Alumni Profile: Katie Pollard
January 23, 2025
By Rose Miyatsu
July 2025 will mark the 25th anniversary of the UC Santa Cruz Genome Browser, one of the most widely used resources for genomics worldwide. Originally built to allow researchers to explore a single human DNA sequence assembled by the Human Genome Project Consortium (HGPC), it is now accessed by tens of thousands of researchers a day to visualize, annotate, and study genomes of thousands of different species from humans to viruses.
In celebration of this amazing resource, we are spotlighting alumni who worked on the Browser over the course of its history. Katie Pollard, a former postdoc at the UC Santa Cruz Genomics Institute, is currently the Director of the Gladstone Institute of Data Science and Biotechnology, Professor of Epidemiology and Biostatistics at UC San Francisco, and Investigator with the Chan Zuckerberg Biohub San Francisco. She worked on the chimpanzee genome in the early years of the Browser, a project that led her to an important discovery about the difference between humans and primates. She spoke with us about the importance of the Human Genome Project and the Browser both to her own career and to the field of genomics as a whole.
The start of a new discipline
When Katie Pollard first began working toward her Ph.D. in biostatistics at UC Berkeley in the late 90s, the human genome had not yet been sequenced. Then, on July 7, 2000, UC Santa Cruz published the HGCP’s first draft of a sequence online. Suddenly, a whole new field of genomics sprung into being. It was an inspiring accomplishment, and led Pollard to shift her research focus.
“When [then UC Santa Cruz Professor of Computer Science] David Haussler’s team and others analyzed the human genome for the first time, it was really pivotal in my career,” Pollard said. “I switched from an interest in epidemiology to cancer genomics.”
Pollard’s Ph.D. thesis ended up focusing on computational and statistical methods for analyzing DNA “microarrays,” which were the first technology for looking at how genes get turned on and off in the human body, and using them to identify the differences between cancer and a healthy tissue. After finishing her Ph.D., Pollard considered a number of different postdoctoral positions in genomics, but the opportunity she found herself most drawn to was working at UC Santa Cruz with Todd Lowe, who is currently a professor of biomolecular engineering at UC Santa Cruz, and David Haussler, currently a distinguished professor of biomolecular engineering and the founding scientific director of the UC Santa Cruz Genomics Institute.
“The reason I was super excited was that there was clearly something going on there at the time that was different from other places,” Pollard said. “The idea that scientific data was not just a text file on a computer, but that you needed to build tools to visualize it so that anyone could interact with it, was such a draw for me.”
Using the Browser to discover what makes us human
When Pollard began her postdoctoral fellowship, the UCSC Browser was still in its infancy. It had been built to accommodate the HGPC’s completed human genome sequence, and researchers had quickly added a mouse and rat genome to the platform. Pollard began working on the chimpanzee genome.
“I was super excited when I was invited to start working on the chimpanzee genome because as an undergraduate I had studied comparative primatology and the evolution of humans from a very different perspective. The idea that we could look at the genetic basis for what makes us human and connect that to behavior and other physical differences was super tantalizing,” Pollard said.
During her fellowship, Pollard compared the human and chimpanzee genomes to make an astounding discovery about rapidly evolving regions in the human genome — the parts of the genome that distinguish humans from closely related species and could help explain the emergence of our unique brains. Scientists expected that these regions would be located in protein-coding regions that were already well characterized and understood, but Pollard revealed that nearly all of the regions that had been fastest to evolve were actually outside protein-coding regions. This pivotal discovery would not have been possible without using the UCSC Browser’s early annotations of gene expression, known as expressed sequence tags (ESTs).
“It was a really big deal because genes weren’t even properly annotated at the time,” Pollard said. “That really set my whole research career in a different direction — instead of focusing on proteins, I began focusing on how proteins get turned on and off in evolution and in disease.”
The legacy of the UCSC Genome Browser
Pollard’s important discovery as a postdoc was only the beginning of a rewarding career in uncovering how genomes evolve and how they lead to disease. After her two-year postdoc at UC Santa Cruz concluded, she became an assistant professor at UC Davis before ultimately moving to San Francisco, where she is currently a professor of Epidemiology and Biostatistics at UC San Francisco and director of Data Science & Biotechnology at the Gladstone Institutes, an independent biomedical research institute. In 2017, she joined the Chan Zuckerburg Biohub as an investigator. In all that time, Pollard says that the UCSC Genome Browser has continued to be vital to her work.
“The way the Browser was set up and continues to evolve makes it an incredibly useful resource,” said Pollard. “Today when someone in my lab comes in with an interesting result or with a question, the first thing I do is look up that genome sequence in the Browser and figure out what we know about it.”
Pollard believes that the impact of the Browser has only grown since the early days of the human genome, which she attributes to the Browser’s strong, diverse team that was able to continually innovate to accommodate a torrent of new data.
“I think that the biggest challenge is that what seemed like the best solution when you had one human genome and very little information about it is not the solution that we need today,” Pollard explained. “Data generation exploded after the Human Genome Project… hundreds of thousands of people have had their genomes sequenced now, and we don’t only sequence the DNA, we sequence the RNA, and we don’t only sequence the RNA in one tissue, we sequence it in many different tissues, and not just in that tissue but in all the cell types of that tissue at a single-cell resolution. We’ve also been incorporating proteomics, metabolomics, and imaging data. The amount and diversity of the different kinds of data have exploded since that first human genome was sequenced.”
UC Santa Cruz has risen to this “big data” challenge time and time again, continually evolving the Browser to make new data types easier for scientists to explore. This effort has involved an interdisciplinary team of experts in the biological domains, engineering, data visualization, and user interface.
“Santa Cruz has always been pushing to figure out what the next challenge in data science is,” Pollard said. “In a way you may think that the technology did not change. There is still a UCSC Genome Browser that has a similar look and feel to how it did two decades ago, but the functionality of that browser is so different, and so is the scale and type of data that is available in it. UC Santa Cruz has continued to innovate on data curation and making data easy to explore and query for other scientists.”