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 Browser, Genome 10K, Global 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. Currently, UCSC Genomics Institute is moving into clinical settings for treatments and diagnostics of illnesses.


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.


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…

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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.

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.

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Environmental Genomics and Nature

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 Shapior 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.

Center for Big Data in Translational Genomics

The Center for Big Data in Translational Genomics is a multi-institution collaboration coordinated by UC Santa Cruz to create scalable structures for the broad application of genomics in biomedicine. UC Santa Cruz identifies this program as one of the NIH Big Data to Knowledge (BD2K) centers.

GENCODE

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

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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.

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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.

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.


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.

UCSC Genome Technology Center

Pourmand research follows a certain philosophy. They state that the best way to increase findings is to develop cutting-edge tools which lead to great advances in knowledge. Using newly developed technologies demonstrate these advances.


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.


GSID HIV Data Browser

The GSID HIV Data Browser was developed in collaboration with the Genome Bioinformatics Group at the University of California, Santa Cruz (UCGBG). The efforts come from a cross-departmental team within the Center of Biomolecular Sciences and Engineering (CBSE).

Under the guidance of Jim Kent and Fan Hsu, UCGBG developed a relational database. The library contains significant clinical data and sequence information from infected subjects which participated in the VAX003 and VAX004 Phase III clinical trials.


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.

Xena

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


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 Cancer Genomics Hub

CGHub rapidly grew to be the largest database of cancer genomes in the world. It stores more than 2.5 petabytes of data, and serves downloads of approximately 3 petabytes per month.