Project Portfolio

The UC Santa Cruz Genomics Institute brings together data sharing, biotechnology, and massive computing power in efforts to expand the limits of genomics in medicine and conservation science.

Our software and technologies are used by researchers all over the world to push the boundaries of genomic science. Below is a portfolio of some of our larger current projects in the areas of genome sequencing, human health, conservation, tool and platform development, and exploring the ethical and societal implications of genomics.

Genomics and Health

One of the great motivations for understanding our genome is to improve human health outcomes. Researchers at the GI are focused on improving human health through research on pathogens, cancer genes, and by observing the ways our cells develop and where that development can go wrong.

A group photo of a team holding a "Treehouse Childhood Cancer Initiative" Banner

Treehouse Childhood Cancer Initiative

The Treehouse Childhood Cancer Initiative was established to analyze genomic data of children with cancer with the use of large sets of data for pediatric and adult cancers. This allows researchers to identify situations where an available drug can be predicted to work for a specific patient’s tumor.

 

The Center for Live Cell Technology.

The Center for Live Cell Technology aims to transform cell culture and organoid research by enabling automated, consistent growth chambers, and remotely controlled, continuous, and non-invasive phenotypic analysis (optical, chemical, physiological). Computer and mechanical engineers, cell biologists, and clinicians collaborate to build affordable solutions that will be available to local and remote researchers alike as well as to educators around the world.

UCSC researchers are pioneering use of these technologies for research on brain evolution and disease, including childhood gliomas.

BRCA Exchange

We are developing the BRCA Exchange– a comprehensive and global data location to track variation within the BRCA genes. The database also aims to collect individual-level evidence for specific classification. The scientific and medical communities have a tremendous and urgent need for such a comprehensive library of varying data.

Covid molecules with spikey proteins on their surfaces

Pathogen Genomics

The 2019 global pandemic has made pathogen genomics a new area of priority for the Genomics Institute. We are proud that our UShER tool was used to help identify Covid-19 variants and is currently the default linage tool used by the CDC.

Braingeneers

Braingeneers are using brain organoids, multicellular tissues derived from pluripotent stem cells, to uncover how genetic changes led to the development of the human brain. Novel use of artificial intelligence (AI) enables us to optimize organoid culture, and to analyze normal and perturbed human neural circuit development in ways that were never possible before.

A cluster of blue, green, and red cells

Molecular, Evolutionary, and Stem-Cell Biology

Our bioinformatics research generates an increasing number of very specific hypotheses about the evolution and function of human genes. Through wet-lab experiments, we explore and validate predictions generated from computational genomic research.

Global Alliance for Genomics and Health

In 2013, Scientific Director David Haussler co-founded the Global Alliance for Genomics and Health (GA4GH) to create a common framework for the responsible, voluntary, and secure sharing of genomic and clinical data. Today it is a large international nonprofit alliance of 600+ leading organizations working in healthcare, research, patient advocacy, life science, and information technology.

SSPsyGene

The UCSC Genomics Institute is leading a consortium to create a comprehensive catalog of 250 genes related to neurodevelopmental and psychiatric disorders, funded by the National Institute of Mental Health.

The project, “Scalable and Systematic Neurobiology of Psychiatric and Neurodevelopmental Disorder Risk Genes” (SSPsyGene), will include four collaborating data generating centers to functionally characterize the contribution of 250 genes to neurodevelopmental and psychiatric disorders in various human cell and zebrafish models. The Genomics Institute is serving as the Data Resource and Administrative Coordinating Center for the four centers. Our collaboration will result in a comprehensive phenotypic catalog across biological scales.

Live Cell Biotechnology Discovery Lab

Our new Live Cell Biotechnology Discovery Lab is a maker space dedicated to creating the next generation of technologies for remote, project-based education. The lab, which occupies part of the second floor of the UCSC Westside Research Park, is inspired by an effort to improve access to STEM education through collaborations with hispanic-servicing high schools both locally and in Latin America. Mohammed Mostajo-Radji directs the lab.

GENCODE

UC Santa Cruz is a part of the GENCODE consortium, which aims to build an “Encyclopedia of genes and genes variants” that will map protein-coding genes within the human genome.

Nanopore diagram

Nanopore Sequencing Technology

Investigators at the UC Santa Cruz Genomics Institute including Miten Jain, Benedict Paten, Mark Akeson and David Deamer have spent years developing a mobile phone sized MinION™ DNA sequencer (licensed and marketed by Oxford Nanopore); their work was reported in Nature Methods on February 16, 2015. With the sequencer’s features of long-reads and portability, the MinION is ready to revolutionize the field of genomics.

T2T

Founded by UC Santa Cruz Genomics Professor Karen Miga with NIH Researcher Adam Phillippy, the Telomere-to-Telomere consortium aims to generate the first truly complete assembly of a human genome, filling in the gaps in chromosome regions that were too complicated and costly to complete during the initial Human Genome Project.

Diversifying the Human Genome

Eliminating all gaps is only part of the challenge of creating a robust reference genome. Most current reference DNA has been collected from people of European descent, which cannot encompass all of human diversity. UC Santa Cruz’s David Haussler, Karen Miga, and Benedict Paten chair multiple working groups in the Human Pangenome Reference Consortium that is working to create a wider range of reference sequences.

Conservation Genomics

 

How can genomics aid conservation efforts to protect our most vulnerable species, preserve our environment, and understand the world around us? UC Santa Cruz researchers are engaged in a number of projects to catalog past and current biodiversity to inform conservation strategies around the globe.

Vertebrate Genome Project

The Vertebrate Genome Project aims to assemble a genomic zoo—a DNA sequence collection representing 10,000 vertebrate species genomes.

UCSC Paleogenomics Lab

The Paleogenomics Lab is a joint venture between Beth Shapiro and Richard (Ed) Green. Their research focuses on the evolutionary and ecological questions that connect with the study of genomics.

CALeDNA

The UC Santa Cruz Genomics institute is proud to be a partner of the CALeDNA program, headquartered at both UCLA and UC Santa Cruz. The project aims to collect soil and sediment samples from across California to assess the biodiversity of different habitats throughout the state and harness the potential of eDNA for conservation.

Genomics Technology Development

Genomic studies in health, conservation, and human sequencing would not be possible without platforms and technologies for sharing massive amounts of data. From software that can display over ten million Covid-19 sequences on a single phylogenetic tree to nanopore technologies that are allowing clinicians to rapidly sequence patient genomes in under six hours, our technology is helping to create a revolution in the field of genomics.

Computational Nanopore Genomics

Investigators at the UC Santa Cruz conceptualized and patented the technology licensed by Oxford Nanopore’s MinION™ DNA sequencer. With the sequencer’s features of long-reads and portability, the MinION is ready to revolutionize the field of genomics. Nanopore sequencing has been used in projects like the Telomere to Telomere completion of a human genome and a world record in fastest genome sequencing.

High-throughput Genomics

Genomics is in transition. Large projects like The Cancer Genome Atlas have generated petabyte-scale datasets that very few groups have the capacity to analyze independently. We have joined with UC Berkeley’s AMP lab to pioneer ADAM, a genomics platform built on Apache Spark that can radically improve the efficiency of standard genomic analyses.

Dockstore

Dockstore, jointly developed and maintained by the UC Santa Cruz Genomics Institute, acts as an app store for bioinformatics analysis tools and is used by scientists worldwide. It provides a global cloud library of analytical workflows, so that researchers can easily find and use existing analysis tools, facilitating large-scale biomedical research collaborations.

UC Santa Cruz Storage Systems Research Center

The Center for Research in Storage Systems (CRSS) is a partnership between academia and industry. The collaboration explores and develops new technologies and techniques. This mission will improve the maintenance, expansion, security, life span, and performance of storage systems.

UCSC Biosensor & Biotechnology Group

The UCSC Biotechnology Group is seizing opportunities to broaden the fields of bioengineering and support other biomedical research. They have developed a new nanopipette technology that can be used to study the genomics of individual cells such as neurons while they are still alive. This method now makes it possible to look into the basic mechanisms of neurodegeneration. 

Browsers

Researchers at UC Santa Cruz were the first to assemble the human genome sequence, publish it on the web, and create a human genome browser, which evolved into what is now known as the UCSC Genome Browser. It is now an essential tool in biomedical science.

UCSC Genome Browser

For more than 20 years, the UCSC Genome Browser has been a free resource providing genomic scientists with graphical tools to display genome sequences. This interactive web-based “microscope” allows researchers to view all 23 chromosomes of the human genome at any scale, from a full chromosome to an individual nucleotide. It receives over a million hits daily and has become an essential tool for genomic researchers.

UCSC SARS-CoV-2 Genome Browser

A one-stop shop for COVID-19 research, the UCSC SARS-CoV-2 Genome Browser (“the virus browser”) is built on the strength of the UCSC Genome Browser to display the genome sequencing of thousands of viral samples, helping researchers study mechanisms of infection, transmission, mutation and variation, as well as the response of the human immune system.

Xena

UCSC Xena is a bioinformatics tool which visualizes functional genomics data from multiple sources all at once, including public and private data.

UCSC Cell Browser

Single-cell analysis is the current hot topic in genomics right now. This is because new droplet-based machines have brought single-cell gene expression assays into the < $1000 range, bringing them within reach of most research groups. Genomic analysis generally creates too many data points to show everything in a single image: For example, if you sequence 100.000 cells and the machines measure 20,000 genes per cell, the resulting data table has billions of values. 

 

 

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It’s impossible for a human to get much out of such a table without some tool to help them. Researchers need interactive solutions to help them visualize the data and share it with others via the web. The UCSC Cell Browser, created by the UCSC Genome Browser team, is one of the solutions being developed right now to address this challenge. The UCSC Cell Browser works like a map viewer, but it plots circles instead of landscapes. Every circle represents a cell. Users can color the circles to designate gene expression; usually brighter values mean higher expression of a gene. You can also color-code according to annotations added manually by researchers, like patient age or body part of the cell. We are working to enhance the UCSC Cell Browser, improving the annotation interface and interactivity.

UCSC Ebola Virus Genome Browser

The 2014 Ebola epidemic in West Africa has stirred international response, renewing efforts to develop compelling preventative and treatment options. In response to requests for help from vaccine researchers, we have fast-tracked the UCSC Ebola Genome Browser. The browser is built with viral sequences from previous outbreaks, including the 2014 outbreak. This site also provides related tools and information which can be used to further the understanding of Ebola.

Ethics & Societal implications of Genomics

UCSC Science & Justice Research Center

The UC Santa Cruz Genomics Institute collaborates with social scientists and ethicists to address bioethical and privacy issues in genomics studies. These conflicts affect patients, families, physicians, counselors, business, and government.