Leadership

Isabel Bjork

Isabel Bjork

Director of Operations, UC Santa Cruz Genomics Institute Director, Pediatric Cancer Programs, Treehouse Childhood Cancer Initiative

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As Director/Operations and Director of Pediatric Cancer Precision Medicine at UC Santa Cruz, Isabel facilitates the partnerships and funding that supports the work of the Treehouse Childhood Cancer Initiative. Prior to joining UC Santa Cruz, Isabel taught at the Monterey College of Law and was a research associate at the University of York.

David Haussler

David Haussler

Scientific Director, Faculty

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Scientific Director UCSC Genomics Institute
Investigator Howard Hughes Medical Institute

David Haussler develops new statistical and algorithmic methods to explore the molecular function, evolution, and disease process in the human genome, integrating comparative and high-throughput genomics data to study gene structure, function, and regulation (CV,  publications). As a collaborator on the international Human Genome Project, his team posted the first publicly available computational assembly of the human genome sequence. His team subsequently developed the UCSC Genome Browser, a web-based tool that is used extensively in biomedical research. He is Santa Cruz Campus co-director of QB3, an HHMIInvestigator, and on scientific advisory boards of the Broad InstituteNYGC and CZI. He also co-founded the Genome 10K Project, co-founded the Treehouse Childhood Cancer Project, and is a co-founder of the Global Alliance for Genomics and Health (GA4GH), a coalition of the top research, health care, and disease advocacy organizations. He is a member of the National Academy of Sciences and the American Academy of Arts & Science.

Please visit the Haussler lab website for more information. See also my CV and publications.

Ann Pace

Ann Pace

Director, Research Development & Finance

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Ann Pace currently co-leads the UC Santa Cruz Genomics Institute, where she also oversees research development and finances, managing $22M in research funding. Ann started her career as a pharmaceutical scientist at Pfizer Central Research, working on dosage form development. She received her Ph.D. in Cellular and Molecular Pharmacology at UCSF, focusing on how specific genetic changes lead to tumor growth. She continued in molecular biology as an NIH postdoctoral scholar at Stanford. Ann went on to work in the gene sequencing group at the biotech company Hyseq. Ann returned to academia to help start a new interdisciplinary effort at UCSC – the Center for Biomolecular Science and Engineering. She has been instrumental in establishing a biotech incubator in Santa Cruz. You can see her publications and patents here.

Benedict Paten

Benedict Paten

Associate Director, Director of Comparative Genomics, Faculty

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My work involves building computational tools for understanding genomes, and I serve as Director of the UCSC Computational Genomics Lab as well as an Associate Research Scientist within the UC Santa Cruz Genomics Institute. I also direct the Center for Big Data in Translational Genomics, a partnership coordinated by UC Santa Cruz between industry and academic institutions as part of the NIH Big Data to Knowledge (BD2K)project, which is building an infrastructure for researchers and clinicians around the world to analyze massive sets of genomic information for medical use.

At least half of all human diseases are driven by genetic variations whose hallmarks are uncommon on the individual scale, only becoming apparent when we examine data from thousands of individuals. As we develop tools and deploy standards to harness big data in bioinformatics, our goal is to deliver the statistical power necessary for scientists to decipher the relationships between genome, gene expression, and disease.

I came to UC Santa Cruz in 2007, and hold a Ph.D. in computational biology awarded jointly by the University of Cambridge in the UK and the European Molecular Biology Laboratory. Clickfurther to hear me talk about using computational genomics to infer the common ancestor of today’s birds.

Beth Shapiro

Beth Shapiro

Associate Director, Affiliated Faculty

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My research concerns ancient DNA, a field of inquiry only a couple of decades old that uses genomic information from long-dead organisms in order to study how populations and species change through time. The Shapiro lab excavates relatively well-preserved bones in the Arctic, estimates their age using radiocarbon dating or information from depositional environments, samples their DNA, and uses experimental and computational approaches to assemble and compare genomic changes over time.

This process allows us particular insight into how a population or species evolves in response to changes in its habit. As we are currently in a period of rapid climate and habitat change, our research offers new insights into how similar periods of rapid change in the Earth’s past affected the distribution and diversity of organisms. What we learn from the past can then be used to make more informed decisions about how to protect and preserve species and ecosystems in the present day.

I have been at UC Santa Cruz since 2012, and previously held positions at Oxford University and The Pennsylvania State University. I hold a D.Phil. in zoology from Oxford, and a M.S. and B.S. in ecology from the University of Georgia. You can read more about my publications here, includingHow to Clone a Mammoth: The science of de-extinction (Princeton University Press, 2015), and learn more about research into the DNA of extinct species as I describe the technical and ethical challenges scientists would face in trying to clone a mammoth or make a dodo.

Josh Stuart

Josh Stuart

Associate Director, Faculty, Jack Baskin Endowed Chair, UCSC School of Engineering

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The Stuart lab designs computational tools that investigate the networks regulating gene function and how they can be manipulated in the context of human health. We focus on elucidating cancer mechanisms and develop methods that highlight the cells, pathways and processes involved in tumorigenesis. In order to interpret high-throughput biological datasets, we develop algorithms to understand how alterations drive tumor initiation and progression and how mutations influence a patient’s response to treatment. The machine-learning techniques we develop can read through large compilations of data to discriminate between known and novel forms of cancer, allow us to pinpoint cancer’s essential genes, and determine which molecular pathways predict a patient’s sensitivity or resistance to drugs.

As researchers, we embrace large-scale collaboration as the best way to produce knowledge that can improve treatment options for patients. We participate in cancer genomics consortia on the state, national and international levels, including the California Kids Cancer Comparison (CKCC), Stand Up To Cancer (SU2C),and the National Cancer Institute (NCI)’s The Cancer Genome Atlas (TCGA). The predictive models and novel visualization strategies we contribute allow investigators to identify patterns in complex datasets. For example, our Tumor Map plots the genomes of all publicly available tumor samples in a single geographic-style layout, making it easier than ever before for researchers and clinicians to compare new tumors to existing ones.

We are currently adapting this mapping tool for use in CKCC so that it can be consulted in pediatric tumor board meetings to suggest new treatment options for children with cancer. Our commitments to open dialogue, data sharing, and open-source platforms and bioinformatics drive all our research, and we are pleased to work with DREAM to organize cancer-related competitions that identify increasingly effective algorithms for processing and analyzing cancer genome data.

I joined the University of California Santa Cruz in 2003, having earned a Ph.D. in biomedical informatics from Stanford University, and a B.A. in molecular biology and a B.S. in computer science from the University of Colorado, Boulder. I co-lead the PanCancer Analysis project of NCI and the International Cancer Genome Consortium (ICGC), and participate in NCI’s TCGA as co-director of UCSC-Buck Institute’s Genome Data Analysis Center. To learn more, you may visit my website, browse a list of my publications, or hear me speakabout my work.