to analyze the data."
April 28, 2020
Assistant bioengineering professor Patrick Hsu, an investigator at Berkeley's Innovative Genomics Institute (IGI) is co-leading a massive UC Berkeley-UCSF joint effort to study more than 120 antibody test kits for their effectiveness in identifying people who may be immune to COVID-19. "These tests are widely available, and many people are buying and deploying them, but I realized that they had not been systematically validated, and we needed to figure out which ones would really work," Professor Hsu says. "This is a huge, unmet need for public health." Praising the project's enormous team of researchers, he says: "This is a huge, huge community effort. ... A lot of people really came together. One of the things I think is cool about this study is how many people repurposed themselves from what we normally do to respond to this pandemic." For more on this, see our press release at Berkeley News. Stories on this topic have appeared in dozens of sources, including Yahoo! News and Science Blog.
April 27, 2020
For the past few weeks, more than 50 scientists have been working diligently to do something that the Food and Drug Administration mostly has not: Verifying that 14 coronavirus antibody tests now on the market actually deliver accurate results, this reporter writes, speaking of tests co-led by assistant bioengineering professor Patrick Hsu, an investigator at the Innovative Genomics Institute (IGI), a joint research collaboration between Berkeley and UCSF that is focused on CRISPR gene-editing technology. The team has found that only 3 of the 14 leading blood antibody tests they tested provided consistently reliable results, and even those three were flawed. The results are especially troublesome for their rate of false-positive results. I realized, 'Gosh this is really the Wild West,'" Professor Hsu says. "We needed to figure out which of these would really work." The accuracy of antibody tests is particularly important as states consider how they'll reopen safely, because they are critical for determining who is immune and would be safe to return to work. For more on this, see our press release at Berkeley News. Stories on this topic have appeared in dozens of sources, including U.S. News & World Report and KPIX TV--link to video.
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