BME 280B Seminar: Speaker Julian Lucas & Speaker Theo Kell
Title of Talk 1: Enabling Population-Scale Analysis of Human Centromere Diversity
Presenter 1: Julian Lucas, Graduate Student in Miga Lab, University of California, Santa Cruz
Description: Centromeres are essential for chromosome segregation, yet their repetitive DNA has long been a blind spot in human genomics. Until recently, they were largely missing from reference genomes, and they are still omitted from many genomic analyses due to their rapid sequence divergence. Reference-quality assemblies from the Human Pangenome Reference Consortium (HPRC) now make it possible to compare centromeres across hundreds of human haplotypes. I will describe how we built these assemblies and developed methods to align their repetitive satellite arrays. Together, these form a centromere pangenome that represents variation and supports analysis such as read mapping, making centromeres accessible to genomics. Our analysis reveals large structural differences in and around centromeres, as well as unexpected patterns in single-base changes that offer clues to how centromeric DNA evolves.
Bio: Julian is a graduate student in Karen Miga’s laboratory at the University of California, Santa Cruz. His research uses pangenomes to characterize variation in human centromeres, with the goal of bringing these historically difficult-to-analyze regions into mainstream human genetics. Recently, he helped lead the assembly effort for Release 2 of the Human Pangenome Reference Consortium (HPRC), which produced reference-quality genome assemblies that better capture human genetic diversity. Before graduate school, Julian worked at biotechnology startups, most recently in non-invasive cancer detection.
Hosted by: Professor Karen Miga, BME Department
Title of Talk 2: Genomics Institute Computing Resources
Presenter 2: Theo Kell, Senior Systems Architect, UC Santa Cruz Genomics Institute
Description: The backbone of the bioinformatics research at the Genomics Institute is its computing infrastructure. Members of the Genomics Institute have access to a wide array of resources, including petabytes of storage capacity, and a supercomputer cluster with over 7,000 cores. There are also systems for hosting public websites, sharing datasets with the world, and collaborating on coding projects. The Genomics Institute IT team works with all stakeholders to make sure that the computing resources are accessible, up-to-date, and optimized for cutting-edge, massively parallel bioinformatics research.
This presentation will give an overview of the computing assets that are available, explain how they are used, and elaborate on best practices. It is intended to be approachable for students who do not yet have experience with programming or using the command line, while also providing a jumping-off point for students who are ready to dive in and begin running code.
Bio: Theo Kell is a Senior Systems Architect at the UC Santa Cruz Genomics Institute. After graduating from the Baskin School of Engineering’s Technology and Information Management program, he worked as an IT System Administrator at Moss Landing Marine Laboratories and Cabrillo College before returning to UCSC to join the Genomics Institute IT team. He has a broad background in Linux/Unix systems, virtualization, cybersecurity, networking, and customer support.