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April 2019

Nanopore Variant Calling Using Deep Neural Networks

April 17, 2019 @ 12:00 pm - 1:00 pm PDT
Engineering 2, Room 215 Santa Cruz,CA95064United States + Google Map

Speaker: Kishwar Shafin, Graduate Student in the Computational Genomics Lab, UC Santa Cruz Genomics Institute Applied Artificial Intelligence Institute Seminar (AAII formerly SCML): Genomic sequencing of an individual genome produces millions of sequence reads. Once aligned to a reference genome, the reads can be used to identify genetic variations. Variant calling is essential in clinical genomics because genetic variants can be associated with genetic diseases. Next-generation short read sequencing technology is widely used for variant calling, but the short-reads are…

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May 2020

BME Seminar: The Genomics of SARS-CoV-2 (COVID-19)

May 14, 2020 @ 11:40 am - 1:00 pm PDT

Abstract: Researchers are generating molecular data pertaining to the SARS-CoV-2 virus at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in formats that can be quickly compared.  The UCSC SARS-CoV-2 Genome Browser  (https://genome.ucsc.edu/covid19.html)  is an adaptation of our genome browser visualization tool.  Molecular data, curated from published studies, database submissions, and selected preprints are mapped to the viral genome and grouped together…

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Following the Trial of Discovery

May 22, 2020 @ 12:00 pm - 1:30 pm PDT

We often hear advice about how to develop a research project such as "identify a problem" ; "brainstorm with a collaborator"; "make a list of keywords"; and "read background literature." All of this is great advice. But turning an inspiration into a workable, and more importantly, a fundable project is a complex process that requires more than following a formula or series of steps. In this presentation, graduating seniors Preet Kaur and Devin Virassammy will share their experiences in developing…

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February 2021

Environment x Everything Interactions: From Protein Evolution to Epidemic Dynamics & Beyond

February 8 @ 3:00 pm - 4:30 pm PST

In this seminar, C. Brandon Ogbunu will discuss how an appreciation for environmental interactions in complex systems manifests across my research program. To highlight this, he will focus on two main areas: (1) evolutionary dynamics in antibiotic resistance, and (2) the ecological determinants driving transmission in modern epidemics. In closing, he will outline future directions in my quest to understand how the environment crafts complex systems, which includes work in the scientific communication, health justice, and storytelling spaces. All are…

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Genomics Science Series: Postdoctoral Scholars Jonas Sibbesen & Jean Monlong

February 10 @ 1:20 pm - 2:20 pm PST

  Join us Wednesdays Winter 2021, for a Genomics Science Seminar Series! Up next:  UC Santa Cruz Genomics Institute Postdoctoral Scholars Jonas Sibbesen & Jean Monlong present Using pangenome graphs for variant-aware genomic and transcriptomic analyses Join via Zoom Meeting ID: 973 7468 9859 Passcode: 456371 One-tap mobile +16699006833,,97374689859#,,,,*456371# US (San Jose) Add to your calendar This event coincides with BME 281C, Instructors: David Haussler, Josh Stuart. Registration is open to all UCSC students. See Canvas for details.

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