Our Team
David Haussler Scientific Director
David’s titles include:
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 HHMI Investigator, 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.
Please follow these links to see my CV and publications.
Isabel Bjork Director, Treehouse Childhood Cancer Initiative
Ann Pace Director, Research Development
Zia Isola Director, Diversity Programs
Robert Currie Chief Technical Officer
Jim Kent Jim Kent directs the UCSC Genome Browser project. The project started in 2000 when he created the computer program that assembled the first working draft of the human genome sequence from information produced by sequencing centers worldwide and then participated in the informatics associated with the finishing effort. His team participates in the public consortium efforts to produce, assemble, and annotate genomes. You can find more about my research and publications here.
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. Click further to hear me talk about using computational genomics to infer the common ancestor of today’s birds.
Mark Akeson Faculty
Our research in the Nanopore Technology group focuses on developing methods for more efficient, detailed transcriptome and genome sequencing. The next-generation sequencing (NGS) instruments that have revolutionized modern genomics cannot read RNA directly, nor can they resolve the long, repetitive sequence gaps and structural variants in the human genome. We are working to bridge these technical gaps with nanopore strand sequencing, a process we co-invented in 1989 that reads an individual DNA or RNA strand as an applied electric field drives the strand through a biological nanopore. The rate at which each strand moves through the nanopore is controlled by a processive enzyme at the pore orifice. Changes in ionic current, each associated with a unique ‘word’ 3-6 bases long, are detected with single-nucleotide precision and algorithms read the changing current to call the strand’s bases and infer their sequence.
Recently, we have worked with Oxford Nanopore Technologies (ONT) in their efforts to develop a commercial nanopore DNA sequencer, drawing on fundamental methods we established at UC Santa Cruz. This device, the MinION, weighs 100 grams and is being tested in 1000 laboratories worldwide to identify bacterial strains in clinics, pinpoint Ebola infections at the point of care in West Africa, and detect splice variants in human samples.
Over the next five years, we will use the MinION along with ONT’s high-throughput PromethION to investigate cellular differentiation, neurological disorders, and cancer. Specifically, we have four goals: 1) to read genomic DNA strand exceeding 300,000 bases, 2) to improve the platform’s sequencing accuracy by resolving the homopolymeric tracts in MinION DNA reads so that it approaches the 99.99% (Phred score 40) required for analyzing human DNA samples, 3) to read mRNA splice variants directly, and 4) to resolve age-related sequence and structural changes by achieving direct, complete reads of human mitochondrial DNA.
I joined UC Santa Cruz in 1996 from a position at the National Institutes of Health in molecular biology, and hold a Ph.D. in soil microbiology from UC Davis, as well as a B.A. in twentieth century European history with a minor in biology from UC San Diego. See my publications, or hear me describe my research.
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.
Dr. Andy Hospodor has worked for IBM, Quantum (now Maxtor), and Western Digital, among other companies, since receiving his Ph.D. from Santa Clara University. His research interests include interconnection network architectures for storage systems and scalable storage for computational grids.
In addition to researching Shingled Write Disks, Dr. Hospodor is the Executive Director of the Storage System Research Center (SSRC), and is helping to deepen the connections between the SSRC and industry. You can find more about his research and publications here.
I am currently Associate Director of the Genome Browser and have worked with the Browser Group with shifting responsibilities since 2003. In recent years I have been conducting trainings and workshops on how to use the Genome Browser and its associated bioinformatics tools. I have also been interacting with the medical genetics community to acquire useful datasets for the Browser and to learn about how to make it more useful to the scientific community. Before joining the team I taught courses in organic chemistry, molecular biology, biochemistry and genetics at UCSC.
The Lowe Lab uses a mixture of computational and experimental genomics to Identify and characterize of non-coding RNA (ncRNA) genes, and study the unique biology of archaeal “extremophiles” – microbes that live at the edge of the limits of life (high/low temperature, pH, salt, pressure).
On the experimental side, we do ncRNA discovery via next-generation RNA sequencing, and analysis of transcriptional profiles using hybridization to in-house generated DNA microarrays, augmented by traditional molecular biology characterization. We believe tight integration of theoretical and experimental approaches is the quickest, most efficient path to discovery. We have also created full genome DNA microarrays for two of the most extreme hyperthermophilic Archaea sequenced to date, Pyrococcus furiosus and Pyrobaculum aerophilum, which natively grow at boiling temperatures.
On the computational side, we develop and refine methods to detect RNA genes in genomic sequence using probabilistic models and comparative genomics. We also analyze RNA-seq data for novel transcript detection, and extremophile array data to predict functional roles for genes of unknown function, identify the major players in various cellular stresses, and develop robust functional clusters. To learn more about my research please see my list of publications.
Jenny Reardon is professor of Sociology and faculty affiliate in the Center for Biomolecular Science and Engineering at UC Santa Cruz. She founded and directs the Science and Justice Research Center at UCSC. She is the author of Race to the Finish: Identity and Governance in an Age of Genomics (Princeton University Press, 2005) and is currently working on a second book manuscript entitled The Postgenomic Condition: Ethics, Justice, Knowledge After the Genome (forthcoming with Chicago University Press). You can find more about her research and publications here.
The Sanford lab studies how RNA binding proteins (RBPs) influence the interpretation of genetic information in mammals. Many human diseases arise as a result of aberrant interactions between RNA and RBPs. We apply genomic and biochemical approaches to identify RBP interaction sites and determine their functional significance.
Our current work focuses on two different classes of RBPs that are associated with cancer. We aim to determine which RNA sequences engage oncogenic RBPs in cancer cells, allowing us to identify these RBP’s RNA targets and molecular functions. We hope the results of our research will yield new RNA-based diagnostics and therapies for cancer.
I joined UC Santa Cruz in 2008 and have also held positions at Indiana University School of Medicine and the Medical Research Council Human Genetics Unit in Edinburgh, UK. I received my Ph.D. and B.A. from Case Western Reserve University. You can find a list of my publications here, or listen to me describe my research.
I study the adaptive immune system, using a combination of big data genomics and methods from molecular biology to reveal how the immune system works as a whole. Analyzing the distinct genomes of each of the human body’s hundreds of millions of immune cells has yielded a wealth of new immunological information, but the resulting data is highly complex and generating and processing it can be expensive. When I started the Vollmers lab at UCSC, I wanted to develop a protocol to achieve high accuracy in reading the complete transcripts of antibody heavy chains.
We designed a pipeline integrating advanced molecular biology with computational tools we developed that assembles raw sequencing read data into antibody heavy chain sequences.
This streamlined molecular biology pipeline allows us to produce a final sequencing library from RNA over the course of a single day in the lab. Our publicly available computational tools, in turn, make it easy for other scientists to analyze the data in these sequencing libraries. By facilitating quicker, less expensive, and more accessible immunogenomic analysis, our research helps molecular biologists increase our knowledge of how the immune system works, making way for new treatments for cancer, autoimmunity, immunodeficiency and other diseases.
I came to UCSC in 2014, and previously held a postdoctoral position at Stanford University. I earned my Dr. rer. nat., or doctorate in natural sciences, from the University of Heidelberg in Germany for research conducted at the Salk Institute for Biological Studies in La Jolla, California. My M.S. and B.S. in biomedical sciences are from the University of Würzburg, also in Germany. Check out a list of my publications, or hear me describe my research.
Jingchun Zhu I earned my Ph.D. in biological and medical informatics from UC San Francisco, and subsequently held a postdoctoral position in the Haussler Lab at UCSC, where I led the development of the UCSC Cancer Genomics Browser. I’m a project lead for UCSC’s Xena visual analysis tool. My interests include improving presentation of genomics data to increase clinician and researcher understanding of disease, creating modular and sharable web-based data visualizations and data hosting. I’m currently involved in UCSC Xena, UCSC Cancer Genomics Browser, the Cancer Genome Atlas (TCGA), International Cancer Genomics Consortium (ICGC), Big Data to Knowledge (BD2K), and the Treehouse Childhood Cancer Initiative. To learn more about our work with Xena, you can watch this short introduction.
My work is in the field of molecular ecology and evolution, two closely related disciplines that use genomics to study how populations adapt to their environments. In the Bernardi lab, we ask and answer questions about the speciation of marine fish, an area of inquiry that has changed rapidly as high-throughput sequencing makes genomic testing increasingly practical. Such genomic information makes it easier than ever before to demonstrate where populations of fishes diverged into separate species, or to show that morphologically indistinguishable fish are actually genetically distinct species. We work in four main areas—identifying the genetic bases of adaptation to local environments, surveying the changing populations in the Mediterranean resulting both from climate change and from fish entering the Mediterranean from the Red Sea via the Suez Canal, studying the sustainability of subsistence coral reef fishing in Yap State, Micronesia, and performing long-term monitoring of the Moorea Coral Reef and its ecology. All this work allows us to gain a deeper understanding of the molecular underpinnings of how fish species adapt to their local environments.
I came to UC Santa Cruz in 1994, following positions at the Pasteur Institute in Tunis, Tunesia, and at Stanford’s Hopkins Marine Station in Pacific Grove. I hold an M.S. and Ph.D. in molecular biology working on the genome organization of fishes from the University of Paris, where I also earned my B.A. You can learn more about my research, or find a listing of my publications.
My research interests include regulation of innate and adaptive immunity, systems biology of human immune responses, and the development of novel vaccines and oligonucleotides-based drugs. I along with my colleague Tim Mosmann defined the principle subtypes of helper T cells, T1h and T2h, based on cytokine expression and function. Some of my other accomplishments include defining the basic mechanism of T cell regulation in asthma and infectious and parasitic diseases and demonstrating the central role of regulatory CD4+ T cells in preventing inflammatory bowel disease.
I earned my A.B. in Microbiology from Indiana University and my Ph.D. in Biology from UC San Diego. In addition to holding the position of Adjunct Professor of Biomolecular Engineering, I am a founding member of the DNAX Research Institute in Palo Alto and am Senior Vice President and Chief Scientific Officer at Dynavax where I pioneered the development of agonists and antagonists for Toll-like receptors.
Ted Goldstein My research focuses on harnessing machine learning and large scale statistical processing of cancer omics data to identify possible targets for precision drug therapies. Currently I am Director of Medbook at UCSC and Scientific Program Director for the Institute of Computational Health Sciences at UCSF, as well as a research collaborator with the Stand Up To Cancer Project Dream Team and the NIH’s Cancer Genome Atlas.
I have been very privileged to work with some fabulous people at Apple, Sun Microsystems, Xerox PARC/ParcPlace Systems and other many fabulous start-up companies and I made major contributions to the development of software tools and operating systems. As Vice President of Development Technologies at Apple, I led the effort to create Xcode, the preeminent developer tool for Mac OS X and iPhone. While at Sun Microsystems, Inc., I created Java Card, the Smart Card in GSM phones and US military and government identification cards. I have been awarded nine patents in information technologies. After many commercial successes as a Vice President of Engineering in the computer industry, I decided I needed a new level of challenge and returned to my first love, biology and bioinformatics.
To learn more about my research see my full list of patents and publications, or hear me describe my vision for Medbook.
My work in plant evolution centers on understanding how both tropical and temperate flowering plants—especially those in California—adapt to new habitats and form new species. Research in the Kay lab combines observations and experiments in the field and the greenhouse with insights from molecular genetics, microscopy, phylogenetic inference, and comparative biology. We work to understand the genetics that underlie plant speciation, focusing on the geographic and ecological settings in which plant species diverge, as well as the adaptations and phenotypic changes that contribute to reproductive isolation. We are especially interested in how plants adapt to their pollinators, soil environment, and local climate, and how these factors affect the overall diversity of a regional flora. Insights from our studies are useful for rare plant conservation strategies and restoration planning.
I came to UC Santa Cruz in 2008, and previously held postdoctoral positions at UC Berkeley and UC Santa Barbara. I earned my Ph.D. in plant biology from Michigan State University, and my B.S. in environmental biology and management from UC Davis. You can learn more about my work and find a list of publications here.
My research on data storage systems provides an essential backbone to the big data genomics centered in the Genomics Institute. I head the Storage Systems Research Center, which works on high performance storage systems, archival storage systems and energy-efficient storage. Other areas of investigation include computer system reliability, mobile computing and cyber security. More broadly, my interests incorporate mathematics and science, looking at operating systems, distributed computing, reliability and fault tolerance, and computer security. Multiple governmental and industrial sponsors have made my research possible, including the National Science Foundation, NASA, the Department of Energy (Office of Science and National Nuclear Security Administration), the Department of Defense, Avago Technologies, Exablox, Hewlett Packard Laboratories, Huawei, Intel Corporation, NetApp, Sandisk, Seagate Technology, SK Hynix, Symantec, Veritas, Toshiba and Microsoft.
Before joining UC Santa Cruz in 1988, I received my Ph.D. and M.S. in computer science from the University of California San Diego, and my B.S. from San Diego State University. On my web page you can find a listing of my publications as well as the recognition my work has received.
My research bridges bioelectrics and DNA sequencing to advance knowledge in the burgeoning field of nanogenomics. As a technology developer, my approach to systems on the subcellular level is distinct from traditional biology or engineering, and by bringing together these two groups of researchers, our work in the Biosensors and Bioelectrical Technology Group allows us to propose solutions to scientific problems that would be less available within the confines of a single discipline. The new technologies we develop open the door to increased knowledge by making it possible to ask new questions, and we direct particular attention to developing medically relevant instruments and assays for single cell characterization and manipulation.
We are proudest of our new RNA/DNA sequencing protocol, which uses a precise, controllable nanopipette that we invented to aspirate a minute amount of nucleic acid (less than 1% of the content of a single cell). Because this specimen is so small and does not damage the cell, even as it remains surrounded by many other cell types, we can sample it repetitively over its lifetime and gain a highly detailed understanding of its function. We have also developed nanogenomic technologies to interpret these samples, conducting a highly sensitive whole transcriptome analysis (WTA) that allows us to monitor the genomics of an individual cell in real time. Together, these sampling and sequencing technologies make it possible to manipulate individual living cells.
I came to UC Santa Cruz in 2008 from Stanford University, and hold a Ph.D. in experimental medicine from the Karolinska Institutet in Solna, Sweden. For more information, see my lists of patents and publications.
Beth Shapiro 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, including How 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.
I study large, endangered, carnivorous mammals, focusing on how different species’ exercise physiology, energetics, feeding habits, movements and genes allow them to survive in changing ecosystems around the globe. Research in our Integrative Carnivore EcoPhysiology (ICE) lab combines field work in Africa, Antarctica and sites closer to home with laboratory measurements of such ecologically significant predators as African lions, elephants, Weddell seals, Hawaiian monk seals, pumas, dolphins and narwhals.
We pair functional genomic data with our physiological and behavioral observations to gauge the heritable limitations on these animals’ survival in response to global climate change. At the same time, the insights we gather into animal biology—from a narwhal’s ability to travel long distances between breathing holes in the sea ice to the way a seal’s heart rate drops while it swims deep in the ocean—may one day help human beings live longer and healthier lives.
I have been at UC Santa Cruz since 1994 and hold a Ph.D. in environmental and exercise physiology and an M.S. in physiology from Rutgers University, as well as a B.A. in biology from Douglass College. See my publications or listen to me speak to learn more about research or read my book The Odyssey of KP2: An Orphan Seal, a Marine biologist, and the Fight to Save a Species (Penguin Press, 2012) to learn more about my work with endangered Hawaiian monk seals.
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.
My work as an immunologist centers on identifying novel genes that regulate the innate immune system’s inflammatory response. While certain patterns of gene expression help support inflammation that helps our bodies maintain homeostasis and protects us from microbes, uncontrolled inflammation can result in diseases like cancer, lupus, or rheumatoid arthritis.
In the Carpenter lab, we approach this gene expression by looking at the 85% of the human genome that is actively transcribed but does not code for protein, focusing on the largest class of RNA transcripts produced from the genome, the long non-coding RNAs (lncRNAs). There are at least 16,000 different lncRNAs in the human genome, which show greater cell-type and tissue-specific expression patterns than protein-coding genes, and are involved in remodeling chromatin, transcribing genes, and regulating gene expression after transcription. Our work focuses on lncRNAs expressed in macrophages and dendritic cells and determines their role in inflammatory signaling. We identify differentially regulated lncRNAs using deep sequencing technology, study lncRNA localization using fluorescence in situ hybridization, and carry out loss and gain of function experiments using Cas9/CRISPR technologies to understand how these lncRNAs regulate gene expression in our pathways of interest. Our research offers new insight into the molecular mechanisms that promote, adjust, or restrain the inflammatory program, and may help develop new therapies for human diseases.
Before coming to UC Santa Cruz, I held positions at UCSF, UMass Medical Center, as well as the Irish-based company Opsona Therapeutics. I earned my PhD and my BA Mod in biochemistry and immunology from Trinity College, Dublin. I describe my research on rheumatoid arthritis, other inflammatory diseases and lncRNA further on my website.
The Paleogenomics lab investigates the biology of ancient genomes. Genomic material gleaned from preserved biological remains poses specific research challenges that we address with comparative genome analysis and methods for computationally reconstructing longer sequences of genomic data. Our recent projects stretch backward in time and reach toward the future, from a genome-scale analysis of archaic human DNA, to the comparative genomics of Crocodilia, and the Genome 10K Project, which aims to sequence and compare the complete genomes of 10,000 different vertebrate species. We apply high-throughput sequencing to address questions in molecular biology, including population genetics, alternative splicing, and how gene expression evolved.
Before coming to UC Santa Cruz in 2010, I held postdoctoral appointments at UC Berkeley and as a NSF fellow at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. I hold a Ph.D. in molecular and cell biology from UC Berkeley and a B.S. in genetics from the University of Georgia, Athens, and am also the president of Dovetail Genomics, Inc. You can learn more by reading my publications, or listen to me describe our research on the genomes of early humans.
My research addresses fundamental questions regarding stem cell identity and the role of long non-coding RNAs (lncRNAs) in epigenetic reprogramming and cancer. The Kim lab uses single-cell RNA sequencing and other powerful genomic tools to examine an individual cell’s entire repertoire of protein-coding and non-coding genes, and we have uncovered novel lncRNAs that are dynamically expressed as cells are reprogrammed to a stem-cell state. We investigate how the tens of thousands of lncRNAs in the human genome mediate epigenetic reprogramming using induced pluripotent stem cells and mouse models of cancer. By discovering how lncRNAs help stem cells acquire and maintain identity, particularly in the context of tumorigenesis, we aim to develop new approaches to better diagnose and treat aggressive, poorly differentiated cancers.
Prior to joining the faculty at UC Santa Cruz in 2016, I was a Beckman Fellow at the California Institute of Technology and a Damon Runyon Cancer Research Foundation Fellow at Harvard Medical School and Massachusetts General Hospital. I received my BS in biology from the California Institute of Technology and my PhD in biological sciences from the City of Hope Comprehensive Cancer Center in Duarte, CA, where my work received the National Academy of Sciences’ Cozzarelli Prize for scientific excellence and originality. You can find more about my research and publications here.
As an evolutionary biologist and geneticist of marine populations and ecologies, my research focuses on the origins of speciation as well as the natural forces shaping the divergence of populations and the propagation of species. In particular, I study sea urchins, looking at a combination of neutral and selected genes to study the adaptation and speciation of these globally distributed and genetically deeply resourced animals. Applying genomics to evolutionary biology sheds light on how natural selection, population structure, and historical demography can affect polymorphism within species as well as divergence between species, and offers new insights into the origins and incredible diversity of the tree of life.
Our work in the Pogson lab has developed techniques that can help reveal the processes that influence selection by focusing on DNA polymorphism. We have developed a set of 22 nuclear restriction fragment length polymorphisms (RLFPS) in the Atlantic deep-sea scallop, Placopecten magellanicus, and have been able to show that polymorphic enzyme loci, not degree of heterozygosity, directly contribute to the scallops’ growth rate and overall fitness. More widely, we investigate the evolutionary dynamics of mitochondrial DNA (mtDNA) polymorphism, examining the relation between growth rate and large-scale (1.45 kb) mtDNA repeated sequences in scallops, as well as the evolution of biparental mtDNA inheritance in Mytilus mussels. We also look at the genetic basis of variation in physiological performance in different stocks of the conservationally vulnerable and commercially important Atlantic cod, Gadus morhua, and analyze variation at electrophoretic, mtDNA, and nuclear RFLP loci to measure the extent of population structure and gene flow. You can find more about my research and publications here.
Sofie SalamaResearch Investigator
I direct the Haussler Wet Lab, which is a portion of Professor David Haussler’s research group at UCSC and is primarily funded by the Howard Hughes Medical Institute. We work closely with the computational group, the Haussler Dry lab, to understand the evolution and function of non-protein coding regions of the human genome. A major focus is on identifying DNA elements and non-coding RNAs that play a role in specifying cortical neuron development. We use embryonic or induced pluripotent stem cell neural differentiation assays with human and primate stem cells followed by genomic characterization of this process using RNA-Seq, ChIP-Seq, etc.
This approach allows us to identify both primate- and human-specific features of this important developmental pathway. In addition, we are examining the role of transposable elements in modifying our genome in both deleterious and beneficial ways. We study the cellular machinery that controls the proliferation of these elements and whether deregulation of these elements during reprogramming alters the genome of induced pluripotent stem cells. You can find more about my research here.
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 speak about my work.
Wet Lab/Systems BIology