Project Portfolio

The UC Santa Cruz Genomics Institute leads a variety of efforts that revolutionize our understanding of health and nature.

Browse our project portfolio below. Or, visit our research group websites; UCSC Genome BrowserGenome 10KGlobal Alliance for Genomics and Health, the Stem Cell HubComputational Genomics Laboratory (CGL), Treehouse Childhood Cancer Initiative and BRCA Exchange.

Genomics and Health

The UC Santa Cruz Genomics Institute provides framework for the next great leap in genomics. We unlock the world’s genomic information in hopes of developing targeted disease treatment.

Global Alliance for Genomics and Health

The Global Alliance for Genomics and Health (GA4GH) is an international effort to undertake, share, and standardize the secure and ethical sharing of genomic information. GA4GH strives for the betterment of global health outcomes.

 

 

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.

 

 

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Treehouse promotes the sharing of pediatric cancer genomic data. In addition, they support the translation from these findings into the clinical setting. Cofounded by Dr. Olena Morozova, a researcher at the Genomics Institute, the Initiative has grown rapidly and recently received a major grant from St. Baldrick’s Foundation.

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.

Human Genome Variation Map

The human genome variation map is a genome graph for the leukocyte receptor complex built from 30 concealed human haplotypes. In 2000, UC Santa Cruz researchers posted the first draft of the human genome on the internet. Since then, the current model of human genetics has not changed…

Environmental Genomics and Health

How can genomics aid conservation efforts to protect our most vulnerable species, preserve our environment, and understand the world around us?

Genome 10K

The Genome 10K project aims to assemble a genomic zoo—a DNA sequence collection representing 10,000 vertebrate species genomes. There is approximately one for every vertebrate genus.

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.

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.

Genomics Platform and Technology Development

From decoding cancer to preserving species, our open-source genomics platform is essential in unlocking today’s most challenging medical and scientific issues around the world.

Haussler Lab

On July 7, 2000, David Haussler and his team launched the first working draft of the Human Genome on the internet, ensuring that it would remain in the public domain forever. The Haussler Lab continues disrupting the field of genomics by innovating statistical and algorithmic methods to accelerate our understanding cancer, human development, evolution, and many other areas of active research.

Computational Nanopore Genomics

In collaboration with the UCSC Nanopore group, we are developing algorithms and code to analyze nanopore data. We predict that low-cost nanopore sequencing will allow us to decode virtually complete genomes replete with methylation information and haplotype phasing.

Dockstore

Dockstore, developed by the Cancer Genome Collaboratory, is an open platform for sharing Docker-based tools described with the Common Workflow Language used by GA4GH.

GENCODE

The GENCODE project publishes high quality content for human and mouse genomes.

California Institute for Regenerative Medicine Stem Cell Hub

UC Santa Cruz runs the Data Coordination and Management program (the Stem Cell Hub) for the California Institute for Regenerative Medicine (CIRM) Center of Excellence in Stem Cell Genomics. The center applies genomics to stem cell research to gain a deeper understanding of disease processes in cancer, diabetes, heart disease, and mental health. These understandings can ultimately lead to safer, more effective ways of using stem cells in medical research and therapy.

UCSC Biosensor & Biotechnology Group

Nader Pourmand’s research is motivated by the philosophy that the best way to accelerate discovery is to develop innovative tools that will enable sweeping advances in knowledge, and to demonstrate such advances through the application of newly developed technologies. The UCSC Biotechnology group is seizing opportunities in Bioengineering and Biology to broaden the field and support other biomedical research.

High-throughput Genomics

Genomics is in transition. Increase in information is motivated by the need for great sample sizes. As a result, data becomes statistically significant with this growth. This event is said to exceed Moore’s law.

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.

Browsers

 

Researchers at UC Santa Cruz were the first to assemble the human genome sequence, publish it on the web, and create the Human Genome Browser. It is now an essential tool in biomedical science.

UCSC Genome Browser

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. More than 130,000 biomedical researchers throughout the world use this browser each month.

Neanderthal Browser

Neanderthals are the closest extinct relatives of humans. They lived several hundred thousand years ago until their disappearance approximately 30,000 years ago. The Neanderthal genome sequence (published by Green et al. in Science May 2010) is made up of short sequence fragments (with average lengths of 50 base pairs) mapped to the human reference genome.

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.

UCSC Cell Browse

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.

Xena

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