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DTSTART;TZID=America/Los_Angeles:20260925T130000
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SUMMARY:Mastoras\, M. (BMEB) - Polishing genome assemblies and leveraging their improved quality to study centromere variation
DESCRIPTION:A complete and accurate genome reconstruction serves as the foundation for studying an organism’s biology and the mechanisms underlying disease. It is particularly critical for reference genomes\, which provide a universal coordinate system for downstream genomic analysis. Errors or missing sequences in a reference genome create bias in all of the studies built on top of them. The Human Pangenome Reference Consortium (HPRC) seeks to address this bias by transitioning the field to a pangenome reference\, a graph based collection of many genome assemblies\, providing a better representation of variation in the human population. Removing errors in the HPRC assemblies is critical to ensure the pangenome serves as a robust standard for genomic variant discovery. In the first part of my thesis\, I improve the base level accuracy of the HPRC release 2 assemblies (HPRC2) with a machine learning model for assembly polishing called DeepPolisher. Next\, I make additional contributions to reference-based genomic analysis by polishing reference genomes of other model organisms\, and helping to develop a new method for de-novo assembly and variant calling from a single-flow cell nanopore sequencing protocol. Finally\, I take advantage of the highly accurate\, near complete assemblies from HPRC2 that I improved with DeepPolisher to study a region only recently made accessible to genomics analysis: the human centromere. I apply the tool Centrolign\, the first ever multiple-sequence-aligner for centromeres to the HPRC2 assemblies\, establishing precise estimates of mutation rates and spatial variation patterns across centromeric arrays. \nEvent Host: Mira Mastoras\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics \nAdvisor: Benedict Paten \nZoom: https://ucsc.zoom.us/j/98960011053?pwd=mFKCwtSIhvT5FvEURbE85lRbbMvzuo.1 \nPasscode: 118488
URL:https://live-events-ucsc.pantheonsite.io/event/mastoras-m-bmeb-polishing-genome-assemblies-and-leveraging-their-improved-quality-to-study-centromere-variation/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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DTSTART;TZID=America/Los_Angeles:20260925T180000
DTEND;TZID=America/Los_Angeles:20260925T220000
DTSTAMP:20260911T232254Z
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SUMMARY:Boardwalk Frolic
DESCRIPTION:Kick off your UCSC experience with a night of fun at the Santa Cruz Beach Boardwalk! The Boardwalk Frolic is a private event just for new UCSC students—featuring free rides\, games\, and the chance to connect with fellow Banana Slugs right on the beach. Enjoy the lights\, the ocean breeze\, and one of Santa Cruz’s most iconic spots as you make new memories and new friends. \n  \nPurchase tickets in advance to avoid long wait lines at the Boardwalk! \n$20 for all UCSC Students* – purchase your ticket here! \n*Ticket price increases to $40 after 4\,500 student tickets are sold. \n\nUnlimited rides\n$10 MyBoardwalk Card valid for food\, games\, and retail\nFree mini golf\, laser tag\, fright walk\, and laser maze\nFree arcade play\nFree parking\nCampus shuttles to and from the Boardwalk\n\nShuttle Info (Campus shuttle pickup locations TBD): \nCampus to Boardwalk: Buses run from 4:30 p.m. – 8 p.m. ONLY. \nBoardwalk to Campus: Buses run from 8 p.m. – 11 p.m. ONLY*. \n*Shuttles going back to campus from the Boardwalk will stop running after 11 p.m. Any student who is not in line for a bus before 11 p.m. will need to arrange for their own ride back to campus. Santa Cruz Metro city busses also stop running at 11 p.m. \n 
URL:https://live-events-ucsc.pantheonsite.io/event/boardwalk-frolic/
LOCATION:Santa Cruz Beach Boardwalk
CATEGORIES:Social Gathering,Undergraduate
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