Genomics Technologies & Platforms

The UC Santa Cruz Genomics Institute brings genomics, data sharing, biotechnology and massive computing power together in efforts to change the limits in medicine. The work is essential and fundamental for the future of targeted disease treatment. In addition, genomics technologies create a groundbreaking opportunity for scientists to compare known information in one case to known information in millions of others.

UCSC Genome Browser

UC Santa Cruz holds special strength in bioinformatics– a variety of ways to investigate and analyze biological data with the use of computational, mathematical, and statistical approaches. The largest product of this expertise is the UCSC Genome Browser. The browser serves as an interactive web-based “microscope”, allowing researchers to view all 23 chromosomes of the human genome at any scale, from a complete chromosome to an individual nucleotide.

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Computational Genomics Laboratory (CGL)

The Computational Genomics Lab is led by staff, research scientists, and engineers of the UC Santa Cruz Genomics Institute. The lab currently focuses on developing technology which organizes isolated genomic information with advanced communication standards. This creation in the field of genomics technologies will lead to a higher amount of completely and accurately processed genomes. This makes it easier to find and share many genomic systems. Using the newly made process, the Computational Genomics Library will become closer to finishing the RNA libraries of humans and mice.

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Global Genomics Platforms and Standards

UC Santa Cruz is a partner in the Global Alliance for Genomics & Health. The alliance is an international organization for research, healthcare, and disease advocacy groups that aim to standardize and safely share genomic/clinical data. David Haussler co-leads their Genomic Data Working Group, which concentrates on data representation, storage, and analysis. The group is working with platform development partners and industry leaders to develop communication standards in genomics technologies. This includes projects such as the Human Genome Variation Map (HGVM), which aims to offer a new and thorough representation of human genome variations.

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Human Cell Atlas Data Coordination

UC Santa Cruz Genomics Institute will collaborate with the Broad Institute of MIT & Harvard and the European Bioinformatics Institute (EMBL-EBI) to build a data coordination platform for the Human Cell Atlas Initiative. This initiative is an extensive plan to map and characterize every cell type in the human body. The Chan Zuckerberg Initiative (CZI) is funding this project.

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Center for Big Data in Translational Genomics

The Center for Big Data in Translational Genomics is a multinational effort between academia and industry for genomics technologies. They pursue to create models and tools that will help study vast amounts of genomic information. The studies may lead to the analysis of genomes and gene expression from thousands of individuals, uncovering causes of gene variants for cancer and disease. Such knowledge will be vital in the development of precise methods for diagnosis and treatment. The center aims to make software solutions interactive by developing standard application programming interfaces (APIs) and tools at multiple levels, from raw sequence data to genetic variation and functional data.

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A nanopipette is so small it can penetrate a single cell without causing serious damage. This technology enables scientists to measure and track changes in gene expression and metabolic states in a single cell over time.

Single-cell Genomic Studies

UC Santa Cruz professor of biomolecular engineering Nader Pourmand developed a unique approach to tracking the long-term genomics of single cells in living organisms. His team developed a new nanopipette technology, which can be used to study the genomics of individual cells such as neurons. This method now makes it possible to look into the basic mechanisms of neurodegeneration.

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Nanopore Portable DNA Sequencing

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.

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