Month: March 2021
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Unlocking the Covid Code
Scientists can now sequence an entire genome overnight. This technology has been the key tool in identifying and tracking Covid variants. Jon Gertner | New York Times | March 25, 2021 Edward Holmes was in Australia on a Saturday morning in early January 2020, talking on the phone with a Chinese scientist named Yong-Zhen Zhang…
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Warmest welcome to our newest faculty affiliates Greider, Sharma and Shariati and faculty associate director Fehren-Schmitz
The Genomics Institute extends a very warm welcome to our newest faculty affiliates, Carol Greider, Professor of MCD Biology; Upasna Sharma, Assistant Professor of MCD Biology; and Ali Shariati, Assistant Professor, Biomolecular Engineering. Additionally, we are very happy to welcome our newest faculty associate director, Lars Fehren-Schmitz, Associate Professor, UCSC Department of Anthropology. Fehren-Schmitz’s work…
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CIRM Scientific Strategy Advisory Panel meeting | Feb. 22, 2021
Convened jointly by: Maria T. Millan, MD, CIRM President and CEO Jonathan Thomas, PhD JD, CIRM ICOC Chairman This video is of the inaugural meeting of the California Institute for Regenerative Medicine (CIRM) Scientific Strategy Advisory Panel meeting. The panel was created by Proposition 14 that envisioned this group of expert scientists offering thoughts, guidance…
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Nanopore sequencing
Photograph of Professor David Deamer with his second wife, Professor Ólöf Einarsdóttir, a biochemist, shortly after they married in 1992 (credit David Deamer). Brought up in California and then Ohio, Deamer completed a doctorate in lipid biochemistry at Ohio State University School of Medicine in 1965 and then spent two years at the University of…
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Ikenna Anigbogu: Alumnus
Ikenna Anigbogu graduated from UC Santa Cruz in spring of 2020. During his time at UCSC, he was a Research Mentoring Institute (RMI) scholar, a member of the National Society of Black Engineers (NSBE), a peer mentor for the Black Men’s Initiative (BMI), and an iGEM team member. He currently works as a junior research…
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Critics decry access, transparency issues with key trove of coronavirus sequences
Meredith Wadman | Science Magazine | Mar. 10, 2021 In December 2020, software developer Angie Hinrichs at the University of California, Santa Cruz (UCSC), applied for access to a labor-saving data feed from GISAID, a nonprofit database of viral sequences including those of the pandemic coronavirus, SARS-CoV-2. She wanted GISAID’s data so she could display mutations on…
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UShER: Ultrafast Sample placement on Existing tRees
See your #SARS-CoV-2 sequence placement on a global phylogenetic tree, performed by Ultrafast Sample placement on Existing tRees (UShER) (Turakhia et al.) UShER generates local subtrees, displaying the most similar complete, high-coverage samples from GISAID or public sequence databases (NCBI Virus / GenBank, COG-UK and the China National Center for Bioinformation) in the context of…
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No ‘variants of concern’ in first Santa Cruz County tests, though bulk of samples show California strain
Mallory Pickett | March 1, 2021 | Lookout Santa Cruz UC Santa Cruz scientists said Monday that they had completed genomic sequencing of 84 COVID-19 samples from Santa Cruz County, with none of the CDC’s three official “variants of concern” turning up. But approximately 65% of the samples contained the so-called California variant, known as…
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Share pandemic sequences openly and fast
Nature | David Haussler, Max Haeussler, Angie Hinrichs, Russell Corbett-Detig & Isabel Bjork | March 3, 2021 We agree that urgent research on SARS-CoV-2 sequence data is being slowed by antiquated regulations and those who put data ownership and priority over the common good (see Nature 590, 195–196; 2021). In 2006, to address this problem…