BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//Events - ECPv6.18.2//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
X-WR-CALNAME:Events
X-ORIGINAL-URL:https://events.ucsc.edu
X-WR-CALDESC:Events for Events
REFRESH-INTERVAL;VALUE=DURATION:PT1H
X-Robots-Tag:noindex
X-PUBLISHED-TTL:PT1H
BEGIN:VTIMEZONE
TZID:America/Los_Angeles
BEGIN:DAYLIGHT
TZOFFSETFROM:-0800
TZOFFSETTO:-0700
TZNAME:PDT
DTSTART:20250309T100000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0700
TZOFFSETTO:-0800
TZNAME:PST
DTSTART:20251102T090000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0800
TZOFFSETTO:-0700
TZNAME:PDT
DTSTART:20260308T100000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0700
TZOFFSETTO:-0800
TZNAME:PST
DTSTART:20261101T090000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0800
TZOFFSETTO:-0700
TZNAME:PDT
DTSTART:20270314T100000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0700
TZOFFSETTO:-0800
TZNAME:PST
DTSTART:20271107T090000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261112T114000
DTEND;TZID=America/Los_Angeles:20261112T131500
DTSTAMP:20261106T174908Z
CREATED:20261105T221644Z
LAST-MODIFIED:20261106T174908Z
UID:10018055-1794483600-1794489300@events.ucsc.edu
SUMMARY:BME 280B Seminar: Student Lab Rotation Talks - CHEM and BME
DESCRIPTION:Welcome to the 7th week of our BME 280B seminar series\, a weekly seminar covering topics of current research in computational biology and bioinformatics. \nPlease join us this week to learn more about the current projects in our CB3 and BME labs. Open to all\, food is provided. Class enrollment is not required. \nStudents are encouraged to attend to learn more about which labs to join and what projects beginning researchers are given. All is welcome to learn about the new directions in our research labs. \nThis week’s speakers include: \nCHEM: \nSamuel Catania \nClara Hansen – “Investigating Microenvironment Driven Invadopodia Development for Application in Tensile Expansion Mass Spectrometry (TExMS) \nTilly Lobdell – “Exploring Kainoid Synthase Cyclization on Homologated Substrates” \nAriana Negroni Santiago – “Model Building of the Banana Slug 60s Ribosomal Subunit” \nLorenzo Ramirez \nBME: \nAditi Arun \nSebastian Alarcon \nRaghav Bhargava  – “The Importance of Spatial Null Models for Detecting Isolation by Environment” \nSophia Wang – “A Seed Evaluation Framework and Minimaxmers: Frequency-Aware Seed Selection for vg Giraffe” \nDescription: Pangenome graph mappers such as vg Giraffe start by sampling short k-mers (“seeds”) from each read\, and the seeding scheme shapes both speed and accuracy. In this rotation project in the Paten lab\, I built two things. The first is seed-eval\, a reproducible framework that takes any seeding scheme\, builds its index\, maps simulated and real reads\, and reports accuracy with paired statistical tests\, mapping-quality behavior\, repeated speed measurements\, and memory. The second is an implementation of minimaxmer in vg Giraffe. Minimaxmers are a frequency-aware seeding scheme proposed by Yoshihiko Suzuki that use genome and sequencing-read k-mer counts to prefer informative seeds. Using seed-eval on HG002 PacBio HiFi reads\, I show that minimaxmers reduce seed hits per read by about a quarter without loss of accuracy\, at a cost in speed and memory.
URL:https://events.ucsc.edu/event/bme-280b-seminar-111226/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
ATTACH;FMTTYPE=image/png:https://events.ucsc.edu/wp-content/uploads/2026/10/BE-logomark_localist-1.png
GEO:36.9996638;-122.0618552
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=Physical Sciences Building Physical Sciences Building Santa Cruz CA 95064;X-APPLE-RADIUS=500;X-TITLE=Physical Sciences Building:geo:-122.0618552,36.9996638
END:VEVENT
END:VCALENDAR