BME 280B Seminar: Student Lab Rotation Talks – CHEM and BME
Welcome to the 7th week of our BME 280B seminar series, a weekly seminar covering topics of current research in computational biology and bioinformatics.
Please 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.
Students 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.
This week’s speakers include:
CHEM:
Samuel Catania
Clara Hansen – “Investigating Microenvironment Driven Invadopodia Development for Application in Tensile Expansion Mass Spectrometry (TExMS)
Tilly Lobdell – “Exploring Kainoid Synthase Cyclization on Homologated Substrates”
Ariana Negroni Santiago – “Model Building of the Banana Slug 60s Ribosomal Subunit”
Lorenzo Ramirez
BME:
Aditi Arun
Sebastian Alarcon
Raghav Bhargava – “The Importance of Spatial Null Models for Detecting Isolation by Environment”
Sophia Wang – “A Seed Evaluation Framework and Minimaxmers: Frequency-Aware Seed Selection for vg Giraffe”
Description: 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.