Meet Our Team

Leadership

David Haussler

David Haussler

Scientific Director, Affiliated Faculty

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Scientific Director UCSC Genomics 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 (CVpublications). 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 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-Salama Lab website for more information. See also my CV and publications.

Lauren Linton

Lauren Linton

Executive Director

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Lauren  made a name for herself as one of Science Magazine’s “Unsung Heroes of the Human Genome Project” when she scaled up production at what is now the Broad Institute to make it the lead sequencing institution of the Human Genome Project. She has founded, built, and worked with several academic and non-profit institutes, founded a successful drug discovery biotech, and consulted with numerous biomedical and biotech companies through diverse phases of their development, from early research, fundraising, and scaleup to product launch.

Russ Corbett-Detig

Russ Corbett-Detig

Associate Director for Pathogen Genomics, Affiliated Faculty

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I started at UCSC as an assistant professor in the Department of Biomolecular Engineering in July of 2016. Before that, I was a Chancellor’s Postdoctoral Fellow at UC Berkeley in Rasmus Nielsen’s lab where, among other things, I developed computational methods for infering and for simulating patterns of local ancestry in admixed populations. From 2010-2014, I did my graduate work in Dan Hartl’s lab at Harvard where I studied population genomics of chromosomal inversions, epistasis and comparative patterns of genomic variation.

Read about my lab’s software and publications.

Lars Fehren-Schmitz

Lars Fehren-Schmitz

Associate Director for Genomics and Society, Affiliated Faculty

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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.

Max Haeussler

Max Haeussler

Associate Director for Public Platforms, Affiliated Faculty

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Max Haeussler is the Co-PI of the UCSC Genome Browser. He is also the creator of GBiB and GBiC and works on text mining, CIRM & HCA projects.

Karen Miga

Karen Miga

Associate Director for Human Pangenomics, Affiliated Faculty

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I am the co-lead of the telomere-to-telomere (T2T) consortium and the project director of the human pangenome reference consortium (HPRC) production center at UCSC. My research program combines innovative computational and experimental approaches to produce the high-resolution sequence maps of human centromeric and pericentromeric DNAs. The Miga lab aims to uncover a new source of genetic and epigenetic variation in the human population, which is useful to investigate novel associations between genotype and phenotype of inherited traits and disease.

Please visit my lab website for more information:

www.migalab.com

Benedict Paten

Benedict Paten

Associate Director for Computational Genomics, Affiliated Faculty

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Dr. Benedict Paten is an associate professor in the Department of Biomolecular Engineering at the University of California, Santa Cruz. He received his Ph.D. in computational biology from the University of Cambridge and the European Molecular Biology Laboratory. Dr. Paten’s work is broadly focused on the growing field of computational genomics. He leads the Computational Genomics Lab within the Genomics Institute. He is involved in a number of large-scale genomics efforts; he is currently a PI of the Human Cell Atlas Data Coordination Platform, the NHGRI AnVIL, the NHLBI BioData Catalyst, HuBMAP, GENCODE, and the Human Pangenome Reference Consortium. Through these efforts and many smaller collaborations, he is helping to develop methods to further our ability to read and interpret genomes. 

Sofie Salama

Sofie Salama

Faculty Director for Diversity, Affiliated Faculty

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Sofie Salama’s work involves using pluripotent stem cells from a variety of primate species and high throughput sequencing methods to study how genome evolution affects human development and disease. Since 2004, she has collaborated closely with Professor David Haussler, Scientific Director of the UC Santa Cruz Genomics Institute, directing a Molecular Biology (Wet) Lab that works closely with the Computational Genomics (Dry) Lab. She is also a lead scientist for the UCSC Treehouse Pediatric Cancer Initiative and is a Howard Hughes Medical Institute Senior Scientist. She has funding from NIH-NHGRI to explore the mechanisms by which transposable elements lead to new gene regulatory programs important for the evolution of new traits as well as funding from HHMI, NIH-NIMH, and the Simons Foundation to study the role of human-specific genomic innovations on brain development and disease. With Professor Haussler and Computer and Electrical Engineering Professor Mircea Teodorescu, Salama leads UCSC’s Braingeneers project funded by the Schmidt Futures Foundation. This interdisciplinary team aims to develop stem cell derived 3D cell culture models of the brain to study the development and behavior of human neural circuits at a scale that enables the application of modern artificial intelligence (AI) approaches to this research. Salama received her Ph.D. at UC Berkeley in Molecular, Cell and Development, did postdoctoral research in the Laboratory of Molecular Oncology at the MGH Cancer Center and Harvard Medical School and was a founding scientist and Director of Core Technologies at Microbia Inc. (now Ironwood Pharmaceuticals). Her work has been recognized by the Jane Coffin Childs Memorial Fund for Medical Research.

Beth Shapiro

Beth Shapiro

Associate Director for Conservation Genomics, 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.

Affiliated Faculty

Mark Akeson

Mark Akeson

Emeritus Affiliated Faculty

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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.

Manny Ares

Manny Ares

Affiliated Faculty

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Manny landed in Santa Cruz as an Assistant Professor in 1987 and set about to dismantle the yeast spliceosome using genetics and biochemistry. As the genomic age dawned, he collaborated with David Haussler to create splicing-sensitive microarrays to study global splicing regulation in mammals and yeast. In addition to splicing, the Ares lab is interested in all things RNA, and enjoys numerous collaborations with other Genomics Institute faculty including Mark Akeson to develop methods to improve direct RNA sequencing using nanopores, Benedict Paten on single molecule RNA modification profiling of ribosomal RNAs, and Russ Corbett-Detig on the dynamics of intron gain during eukaryotic genome evolution in the wide-spread marine microalgae Micromonas. For more about the lab’s findings, check this link. Lab Website: http://ribonode.ucsc.edu/

Joshua Arribere

Joshua Arribere

Affiliated Faculty

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The Arribere Lab studies how information is decoded from the genome, focusing on the understudied steps of mRNA translation (protein synthesis) and mRNA decay. We are particularly interested in the question of how the gene expression program deviates from normal for individual mRNAs. One lens we use to attain insight is mRNA quality control pathways in which cells identify and degrade an individual mRNA according to its properties, such as the presence of early stop codons, difficult-to-translate codons, or a lack of any stop codons. Our work has relevance to human health and disease: mutations can alter the pathway of gene expression, alter the protein products and/or their levels, and cause disease. We leverage experimental systems, chiefly the nematode C. elegans and we use both classical (genetic screens, phenotyping) and contemporary (CRISPR/Cas9, deep sequencing, Nanopore full length mRNA sequencing) approaches.

Lab Website: https://arriberelab.mcdb.ucsc.edu/

Giacomo Bernardi

Giacomo Bernardi

Affiliated Faculty

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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.

Angela Brooks

Angela Brooks

Affiliated Faculty

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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.

Susan Carpenter

Susan Carpenter

Affiliated Faculty

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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.

Raquel Chamorro-Garcia

Raquel Chamorro-Garcia

Affiliated Faculty

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A key challenge of the modern world relates to how our contribution to environmental pollution has a pervasive effect on our own health and the health of future generations. This seems to occur, at least partially, due to non-genetic alterations of the germline; however, the mechanisms through which exposure to environmental factors results in diseases in the offspring and future generations remain unclear. The Chamorro-Garcia lab is working on determining how environmental factors such as pollutants, diets, temperature, or stress shape our phenotype with a focus on mechanisms of transgenerational epigenetic inheritance. Their work integrates epigenomic, transcriptomic, and physiological analyses to reveal how environmental stressors lead to the modulation of the expression of the genome.

Raquel Chamorro-Garcia is an Assistant Professor of Microbiology & Environmental Toxicology. Lab website

Brad Colquitt

Brad Colquitt

Affiliated Faculty

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Dr. Brad Colquitt is an Assistant Professor in the Department of Molecular, Cell, and Developmental Biology at UCSC. He completed his postdoc in Dr. Michael Brainard’s lab at UCSF/HHMI, where he studied the cellular and molecular systems that influence birdsong learning and plasticity. Before that, he earned his Ph.D. at UCSF in Dr. Stavros Lomvardas’s lab (now at Columbia University) studying the roles of DNA modifications during olfactory system development.

The Colquitt Lab studies the development and evolution of sensorimotor behaviors, using birdsong and its neural circuitry as a model system. The lab seeks to understand the cellular and molecular basis of behavioral evolution by characterizing the developmental relationships — from neural stem cells to mature neurons — of neurons dedicated to ancestral and derived behaviors. The lab combines advanced molecular techniques, genomics, imaging, and behavioral analysis to understand: (1) the gene regulatory networks that build birdsong neural circuitry during development,  (2) how these networks intersect with experience during birdsong learning, and (3) how modifications to these networks contributed to the evolution of birdsong and other complex learned behaviors. Lab website: www.colquitt-lab.com

Russ Corbett-Detig

Russ Corbett-Detig

Associate Director, Affiliated Faculty

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I started at UCSC as an assistant professor in the Department of Biomolecular Engineering in July of 2016. Before that, I was a Chancellor’s Postdoctoral Fellow at UC Berkeley in Rasmus Nielsen’s lab where, among other things, I developed computational methods for infering and for simulating patterns of local ancestry in admixed populations. From 2010-2014, I did my graduate work in Dan Hartl’s lab at Harvard where I studied population genomics of chromosomal inversions, epistasis and comparative patterns of genomic variation.

Read about my lab’s software and publications.

Omar Cornejo

Omar Cornejo

Affiliated Faculty

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Omar Cornejo is an associate professor of ecology and evolutionary biology who just joined UC Santa Cruz this January. He is an evolutionary geneticist interested in the evolution of pathogens and hosts. In the Cornejo Lab, they study how natural selection drives the adaptation of microbes to their hosts and how hosts develop disease resistance. The lab focuses their analysis on the evolutionary context (historical demographics and especial geological and anthropological events) under which selection drives the gain or loss of genetic variants using study systems in humans and non-human primates, microbiomes, malarial parasites, and plants.

James Doucet-Battle

James Doucet-Battle

Affiliated Faculty

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James Doucet-Battle is an Associate Professor in the Department of Sociology at the University of California, Santa Cruz. He is a graduate of the University of California, Berkeley/ University San Francisco Joint Medical Anthropology Program. His research and teaching interests lie at multiple intersections of science, technology and society studies, diaspora studies, development studies and anthropological approaches to health and medicine. He applies these interests to study the political economy of genomic discourses about race, risk, and health disparities. Funded as a both University of California, Berkeley Chancellor’s and President’s Fellow as well as a Ford Foundation Fellow, he carried out ethnographic research examining racial categorization, risk, and health disparities in Type II diabetes in both New York and the San Francisco Bay Area for his book, Sweetness in the Blood: Race, Risk, and Type 2 Diabetes Minnesota, 2021). A significant focus of this research involved an analysis of the translational challenges facing clinical research and community education outreach efforts towards at risk minority groups, particularly African Americans.

He has published in Transforming Anthropology, the Catalyst Journal of Feminist Technoscience, the Kroeber Anthropological Society Papers, and Feminist Anthropology. He is currently affiliated with the Science and Justice Research Center, the Department of Anthropology, the Global and Community Health Program, and the Theorizing Race after Race Working Group at UC Santa Cruz.

Rebecca Dubios

Rebecca Dubios

Affiliated Faculty

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Rebecca studies the molecular mechanisms of human virus surface and replication proteins using a diverse toolkit of structural and biochemical techniques. She uses her discoveries to design novel vaccines and antiviral therapeutics. Before joining UCSC, she was a postdoctoral fellow at the Pasteur Institute in Paris, France, and at St. Jude Children’s Research Hospital in Memphis, TN. She received her Ph.D. in Biochemistry at UC San Diego and her bachelor’s degree from the University of Colorado Boulder.

Jason Eshraghian

Jason Eshraghian

Affiliated Faculty

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Rebecca studies the molecular mechanisms of human virus surface and replication proteins using a diverse toolkit of structural and biochemical techniques. She uses her discoveries to design novel vaccines and antiviral therapeutics. Before joining UCSC, she was a postdoctoral fellow at the Pasteur Institute in Paris, France, and at St. Jude Children’s Research Hospital in Memphis, TN. She received her Ph.D. in Biochemistry at UC San Diego and her bachelor’s degree from the University of Colorado Boulder.

Lars Fehren-Schmitz

Lars Fehren-Schmitz

Associate Director, Affiliated Faculty

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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.

Winifred Frick

Winifred Frick

Affiliated Faculty

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Winifred Frick is Chief Scientist at Bat Conservation International and an Associate Research Professor in Ecology and Evolutionary Biology at UC Santa Cruz.  As Chief Scientist at Bat Conservation International, she directs high priority research and development of scalable solutions for achieving meaningful conservation outcomes for bats.  With nearly 1400 species, bats are the second most diverse group of mammals on earth, yet many species are threatened by the forces of global change. Her research approach emphasizes empirical field studies coupled with quantitative analyses to address critical data gaps to inform conservation action for bats.  She serves on the steering committee for the Bat1K Project. Lab website: https://frick.eeb.ucsc.edu/

Richard Ed Green

Richard Ed Green

Affiliated Faculty

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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.

Carol W. Greider

Carol W. Greider

Affiliated Faculty

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I received my bachelor’s degree from the University of California at Santa Barbara in 1983 and my Ph.D. in 1987 from the University of California at Berkeley. In 1984, working together with Dr. Elizabeth Blackburn, I discovered telomerase, an enzyme that maintains telomeres, or chromosome ends. In 1988, I went to Cold Spring Harbor Laboratory where, as an independent Cold Spring Harbor Fellow, I cloned and characterized the RNA component of telomerase. In 1990, I was appointed as an assistant investigator at Cold Spring Harbor Laboratory, followed later by appointment to Investigator. I expanded the focus of my telomere research to include the role of telomere length in cellular senescence, cell death and in cancer. 

In 1997, I moved my laboratory to the Department of Molecular Biology and Genetics at The Johns Hopkins University School of Medicine. In 2003, I was appointed as the Daniel Nathans Professor, and Director of the Department of Molecular Biology and Genetics. At Johns Hopkins University, my group continued to study telomerase and determined the secondary structure of the human telomerase RNA. In addition, we characterized the loss of telomere function in mice, which allowed an understanding of short telomere syndromes in humans such as bone marrow failure, pulmonary fibrosis and other diseases. 

In 2009, I shared the Nobel Prize in Physiology or Medicine with Drs. Elizabeth Blackburn and Jack Szostak for our work on telomeres and telomerase. 

In 2020, I established my laboratory at the University of California Santa Cruz where my research group studies fundamental mechanisms of telomere length regulation. 

Read more about my move to UCSC.

David Haussler

David Haussler

Scientific Director, Affiliated Faculty

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Scientific Director UCSC Genomics 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 (CVpublications). 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-Salama Lab website for more information. See also my CV and publications.

Alex Ioannidis

Alex Ioannidis

Affiliated Faculty

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Alex Ioannidis graduated with a degree in Chemistry and Physics from Harvard and completed an M.Phil in Computational Biology in the Department of Applied Math & Theoretical Physics at Cambridge. His Ph.D. is in Computational & Mathematical Engineering from Stanford. Prior to obtaining his Ph.D., he worked on novel superconducting logic and quantum computing at Northrop Grumman. His current research centers on developing computational methods for genomics and precision health, including phenotype prediction with deep learning and privacy preserving algorithms. He also works on statistical genetics methods for diverse populations and has a particular focus on underrepresented populations in Oceania and Latin America.

Vanessa Jonsson

Vanessa Jonsson

Affiliated Faculty

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Vanessa Jonsson is an Assistant Professor of Applied Mathematics.

Kathleen Kay

Kathleen Kay

Affiliated Faculty

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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.

Joanna Kelley

Joanna Kelley

Affiliated Faculty

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Joanna Kelley is a genome scientist whose research examines organismal responses to extreme stressors. Joanna Kelley’s group investigates the genomic basis of adaptation, speciation, and organismal divergence. Her research combines statistical and genomic approaches with environmental, ecological, and functional studies to understand how organisms adapt to novel environments.

Daniel Kim

Daniel Kim

Affiliated Faculty

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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.

Sri Kurniawan

Sri Kurniawan

Affiliated Faculty

David Lederman

David Lederman

Affiliated Faculty

Scott Locky

Scott Locky

Affiliated Faculty

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Scott Lokey received his Ph.D. at the University of Texas, Austin in organic chemistry under the mentorship of Dr. Brent Iverson. His graduate research was centered on the synthesis of molecules that fold into protein-like shapes in water and on poly-intercalators that bind DNA sequence-specifically. He did post-doctoral research at Genentech, where he worked on the synthesis of bioactive cyclic peptides, and then at Harvard Medical School on the synthesis of molecules designed to disrupt cellular processes related to motility. He joined the faculty at UCSC in 2002 in the Department of Chemistry and Biochemistry, where his research group focuses on the relationship between molecular structure and drug-like properties, especially cell permeability. Professor Lokey is also the director of the UCSC Chemical Screening Center, a high-throughput screening facility dedicated to early-stage lead discovery, and is co-founder of Circle Pharma, a biotech startup focusing on the discovery of cyclic peptide inhibitors against intracellular targets.

Lab Website: https://lokey.chemistry.ucsc.edu/

Darrell Long

Darrell Long

Affiliated Faculty

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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.

Todd Lowe

Todd Lowe

Affiliated Faculty

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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.

Aide Macias-Muñoz

Aide Macias-Muñoz

Affiliated Faculty

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Aide Macias-Muñoz is an Assistant Professor in the Department of Ecology and Evolutionary Biology at the University of California, Santa Cruz. Her research focuses on understanding the molecular underpinnings of complex trait evolution. This research lies at the intersection of molecular biology, functional genomics, and evolution. Her lab uses genomics and transcriptomics in invertebrates to determine the similarities and differences in genes encoding similar traits across taxa. Specifically, her lab is interested in investigating which cells and genes are used for sensory system development, regeneration, and evolution.

Before coming to UC Santa Cruz, Aide completed her BA in Integrative Biology with a minor in Chicano Studies from UC Berkeley and a PhD in Ecology and Evolutionary Biology at UC Irvine. She was a George E. Hewitt Foundation Postdoctoral Fellow in the Department of Developmental and Cell Biology at UC Irvine and a UC Santa Barbara Chancellor’s Postdoctoral Fellow in the Department of Ecology, Evolution, and Marine Biology at UC Santa Barbara. Lab Website: https://macias.sites.ucsc.edu/

Rachel Meyer

Rachel Meyer

Affiliated Faculty

Karen Miga

Karen Miga

Associate Director, Affiliated Faculty

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I am the co-lead of the telomere-to-telomere (T2T) consortium and the project director of the human pangenome reference consortium (HPRC) production center at UCSC. My research program combines innovative computational and experimental approaches to produce the high-resolution sequence maps of human centromeric and pericentromeric DNAs. The Miga lab aims to uncover a new source of genetic and epigenetic variation in the human population, which is useful to investigate novel associations between genotype and phenotype of inherited traits and disease.

Please visit my lab website for more information:

www.migalab.com

Eric P. Palkovacs

Eric P. Palkovacs

Affiliated Faculty

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Eric P. Palkovacs is a professor in the Department of Ecology and Evolutionary Biology and the director of the Fisheries Collaborative Program. In his research, he applies genomic tools to understand evolutionary responses to rapid environmental changes, such as fishing and climate change. He also applies genomic tools to support conservation efforts for threatened and endangered species. His work focuses primarily on freshwater and coastal ecosystems. He has a particular interest in the ecology and evolution of anadromous fishes, which migrate between freshwater and marine ecosystems, play an important role in coastal food webs, and serve as an important fisheries resource for people.

Lab Website: https://palkovacs.eeb.ucsc.edu/

Devon Pearse

Devon Pearse

Affiliated Faculty

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Devon Pearse (he/him) is a research geneticist at the NOAA/NMFS Southwest Fisheries Science Center working as part of the Molecular Ecology and Genetic Analysis Team, and adjunct professor of Ecology and Evolutionary Biology at UC Santa Cruz in the Fisheries Cooperative Program. We conduct innovative research addressing a broad array of questions in evolutionary genetics, conservation, and genomics. Much of our work is focused on salmonid fishes, particularly understanding the genomic basis of life-history variation. Our team operates as a cooperative research unit composed of both full-time federal researchers and a variable number of UCSC research staff, and post-doctoral and visiting researchers, undergraduates, and graduate students, most of whom work through the UCSC Fisheries Cooperative Program. We also provide critical scientific review and policy advice regarding specific management actions, as well as the role of science in listing decisions under the Endangered Species Act.

 

I have been an adjunct professor in Ecology and Evolutionary Biology at UC Santa Cruz since 2008, and previously was a postdoctoral scholar at Brigham Young University in Provo, Utah. I earned my PhD in genetics at the University of Georgia in 2001 and a BA in Biology from UC Santa Cruz in 1996.

Benedict Paten

Benedict Paten

Associate Director, Affiliated Faculty

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Dr. Benedict Paten is an associate professor in the Department of Biomolecular Engineering at the University of California, Santa Cruz. He received his Ph.D. in computational biology from the University of Cambridge and the European Molecular Biology Laboratory. Dr. Paten’s work is broadly focused on the growing field of computational genomics. He leads the Computational Genomics Lab within the Genomics Institute. He is involved in a number of large-scale genomics efforts; he is currently a PI of the Human Cell Atlas Data Coordination Platform, the NHGRI AnVIL, the NHLBI BioData Catalyst, HuBMAP, GENCODE, and the Human Pangenome Reference Consortium. Through these efforts and many smaller collaborations, he is helping to develop methods to further our ability to read and interpret genomes. 

Malin Pinsky

Malin Pinsky

Affiliated Faculty

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Malin Pinsky is an Associate Professor in the Department of Ecology & Evolutionary Biology and leads the Global Change Research Group to understand how life adapts to climate change and variability, from genes to communities. His more than 100 publications have appeared in Science, Nature, and other journals, and his research has been covered by the New York Times, Wall Street Journal, and BBC. He is a fellow of the American Association for the Advancement of Science (AAAS), an Earth Leadership Fellow, and an Early Career Fellow of the Ecological Society of America, and he was named one of Science News’ ten scientists to watch in 2019. Pinsky serves on advisory boards for the Beijer Institute of the Royal Swedish Academy of Sciences, the non-profit Oceana, and the Chewonki Foundation. He has a Ph.D. in Biology from Stanford University and an A.B. in Biology and Environmental Studies from Williams College. He grew up exploring tidepools and mountains in Maine. Lab website: https://globalchange.sites.ucsc.edu/

Grant Pogson

Grant Pogson

Affiliated Faculty

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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.

Nader Pourmand

Nader Pourmand

Affiliated Faculty

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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.

Jenny Reardon

Jenny Reardon

Affiliated Faculty

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Jenny Reardon is a Professor of Sociology and the Founding Director of the Science and Justice Research Center at the University of California, Santa Cruz. Her research draws into focus questions about identity, justice and democracy that are often silently embedded in scientific ideas and practices, particularly in modern genomic research. Her training spans molecular biology, the history of biology, science studies, feminist and critical race studies, and the sociology of science, technology and medicine. She is the author of Race to the Finish: Identity and Governance in an Age of Genomics(Princeton University Press, 2005) and The Postgenomic Condition: Ethics, Justice, Knowledge After the Genome(Chicago University Press, Fall 2017). She has been the recipient of fellowships and awards from, among others, the National Science Foundation, the Max Planck Institute, the Humboldt Foundation, the London School of Economics, the Westinghouse Science Talent Search, and the United States Congressional Committee on Science, Space and Technology.

Marco Rolandi

Marco Rolandi

Affiliated Faculty

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Marco Rolandi is a Professor and Chair of Electrical and Computer Engineering at the University of California, Santa Cruz. His laboratory’s research focuses on micro- and nano- biological and bioinspired materials and their integration in bioelectronic and bioprotonic devices. These devices are used to study ionic transport at the biotic abiotic interface and create ion channel mimics, implantable microelectrodes, and synaptic transistors and memories. His specialties include nanolithography, surface chemistry, surface patterning, nanoelectronics, molecular electronics, direct-write, bio-inorganic interfaces, nanotubes, ionic/protonic conductors, and semiconductors. Read more about his research.

Seth Rubin

Seth Rubin

Affiliated Faculty

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My laboratory is studying the molecular mechanisms of cell-cycle control and their relationship to cancer by determining the structure and biochemical function of regulatory proteins. Our approach relies on diverse methods in structural biology, protein biochemistry, and cell biology. Projects in the laboratory focus on the structure and function of cell-cycle transcription factors (E2F, FoxM1, B-Myb, etc.) and the proteins (Rb, MuvB, etc.) and kinases (Cdks, Aurora A, Plk1) that regulate them. The motivation for this work is that structural and biochemical studies will inform fundamental mechanisms underlying cell division and ultimately lead to novel classes of cancer therapeutics.

I came to UCSC as a professor in the Department of Chemistry and Biochemistry in 2006. I received a B.A. in Chemistry from Columbia University, and I did doctoral research in the Department of Chemistry at UC Berkeley, developing novel NMR methods with Professors David Wemmer and Alexander Pines. I was a Damon Runyon Cancer Research Foundation Postdoctoral Fellow at the Memorial Sloan Kettering Cancer Center in the laboratory of Dr. Nikolai Pavletich, where I became interested in mechanisms regulating cancer cell division.

In addition to research, I am committed to teaching, service to the scientific community, and addressing diversity, equity, and inclusion (DEI) in the sciences. I introduced teaching practices in my first-year undergraduate chemistry course, including active learning and developing STEM identity, which have been designed to reduce equity gaps. I also developed a Coursework Undergraduate Research Experience (CURE) laboratory class in cancer biochemistry that I have taught since 2022. I am the faculty director of UCSC’s NIH-funded Maximizing Access to Research Careers (MARC) program and PI of the associated T34 training grant.

Lab Website: https://rubinlab.sites.ucsc.edu

Shelbi Russell

Shelbi Russell

Affiliated Faculty

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Shelbi Russell’s research uses contemporary intracellular symbiotic associations between bacteria and animals combined with synthetic biology to study how symbioses are maintained across generations. During her Ph.D. program in Colleen Cavanaugh’s lab at Harvard University, she built tools and datasets to answer long-standing questions in bacterial symbiont genome evolution. To study the cellular and molecular basis for host and symbiont association from generation-to-generation, Shelbi performed her postdoctoral training in Bill Sullivan’s lab at UCSC. 

The UCSC Russell lab will reveal the cellular and molecular mechanisms underlying symbiont association, characterize how symbiont transmission influences genome evolution, and engineer new symbiont strains and infections with enhanced properties for host control. Shelbi is passionate about teaching and mentorship, and has strived to include diverse trainees in her research and publications throughout her career. She strongly supports faculty and undergraduate research opportunities at UCSC, and is thrilled to help train the next generation of scientists.

Sofie Salama

Sofie Salama

Faculty Director, Affiliated Faculty

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Sofie Salama’s work involves using pluripotent stem cells from a variety of primate species and high throughput sequencing methods to study how genome evolution affects human development and disease. Since 2004, she has collaborated closely with Professor David Haussler, Scientific Director of the UC Santa Cruz Genomics Institute, directing a Molecular Biology (Wet) Lab that works closely with the Computational Genomics (Dry) Lab. She is also a lead scientist for the UCSC Treehouse Pediatric Cancer Initiative and is a Howard Hughes Medical Institute Senior Scientist. She has funding from NIH-NHGRI to explore the mechanisms by which transposable elements lead to new gene regulatory programs important for the evolution of new traits as well as funding from HHMI, NIH-NIMH, and the Simons Foundation to study the role of human-specific genomic innovations on brain development and disease. With Professor Haussler and Computer and Electrical Engineering Professor Mircea Teodorescu, Salama leads UCSC’s Braingeneers project funded by the Schmidt Futures Foundation. This interdisciplinary team aims to develop stem cell derived 3D cell culture models of the brain to study the development and behavior of human neural circuits at a scale that enables the application of modern artificial intelligence (AI) approaches to this research. Salama received her Ph.D. at UC Berkeley in Molecular, Cell and Development, did postdoctoral research in the Laboratory of Molecular Oncology at the MGH Cancer Center and Harvard Medical School and was a founding scientist and Director of Core Technologies at Microbia Inc. (now Ironwood Pharmaceuticals). Her work has been recognized by the Jane Coffin Childs Memorial Fund for Medical Research.

Jeremy Sanford

Jeremy Sanford

Affiliated Faculty

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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.

Holger Schmidt

Holger Schmidt

Affiliated Faculty

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The main research theme in the Applied Optics Group at UC Santa Cruz is single particle optics. We develop new, highly sensitive methods to study single particles with optical methods. We use these and other established techniques to gain new understanding of these particles and light-matter interactions in general. Due to theQ versatility of optical methods, we can investigate different types of particles. Our focus areas include single biomolecules (integrated optofluidics); single nanomagnets (nano-magneto-optics); and single photons (atomic spectroscopy on a chip). We are affiliated with the California Institute for Quantitative Biomedical Research (QB3) and the Storage Systems Research Center (SSRC). I direct the W.M. Keck Center for Nanoscale Optofluidics, whose mission is to incorporate nanoscale features in optofluidic devices to enable new studies of bioparticles and biological processes. You can read more about my research on the Applied Optics Group‘s website.

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.

Tal Sharf

Tal Sharf

Affiliated Faculty

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Tal Sharf is an Assistant Professor of Biomolecular Engineering. His research involves using human brain organoids to uncover the assembly and wiring of neuronal circuits.

Ali Shariati

Ali Shariati

Affiliated Faculty

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I joined the BSOE faculty as an assistant professor in Biomolecular Engineering in Fall 2019. My research aims to understand how stem cells decide to choose between two conflicting fates: division versus differentiation. I combine emerging genome-editing technologies with single cell imaging to determine regulatory principles of cell fate decisions in pluripotent cells. Learn more about me here.

Upasna Sharma

Upasna Sharma

Affiliated Faculty

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I joined the UCSC faculty in 2018 as an assistant professor of molecular, cell, and developmental biology. My group studies the process by which our experiences and lifestyle influence health and longevity in future generations. Such inheritance, known as epigenetic inheritance, is not a result of mutations or other genetic changes to the DNA passed down in the chromosomes but is thought to be mediated by epigenetic factors that change how genes are expressed. As epigenetic factors can be modulated by environmental conditions, across-generational epigenetic inheritance is potentially mediated via alterations to the gamete “epigenome”. In the Sharma Lab, we are studying how our environmental conditions modulate specific epigenetic factors in germ cells and how those factors influence the development of offspring. We are using a unique and powerful combination of genomic, molecular, genetic, and reproductive approaches to address this question.

Understanding the mechanism of intergenerational epigenetic inheritance of parental environmental effects has significant implications for the epidemiology of common metabolic diseases such as diabetes, which have both genetic components as well as contributions from a patient’s lifestyle and environment. In 2019, I received the NIH Director’s New Innovator Award from the National Institutes of Health to support my group’s research in this area. Read more about this work.

Shaheen Sikandar

Shaheen Sikandar

Affiliated Faculty

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The Sikandar lab is interested in tackling questions pertaining to functional consequences of heterogeneity in stem cells in normal and cancer tissues. We use a combination of computational and wet-approaches to study stem/progenitor cells in the mammary gland and tumor initiating cells in breast cancer. We are particularly interested in answering the following questions (1) Can we map subpopulations of cells to different tumor specific functions with an emphasis on metastasis? (2) What are the intrinsic and extrinsic molecular mechanisms underlying tumor heterogeneity and transitions between different cell states? (3) And how does stem cell heterogeneity in the normal mammary gland evolve with aging and pregnancy? We address these questions in the lab using diverse experimental approaches such as patient-derived xenografts, organoid assays, mouse models and single cell transcriptomics.

Lab website: https://www.sikandarlab.com/

Michael Stone

Michael Stone

Affiliated Faculty

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The Stone Research Group at the University of California Santa Cruz is broadly interested in nucleic acid (RNA and DNA) structure and function. A primary research focus for the group is human telomerase – a specialized protein-RNA complex enzyme that maintains the telomere DNA at the ends of chromosomes. Telomerase function has direct biomedical significance. Telomerase loss-of-function mutations cause human diseases (telomeropathies) characterized by failure of highly proliferative tissue types. In contrast, telomerase is overactive in the majority of human cancers. We are also interested in the structure and dynamics of telomeric chromatin, and how these properties impact telomere and telomerase function. More recently, we have begun to explore new areas of RNA structure and function, including several long-non coding RNAs and the structural basis for exon definition during RNA splicing.

Josh Stuart

Josh Stuart

Affiliated Faculty

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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.

My passion is to develop computational approaches that aid in the discovery of new fundamental biology to enlighten our understanding of evolution, cell fate decisions, and disease mechanisms. I have a particular interest in probablistic approaches that infer and leverage genetic pathway information to ground our analysis in intuition. Read about my lab here.

Mircea Teodorescu

Mircea Teodorescu

Affiliated Faculty

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I am a faculty in the Computer Engineering Department. My current research group consists of graduate and undergraduate students with research focused on several parallel tracks, which span Computer Engineering, Computer Science, Mechanical Engineering and Bio-molecular Engineering.

My lab focuses on developing computational solutions and physical prototypes for robotics applications . We conducts research in the areas of dynamics, vibrations and contact mechanics with applications in bio-engineering, environmental sciences, aerospace, assistive technology, arts etc.

The lab develops detailed computational solutions (slow, but vital for understanding the physical phenomena) as well as simplified ones (fast but accurate only within a well-defined range of input parameters), which are ideal for integration in higher level system simulations. We use 3D printing and other rapid prototyping techniques to develop the micro- and macro-scale mechanical base structures and we develop the electronics using a combination of off-the-shelf hardware and embedded systems built in-house.

Olena Morozova Vaske

Olena Morozova Vaske

Affiliated Faculty

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Changing the story for children affected by cancer has become my lifelong commitment and focus of my research career. Early genomic studies demonstrated that childhood cancers are different from adult cancers and that simply using adult analysis methods would not work for the kids. This motivated us to build on the extraordinary bioinformatics expertise at UC Santa Cruz and launch Treehouse, an initiative that uses comparative cancer genomic analysis to help children treated in the clinic today. I am hopeful that our work will help change the landscape of pediatric cancer genomics and genome-guided medicine.

Jairo Velasco

Jairo Velasco

Affiliated Faculty

Christopher Vollmers

Christopher Vollmers

Affiliated Faculty

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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.

Terrie Williams

Terrie Williams

Affiliated Faculty

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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.

Aiming	Yan

Aiming Yan

Affiliated Faculty

Hsien-Wei (Andy) Yeh

Hsien-Wei (Andy) Yeh

Affiliated Faculty

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Andy Yeh’s research lies at the intersection of protein engineering, protein probes/sensor design, analytical chemistry, organic synthesis, and cell reprogramming. Andy received the NIH K99/R00 Award for his work in designing molecular switches capable of building protein biosensors to guide rapid diagnostic tests. At the interface of protein science and chemistry, his goal is to create next generation luminescent probes to dissect complex biological systems.

Research Investigators

Benjamin Abrams

Benjamin Abrams

Ph.D. Facility Manager

Melissa Cline

Melissa Cline

Associate Research Scientist

Max Haeussler

Max Haeussler

Associate Director

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Max Haeussler is the Co-PI of the UCSC Genome Browser. He is also the creator of GBiB and GBiC and works on text mining, CIRM & HCA projects.

Ann McCartney

Ann McCartney

Assistant Researcher

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Dr. Ann Mc Cartney is a research investigator in the Miga Lab. She obtained her PhD from Dublin City University and has since carried out a Postdoctoral Research Fellowship in Manaaki Whenua for Genomics Aotearoa, and Postdoctoral Research Fellowship Genome Informatics Section in the NHGRI where she also conducted a detail in the NIH Office of Science Policy. Her multidisciplinary training in both human and biodiversity genomics across knowledge systems has fueled her research on positioning genomic infrastructures, procedures and systems inside of the socio-political reality they exist within.

Currently, she acts as the Director of the European Reference Genome Atlas’ Pilot Project and Director of Partnerships and Strategy for MyAfroDNA Biobank. She also is a co-organiser of IndigiData, the chair of the Traditional Knowledge and Biocultural Labels technical implementation working group, and leads data sharing and management policy development for Earth BioGenome Project.

To date, her research has focused on developing engagement frameworks, guidelines and recommendations to support genomics researchers and projects to build sustained partnerships with communities that have, and continue to be left outside of genomics. Alongside Local Contexts and the Native Biodata Consortium, Ann also works on decolonising, redesigning and revolutionizing metadata standards to mainstream the interoperable disclosure of Indigenous knowledge and biocultural interests into collections, biobanks, and digital infrastructures.

Mohammed Mostajo Radji

Mohammed Mostajo Radji

Assistant Research Scientist

Jouni Siren

Jouni Siren

Assistant Research Scientist

Jingchun Zhu

Jingchun Zhu

Research Investigator

Technical & Research Staff

Benjamin Abrams

Benjamin Abrams

Ph.D. Facility Manager

Brandy Baird

Brandy Baird

Nanopore Production Specialist

Galt Barber

Galt Barber

Senior Software Developer

Holly Beale

Holly Beale

Lead Computational Biologist

Lon Blauvelt

Lon Blauvelt

Software Engineer

Heather Borgard

Heather Borgard

Sr Bioinformatics Systems Analyst

Anouk van den Bout

Anouk van den Bout

Assistant Specialist

Jonathan Casper

Jonathan Casper

Software Developer

Catharina Casper-Lindley

Catharina Casper-Lindley

Center for Live Cell Technology Program Manager

Abraham Chavez

Abraham Chavez

Junior Software Engineer

Hiram Clawson

Hiram Clawson

Senior Software Developer

Brian Craft

Brian Craft

Senior Software Engineer

Mark Diekhans

Mark Diekhans

Technical Director

Hongxu Ding

Hongxu Ding

Postdoctoral Scholar

Kivilcim Doganyigit

Kivilcim Doganyigit

Junior Scientist

Noah Dove

Noah Dove

Junior Software Engineer

Clayton Fisher

Clayton Fisher

Senior Project Manager & Engineering Manager

Jorge Garcia

Jorge Garcia

System Administration Supervisor

Mary Goldman

Mary Goldman

Design & Usability Engineer

Jairo Navarro Gonzalez

Jairo Navarro Gonzalez

Sr. Quality & User Support Analyst

Angela Hinrichs

Angela Hinrichs

Senior Software Architect

Solomon Katzman

Solomon Katzman

High-Throughput Sequencing Analyst

Ellen Kephart

Ellen Kephart

Software Engineer

Brian Lee

Brian Lee

Quality Assurance Manager

Christopher Lee

Christopher Lee

Software Engineer

Geoff Lyle

Geoff Lyle

Junior Data Analyst

Duncan McColl

Duncan McColl

Junior Software Engineer, Systems Biology

Lou Nassar

Lou Nassar

Quality Assurance Manager

Adam Novak

Adam Novak

Senior Software Engineer

Ash O'Farrell

Ash O'Farrell

Bioinformatics Systems Analyst

Nneka Olunwa

Nneka Olunwa

Senior Security Compliance Officer

Charles Overbeck

Charles Overbeck

Senior Software Engineer

Gerardo Perez

Gerardo Perez

Quality and User Support Analyst

Marc Perry

Marc Perry

Bioinformatician

Brian Raney

Brian Raney

Senior Software Developer

Yohei Rosen

Yohei Rosen

Postdoctoral Scholar

Hannes Schmidt

Hannes Schmidt

Senior Software Engineer

Adriano De Bernardi Schneider

Adriano De Bernardi Schneider

Postdoctoral Scholar

Rachel Schwartz

Rachel Schwartz

Data Wrangler

Jessica Sevetson

Jessica Sevetson

Postdoctoral Scholar

Jonas Sibbesen

Jonas Sibbesen

Postdoctoral Scholar

Daniel Sotirhos

Daniel Sotirhos

Software Engineer

David Steinberg

David Steinberg

Senior Software Engineer

William Sullivan

William Sullivan

Data Wrangler

Kristof Tigyi

Kristof Tigyi

Research Technician

Koorous Vargha

Koorous Vargha

Software Developer

Yvonne Vasquez

Yvonne Vasquez

Junior Specialist

Ivo Violich

Ivo Violich

Senior Bioinformatics Systems Analyst

Ben Vizzier

Ben Vizzier

Program Manager

Ciara Wanket

Ciara Wanket

Sequencing Specialist

Erich Weiler

Erich Weiler

Genomics Systems Architect

Brittney Wick

Brittney Wick

Data Wrangler

Daniel Wilson

Daniel Wilson

Program Manager

Chris Wong

Chris Wong

Programmer, UCSC Pathway Browser

Steve Von Worley

Steve Von Worley

Software Engineer

Cally Lin

Cally Lin

Bioinformatics Programmer

Graduate & Undergraduate Researchers

Mobin Asri

Mobin Asri

Graduate Student Researcher

Nicolas (Nico) Ayala

Nicolas (Nico) Ayala

Undergraduate Data Wrangler

Alex Bagi

Alex Bagi

Graduate Student Researcher

Quinn Brail

Quinn Brail

Graduate Student Researcher

James Casaletto

James Casaletto

Graduate Student Researcher

Krizia Chambers

Krizia Chambers

Graduate Student Researcher

Xian Chang

Xian Chang

Graduate Student Researcher

Allison Cheney

Allison Cheney

Graduate Student Researcher

Kathryn Echandia-Monroe

Kathryn Echandia-Monroe

Undergraduate Student Researcher

Jordan Eizenga

Jordan Eizenga

Graduate Student Researcher

Mateo Etcheveste

Mateo Etcheveste

Genome Browser Outreach Assistant

Marina Haukness

Marina Haukness

Graduate Student Researcher

Ryan Hoffman

Ryan Hoffman

Graduate Student Researcher

Sahar Hosseinzadeh

Sahar Hosseinzadeh

Graduate Student Researcher

Kiana Imani

Kiana Imani

Undergraduate Research Assistant

Nick Keener

Nick Keener

Graduate Student Researcher

Julian Lehrer

Julian Lehrer

Undergraduate Researcher

Wenyu Liang

Wenyu Liang

Graduate Student Researcher

Ryan Lorig-Roach

Ryan Lorig-Roach

Graduate Student Researcher

Hsiang Yun Lu

Hsiang Yun Lu

Graduate Student Researcher

Charles Markello

Charles Markello

Graduate Student Researcher

Nathan Maulding

Nathan Maulding

Graduate Student Researcher

Trevor McGuire

Trevor McGuire

Undergraduate Researcher

John Richard Minnick

John Richard Minnick

Undergraduate Researcher

Christopher Nguyen

Christopher Nguyen

Graduate Student Researcher

Demir Ozcakir

Demir Ozcakir

Undergraduate Researcher

David Parks

David Parks

Graduate Student Researcher

Robin Rounthwaite

Robin Rounthwaite

Graduate Student Researcher

Rojin Safavi

Rojin Safavi

Graduate Student Researcher

Spencer Seiler

Spencer Seiler

Graduate Student Researcher

Lucas Seninge

Lucas Seninge

Graduate Student Researcher

Taylorlyn Stephan

Taylorlyn Stephan

Graduate Student Researcher

Drew Thompson

Drew Thompson

Undergraduate Researcher

Sean Touchstone

Sean Touchstone

Undergraduate Student Researcher

Cesar Veliz

Cesar Veliz

Undergraduate Researcher

Kate Voitiuk

Kate Voitiuk

Graduate Student Researcher

Alana Weinstein

Alana Weinstein

Graduate Student Researcher

Fan (Sarah) Xia

Fan (Sarah) Xia

Undergraduate Researcher

Yuan Xu (Dan) Xu

Yuan Xu (Dan) Xu

Graduate Student Researcher

Bianca Xue

Bianca Xue

Graduate Student Researcher

Viktor Yurevych

Viktor Yurevych

Graduate Student Researcher

Administration & Operations

Samantha Albo

Samantha Albo

Student Assistant, Office of Diversity

Lynn Brazil

Lynn Brazil

Executive Assistant

Jason Burns

Jason Burns

Executive Assistant / Diversity and Inclusion Program Coordinator, Office of Diversity

Krizia Chambers

Krizia Chambers

Communications Assistant

Kimberley Czupil

Kimberley Czupil

Administrative Coordinator

Kelly De La Rosa

Kelly De La Rosa

Student Assistant, Facilities

Maya Eghbali

Maya Eghbali

Student HR Assistant

Nadine Gassner

Nadine Gassner

Associate Director, Research Development

Zia Isola

Zia Isola

Director, Diversity Programs

Linda Knipe

Linda Knipe

Financial Services Specialist

Melaina Legaspi

Melaina Legaspi

Grants Management Specialist

Greta Martin

Greta Martin

Grants Management Specialist

Margaret Mattson

Margaret Mattson

Director of Finance and Operations

Office: WRP 251A

Rose Miyatsu

Rose Miyatsu

Assistant Director of Communications

Tiffany Natali

Tiffany Natali

HR Analyst

Emily O'Daniels

Emily O'Daniels

Grants Management Specialist

Alondra Figueroa Olivo

Alondra Figueroa Olivo

Administrative Coordinator for CDPH and CEGS

Chrissy Camblin

Chrissy Camblin

GI Grant Management Specialist

Labris Marie Willendorf

Labris Marie Willendorf

Academic Personnel Coordinator

Marcus Thayer

Marcus Thayer

WRP Facilities Manager

Adele Poloziouk

Adele Poloziouk

Undergraduate Web Specialist