Portfolio

The UC Santa Cruz Genomics Institute is a leader in an array of efforts revolutionizing 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, Computational Genomics Laboratory (CGL), Treehouse Childhood Cancer Initiative and BRCA Exchange.

Genomics and Health

The UC Santa Cruz Genomics Institute provides the framework for the next great leap in the science of genomics by unlocking the world’s genomic information to drive targeted treatment of diseases. We are moving genomics into clinical settings for disease treatment and diagnostics.


Global Alliance for Genomics and Health

The Global Alliance for Genomics and Health (GA4GH) is an international effort to promote, foster and standardize secure, ethical, privacy-preserving sharing of genomic information for the betterment of global health outcomes.


Human Genome
Variation Map

A genome graph for the Leukocyte Receptor Complex built from 30 underlying human haplotypes Since UC Santa Cruz researchers posted the first draft of the human genome on the Internet in 2000, the current model of human genetics in the genome era has not changed: …Read More

Treehouse Childhood Cancer Initiative

The Treehouse Childhood Cancer Initiative was established to analyze genomic data of children with cancer in the context of large datasets of both pediatric and adult cancers. This allows researchers to identify situations where an available drug is predicted to work for a given patient’s tumor. Treehouse promotes the sharing of pediatric cancer genomic data as well as translation of the findings from this analysis to 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, global data repository to catalogue variation within the BRCA genes and to collect individual-level evidence for their classification. The scientific and medical communities have a tremendous and urgent need for a comprehensive data store of variants.
Read More

Environmental Genomics and Nature

How can genomics aid conservation efforts to protect and better understand our biology, our environment and our most vulnerable species?


Genome 10K

The vertebrate evolutionary tree The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, 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 relating to 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 the bioethical and privacy issues that advances in genomics create for patients, families, physicians, counselors, business, and government.

 
 

Genomics Platform and Technology Development

From decoding cancer to species preservation our open-source genomics platform is the world’s essential resource for unlocking the most challenging medical and scientific issues of our time.

Center for Big Data in Translational Genomics

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

GENCODE

View of a 56 Kbp region of human chromosome 17 where GENCODE annotates one non-coding and 5 protein coding genes. Two genes in the region display tissue-specific gene expression as evidenced by GTEx RNA-seq. Read More

High-throughput
Genomics

Genomics is in transition. The growth in data—driven by the need for vast sample sizes to gain statistical significance and the explosion of clinical sequencing—is far outpacing Moore’s law. Read More


Computational
Nanopore Genomics

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

California Institute for Regenerative Medicine

UC Santa Cruz runs the Data Coordination and Management program 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 the disease processes in cancer, diabetes, heart disease, and mental health. This understanding 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 the GA4GH.

UCSC Genome Technology Center

Pourmand 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.


UC Santa Cruz Storage Systems Research Center

Center for Research in Storage Systems (CRSS)
A partnership between academia and industry exploring and developing new technologies and techniques to improve the manageability, scalability, security, reliability, longevity, 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 — 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 down to an individual nucleotide. More than 130,000 biomedical researchers throughout the world use the 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), which is 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 containing the significant clinical data and sequence information pertaining to the infected subjects participating in the VAX003 and VAX004 Phase III clinical trials.

UCSC Cancer Genomics Hub

CGHub rapidly grew to be the largest database of cancer genomes in the world, storing more than 2.5 petabytes of data and serving downloads of nearly 3 petabytes per month.


ENCODE Project

The ENCODE consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active


Neanderthal Browser

Neandertals are the closest extinct relatives of humans. They lived from several hundred thousand years ago until their disappearance approximately 30,000 years ago. The Neandertal genome sequence (published by Green et al. in Science May 2010) consists of short sequence fragments, usually about 50 base pairs long, mapped to the human reference genome.


UCSC Ebola Virus Genome Browser

The 2014 Ebola epidemic in West Africa has stirred international response and renewed efforts to develop effective preventative and treatment options. In response to a request for help from vaccine researchers, we have fast-tracked the UCSC Ebola Genome Browser built with viral sequences from previous outbreaks as well as the 2014 outbreak. This site also provides related tools and information that can be used to further the understanding of Ebola.

Xena

UCSC Xena is a bioinformatics tool to visualize functional genomics data from multiple sources simultaneously, including both public and private data.