Category: Platforms
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UCSC Genome Browser Alumni Profile: Melissa Cline
Twenty-five years after the Human Genome Project, Melissa Cline has become a prominent figure in the field of cancer genomics. She currently manages the BRCA Exchange, the largest public resource for knowledge on genetic variations that influence heritable breast, ovarian, prostate, and pancreatic cancers. She also co-leads the Genomic Knowledge Standards Workstream for the Global…
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The Human Genome Project’s legacy is still yielding new advances
At the 25th anniversary of the Human Genome Project, the Tech Brew looks back at what it has accomplished, and how its legacy of combining computation and biology has set the stage for future applications in medicine and new advances in AI-powered life sciences at the UC Santa Cruz Genomics Institute.
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Newest Genome Browser features highlight the power of generative AI and machine learning for biology
The UCSC Genome Browser has added two new datasets that leverage the power of generative AI and machine learning to interpret information about genetic variants and more rapidly assess which ones might be harmful to human health. These datasets, from AlphaMissense and VarChat, are available as “tracks” on the two most widely used human reference…
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25 years of the UCSC Genome Browser
When Katie Pollard first began working toward her Ph.D. in biostatistics at UC Berkeley in the late 90s, the human genome had not yet been sequenced. Then, on July 7, 2000, UC Santa Cruz published the HGCP’s first draft of a sequence online. Suddenly, a whole new field of genomics sprung into being. It was…
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Dockstore receives a new update to make sharing workflows even more seamless
Dockstore 1.16 new features include AI-based automatic topic sentence generation, automatic DOI generation and discovery, and improved search results Dockstore is a free and open-source registry for sharing analytical tools and workflows in bioinformatics and adjacent fields of study. Over 4,400 workflows are currently being shared on the platform. Examples include workflows to analyze viral…
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Special Zoonomia issue of Science offers fresh insights on human, and canine, evolution
This article is about a series of 11 papers published in a special issue of Science. The research was made possible in part by the Cactus alignment tool created at UC Santa Cruz and contains exciting discoveries by a number of our scientists. For additional coverage of the Zoonomia papers, please see “DNA analysis can…
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Researchers produce first-ever toolkit for RNA sequencing analysis using a ‘pantranscriptome’
This tool will aid researchers around the world who are working to understand gene expression through RNA sequencing analysis. The tools are publicly available and can be accessed via Github.
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UCSC Genome Browser selected to first-ever Global Core Biodata Resource List
The Global Core Biodata Resources list represents a collection of 37 open-source resources whose long-term funding and sustainability is critical to life science and biomedical research worldwide. The Browser was chosen as a vital tool for researchers in the biosciences.
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UCSC Genome Browser 2023 Update, Future Plans
This coming year represents the first in our new 5-year planning cycle. A major goal during this time is evaluation and adoption of a pangenome graph data format.
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New Educational Module for UCSC Genome Browser
In response to requests from users, we are announcing a new education module in the UCSC Genome Browser training pages. The UCSC Genome Browser is our most widely used genomics tool. Tens of thousands of researchers access it each year to view all 23 chromosomes of the human genome, down to its individual nucleotides. It…
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From concept to commercialization: How UCSC researchers revolutionized DNA sequencing
Nanopore sequencing technology, which has dramatically lowered the cost and increased the accuracy of genomic sequencing over the last two decades, was first patented and developed at UC Santa Cruz. Its inventors reflect on its history, as well as its seemingly unlimited potential for advancing personalized medicine and our understanding of our world.
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The team behind a tree of 10 million Covid sequences
10 million sequences of COVID-19’s genomic code have now been organized into a phylogenetic tree in the UC Santa Cruz SARS-CoV-2 Browser, which is the largest tree of genomic sequences of a single species ever assembled. This accomplishment is impressive for both the computer engineering feat of processing such a massive amount of data and…