Scientific Director, Faculty
Scientific Director UCSC Genomics Institute
Investigator Howard Hughes Medical Institute
Scientific Director QB3
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 Institute, NYGC 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.
Isabel Bjork has served as Director of Pediatric Cancer Precision Medicine, and now as Executive Director of the Genomics Institute. She joined the MDL to contribute strategic and operational expertise to bring essential testing capacity to Santa Cruz. She has a background in international legal reform in developing countries, conflict management, and organizational change. Isabel is a licensed attorney and trained in developmental psychology.
Director, Research Development & Finance
Ann Pace leads the UC Santa Cruz Genomics Institute grant and finance teams. 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 gene sequencing and bioinformatic analysis at a Silicon Valley biotech firm before returning to academia to help start a new interdisciplinary effort at UCSC – the Center for Biomolecular Science and Engineering – and helped shape its evolution into the UC Santa Cruz Genomics Institute. You can see her publications and patents here.
Associate Director, UC Santa Cruz Genomics Institute; Professor and Department Chair, Biomolecular Engineering Department, Baskin Engineering Endowed Chair, UC Santa Cruz
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.
Associate Director, UC Santa Cruz Genomics Institute; Director of Comparative Genomics, Assistant Professor, Biomolecular Engineering, UC Santa Cruz
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.
Associate Director, UC Santa Cruz Genomics Institute; Professor, UC Santa Cruz; Howard Hughes Medical Institute Professor & Investigator
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.
Associate Director, UC Santa Cruz Genomics Institute; Associate Professor, UCSC Department of Anthropology
My research harnesses the wealth of genetic data that has become available in recent years, developing computational approaches to analyze acquired genetic mutations that disrupt pre-mRNA splicing. Placing a particular emphasis on cancer genome alterations, the Brooks lab investigates the mechanisms that regulate alternative splicing, and the functional consequences of splicing dysregulation.
In collaboration with such national and international consortia as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), I am developing computational approaches to analyze genome and transcriptome sequencing data. I am also at work on high-throughput functional studies to identify cancer-related pathways. By providing a more detailed understanding of how cancer genome alterations affect cellular processes, my research aims to help identify new cancer therapies.
Before coming to UC Santa Cruz in 2015, I held a postdoctoral research position at the Dana-Farber Cancer Institute/Broad Institute. I received my Ph.D. in molecular and cell biology from UC Berkeley, and my B.S. in biology with a specialization in bioinformatics from UC San Diego. You can read through my publications.
Faculty Director, Diversity, UC Santa Cruz Genomics Institute; Assistant Professor, Biomolecular Engineering, UC Santa Cruz
Our work in the Human Paleogenomics lab looks at the twin forces of culture and biology in shaping human genomic diversity, demography and health. Since our species emerged around 200,000 years ago, humans have successfully occupied almost all of the planet’s terrestrial ecosystems, adapting to a multitude of novel stress factors, and persisting in an ever-changing world—changes that we humans have been increasingly responsible for in the last 10,000 years or so. Our lab is especially interested in this period, the anthropocene, examining how modern-day humans’ genetic variability has arisen from niche construction and the co-evolution of genes and culture. Rather than inferring our models from modern genomic data, we analyze DNA from ancient humans, pathogens, and associated metagenomes, and remain attentive to the cultural and natural environments those humans inhabited.
Our focus on population history considers the changes in climate and social complexity that have influenced the genetic structure and demography of past human populations. While most of our work has been done in South America, we increasingly study other parts of the world, using ancient human and pathogen DNA to find the demographic and epidemiological effects of European contact on Native American populations, and trace human dispersals in Sub-Saharan Africa, the Caucasus, and Western Europe. We are also interested in gene-culture coevolution from such stressors as nutrition or high-altitude living, host-pathogen coevolution in illnesses like malaria and Chagas disease, and how epigenetic mechanisms that contribute to plasticity also drive evolution on the small and large scales.
I came to UC Santa Cruz in 2013, and previously held positions at Yale University as well as Ruhr University Bochum and the University of Göttingen in Germany. I earned my Dr. rer. nat. (doctorate in natural sciences) at Göttingen, along with M.A. degrees in biology and archaeology. For more information on my research, you can browse a list of my publications.
Advisory Committee for the Genomics Institute
Mark Akeson (BME)
Ed Green (BME)
Darrell Long (ENG)
Mircea Teodorescu (ECE)
Olena Vaske (MCDB)
Jenny Reardon (SOC)
Jennifer Parker (ART)
Jon Ellis (HUM)
Carol Greider (MCDB)
John MacMillan (OR/CHEM)
Holger Schmidt (BSOE/EE)
Richard Durbin, Sanger Institute
Erich Jarvis, Rockefeller University, Vertebrate Genome Project
Sheri Spunt, Sanford University
Peter Goodhand, GA4GH