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DTSTART;TZID=America/Los_Angeles:20261001T114000
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SUMMARY:BME 280B Seminar: Speaker Julian Lucas & Speaker Theo Kell
DESCRIPTION:Title of Talk 1: Enabling Population-Scale Analysis of Human Centromere Diversity \nPresenter 1: Julian Lucas\, Graduate Student in Miga Lab\, University of California\, Santa Cruz \nDescription: 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. \nBio: 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. \nHosted by: Professor Karen Miga\, BME Department \nTitle of Talk 2: Genomics Institute Computing Resources \nPresenter 2: Theo Kell\, Senior Systems Architect\, UC Santa Cruz Genomics Institute \nDescription: 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. \nThis 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. \nBio: 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.
URL:https://events.ucsc.edu/event/bme-280b-seminar-speaker-julian-lucas-speaker-theo-kell-genomics-institute-computing-resources/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260929T133000
DTEND;TZID=America/Los_Angeles:20260929T143000
DTSTAMP:20260925T164513Z
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SUMMARY:Heath\, H. (BMEB) - Linking Altered mRNA Processing to Translational Regulation in Lung Cancer
DESCRIPTION:In lung cancer\, recurrent alterations in RNA processing regulators reshape both the proteins genes encode and the sequences that regulate their production. Understanding how mRNA processing influences protein production requires resolving the coding and regulatory sequences present in individual mRNA isoforms. Transcription start site (TSS) choice\, alternative splicing (AS) \, and polyadenylation site (PAS) choice determine which coding sequences (CDS) and untranslated regions (UTRs) are expressed together. This allows transcripts from the same gene to differ in the structure and abundance of proteins they generate. Short-read RNA sequencing is only able to identify single splicing changes\, failing to link them together\, while long-read RNA sequencing (LRS) reads can span across exons allowing for more confident transcriptome assembly. However\, accurate transcript end detection is not a priority for most LRS transcript assemblers. As a result\, they may miss transcript end changes that could obscure real variations in UTR regulatory sequences. In preliminary benchmarking across multiple cell lines and LRS technologies\, we compared validated transcript-end locations to isoform assemblies. Here we found TSSs and PASs are present in long reads but not recovered by current transcriptome assembly methods\, in addition to incorrect transcript ends. To address these limitations\, I will develop FLAIR-Transcript-End Detection (FLAIR-TED)\, a computational method to improve identification of accurate alternative transcript ends during transcriptome assembly (Aim 1). I will then use FLAIR-TED on long-read polysome fractionation (LRPF) sequencing to identify splicing and UTR sequence differences associated with ribosome association in lung cancer cell-line models – revealing how splicing and UTR choice work together to impact translation and protein production (Aim 2). Finally in matched lung adenocarcinoma (LUAD) primary tumor and normal tissues\, I will examine whether recurrent isoform usage changes favor transcripts with distinct predicted translational efficiencies (Aim 3). Together\, these studies will connect disease-associated mRNA processing changes to the coding and regulatory sequences expressed and their potential translational consequences. \n  \nEvent Host: Harrison Heath\, PhD Student\, Biomolecular Engineering & Bioinformatics \nAdvisor: Angela Brooks  \nZoom: https://ucsc.zoom.us/j/92519872137?pwd=mn1j67FWrojyx6bPt8ekwugm0Tcpaw.1 \nPasscode: 208120
URL:https://events.ucsc.edu/event/heath-h-bmeb-linking-altered-mrna-processing-to-translational-regulation-in-lung-cancer/
LOCATION:Biomedical Sciences\, Biomedical Sciences Building Red Hill Road\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260925T150000
DTEND;TZID=America/Los_Angeles:20260925T160000
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SUMMARY:Malekos\, E. (BMEB) - CRISPR screens of noncanonical ORFs uncover retroviral-derived immune regulators
DESCRIPTION:Ribosome profiling has revealed thousands of noncanonical translation events across mammalian genomes\, yet functional characterization has overwhelmingly focused on proliferative fitness in cancer cell lines. Here\, we present a comprehensive survey of noncanonical translation in the mouse immune system and its functional consequences in macrophages. By performing a unified Ribo-seq meta-analysis across 20 public mouse leukocyte datasets – spanning macrophages\, dendritic cells\, neutrophils\, B cells\, and T cells – we define a compendium of 22\,276 noncanonical coding sequences (CDSs)\, including upstream ORFs (uORFs)\, downstream ORFs\, and ORFs on noncoding RNAs and pseudogenes (ncORFs). Proteogenomic integration with reanalyzed mass spectrometry data prioritizes a high-confidence subset with detectable protein products\, including pseudogene-encoded and lncRNA-encoded zinc finger proteins. To move beyond cataloging\, we carried out two orthogonal CRISPR screens in immortalized bone marrow-derived macrophages: a fitness screen identifying noncanonical CDSs required for macrophage viability\, and a TLR1/TLR2-NFκB reporter screen uncovering CDSs that modulate innate immune signaling. These screens nominate uORFs\, several conserved between mouse and human\, that exert phenotypic effects on par with their cognate coding sequences. We unexpectedly discovered a family of endogenous retroviral envelope-derived proteins translated in adult myeloid cells. Among these\, SYNIR is a full-length syncytin-like membrane glycoprotein that positively regulates NFκB-responsive transcription\, while SEMR is a secreted protein with structural homology to the feline leukemia virus accessory protein FeLIX that drives broad transcriptional remodeling of macrophage gene programs upon knockout. Updated single-cell RNA-seq annotations and an interactive UCSC Genome Browser session integrating Ribo-seq\, proteomics\, and CRISPR screen data are provided as community resources. Together\, these findings expand the functional landscape of noncanonical translation in immunity and establish endogenous retroviral proteins as previously unrecognized regulators of macrophage biology. \nEvent Host: Eric Malekos\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Susan Carpenter
URL:https://events.ucsc.edu/event/malekos-e-bmeb-crispr-screens-of-noncanonical-orfs-uncover-retroviral-derived-immune-regulators/
LOCATION:Biomedical Sciences\, Biomedical Sciences Building Red Hill Road\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260925T130000
DTEND;TZID=America/Los_Angeles:20260925T150000
DTSTAMP:20260911T151906Z
CREATED:20260911T151906Z
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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://events.ucsc.edu/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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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260921T113000
DTEND;TZID=America/Los_Angeles:20260921T123000
DTSTAMP:20260914T191617Z
CREATED:20260914T191617Z
LAST-MODIFIED:20260914T191617Z
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SUMMARY:Headrick\, C. (BMEB) - The Regulation of mRNA Cleavage in Nonsense-mediated mRNA Decay: From Inside (intra-pathway determinants) Out (extra-pathway regulation)
DESCRIPTION:Nonsense-mediated mRNA decay (NMD) is a translation-coupled quality control pathway that degrades mRNAs that harbor a premature termination codon (PTC) and 5-30% of normal cellular mRNAs. The NMD field sits at a pivotal moment with recent developments that endonucleolytic cleavage is the primary mechanism of mRNA decay conserved across metazoans. Discovery of a conserved NMD cleavage mechanism sets the stage for a dissection of mRNA cleavage determinants and regulators. \nTo better understand how mRNA cleavage during NMD is regulated\, I will use degradome-seq based approaches via 5’RACE-seq (Rapid Amplification of 5’ cDNA Ends) to isolate the cleavage products of the NMD pathway. I will first focus my analysis on core NMD factors and helicase UPF1\, the binding site of NMD decay effectors\, to examine how UPF1 enzymatic activity affects mRNA cleavage transcriptome-wide (Aim 1). In parallel\, to assess extra-pathway regulation of mRNA cleavage during NMD\, I will identify endogenous negative regulators of mRNA cleavage (Aim 2). Contemporary models of NMD are deprived of the functional impact of cellular NMD inhibitors. I will access this novel functional space with an innovative application of CRISPR screening and quantitative\, high-throughput NGS\, known as ReLiC (RNA-linked CRISPR) paired with degradome analysis. \n  \nEvent Host: Camille Headrick\, Ph.D. Student\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Joshua Arribere \n 
URL:https://events.ucsc.edu/event/headrick-c-bmeb-the-regulation-of-mrna-cleavage-in-nonsense-mediated-mrna-decay-from-inside-intra-pathway-determinants-out-extra-pathway-regulation/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260828T100000
DTEND;TZID=America/Los_Angeles:20260828T120000
DTSTAMP:20260813T164521Z
CREATED:20260813T164521Z
LAST-MODIFIED:20260813T164521Z
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SUMMARY:Nag\, S. (BMEB) - Personalized Diploid Genome Graphs for Accurate Somatic Variant Discovery
DESCRIPTION:Many somatic variant-calling pipelines begin by aligning tumor and matched-normal sequencing reads to a single linear reference genome\, such as GRCh38. Because every individual differs substantially from this reference\, this approach can introduce reference bias\, causing reads to map incorrectly or not at all and potentially leading to missed somatic variants or germline variants being misclassified as somatic. I propose replacing the generic reference with a personalized diploid genome graph constructed from a donor-specific assembly (DSA)\, which represents both inherited haplotypes of the individual. I will develop this framework by (1) generating haplotype-resolved\, telomere-to-telomere DSAs for cancer reference cell lines\, (2) developing haplotype-aware graph alignment and adapting DeepSomatic to call variants against personalized diploid genomes\, and (3) applying this approach across tissues from SMaHT donors to improve somatic mosaicism detection and characterize shared and tissue-specific mutations. \nEvent Host: Sagorika Nag\, Ph.D. Student\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Benedict Paten \nZoom: https://ucsc.zoom.us/j/99844148597?pwd=amp5Nhmj2UeodTADUdaJwZsKtscRMG.1 \nPasscode: 685655
URL:https://events.ucsc.edu/event/nag-s-bmeb-personalized-diploid-genome-graphs-for-accurate-somatic-variant-discovery/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260827T150000
DTEND;TZID=America/Los_Angeles:20260827T170000
DTSTAMP:20260814T163137Z
CREATED:20260814T163137Z
LAST-MODIFIED:20260814T163137Z
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SUMMARY:Kramer\, A. (BMEB) - Scalable phylo-pangenomics
DESCRIPTION:The COVID-19 pandemic generated genomic data at unprecedented scale\, with tens of millions of SARS-CoV-2 genomes deposited in public repositories and thousands of new sequences added each day. This dissertation develops methods for analyzing genomic datasets at this scale\, unified by the idea that encoding genomes according to their evolutionary relationships can make otherwise intractable computations practical. First\, I evaluate online phylogenetic inference\, in which new genomes are continuously added to an existing tree\, and compare parsimony-based methods with maximum-likelihood approaches under pandemic time constraints. For densely sampled SARS-CoV-2 genomes\, online inference with UShER and matOptimize produces trees comparable to established maximum-likelihood methods while requiring orders of magnitude less time and memory. I then develop tools that make phylogenies containing millions of genomes useful for downstream analysis and visualization. ShUShER enables privacy-preserving phylogenetic placement within a web browser\, allowing laboratories to analyze sensitive sequences without transmitting them to an external server. Treenome Browser co-visualizes the genomic variation of millions of samples alongside their phylogenetic relationships by operating directly on a compressed mutation-annotated tree. Finally\, I describe Panmap\, which uses Pangenome Mutation-Annotated Networks (PanMANs) to place\, align\, and genotype sequencing reads and to estimate haplotype abundances against reference collections containing up to millions of genomes. Panmap produces indexes hundreds of times smaller than graph-based alternatives\, improves genome reconstruction over single-reference workflows at low coverage\, and supports applications ranging from pathogen genome assembly to ancient environmental DNA analysis. Together\, these results show that evolutionary history can serve not only as an object of inference but as a scalable computational infrastructure for phylogenomic and pangenomic analyses as genomic datasets continue to grow. \nEvent Host: Alexander Kramer\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics \nAdvisor: Russell Corbett-Detig \nZoom: https://ucsc.zoom.us/j/91364025182?pwd=Tq95CuaBqrePatRjopy6uJ9bbjsrIH.1 \nPasscode: 318268
URL:https://events.ucsc.edu/event/kramer-a-bmeb-scalable-phylo-pangenomics/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260823T083000
DTEND;TZID=America/Los_Angeles:20260823T170000
DTSTAMP:20260724T220901Z
CREATED:20260605T140000Z
LAST-MODIFIED:20260724T220901Z
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SUMMARY:BIC 2026 | UC Systemwide Bioengineering Symposium
DESCRIPTION:The 26th Annual UC Systemwide Bioengineering Symposium (BIC 2026) is taking place at UC Santa Cruz on August 22-23\, 2026. The event will bring together faculty\, researchers\, students\, industry representatives\, non-profit organizations\, and other stakeholders to explore bioengineering & AI in the heart of the redwood forest. BIC 2026 will foster new collaborations and showcase the latest advancements in bioengineering research and innovation\, including at the intersection with AI. \nRegister here. \n\nDates & Time\n\n\n\nDay 1 (Saturday\, August 22): August 22 @ 8:00 am – 9:00 pm\nDay 2 (Sunday\, August 23): August 23 @ 8:30 am – 5:00 pm\n\n\n\n\nRegistration Fees & Cost\n\nUndergraduate Student: $215 (Early Bird) / $265 (Standard)\nGraduate Student or Postdoc: $270 (Early Bird) / $320 (Standard)\nFaculty or Staff: $320 (Early Bird) / $370 (Standard)\nIndustry or Guest: $420 (Early Bird) / $470 (Standard)\n\nNote: Late bird/Standard rates apply starting June 16\, 2026\, and a 4.00% processing fee is added at checkout.
URL:https://events.ucsc.edu/event/bic-2026-uc-systemwide-bioengineering-symposium/2026-08-23/
LOCATION:Kresge College\, R-3 Suites\, Santa Cruz\, CA\, 95064
CATEGORIES:Conference,Meetings & Conferences,Reception
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260822T080000
DTEND;TZID=America/Los_Angeles:20260822T210000
DTSTAMP:20260724T220901Z
CREATED:20260605T140000Z
LAST-MODIFIED:20260724T220901Z
UID:10014909-1787385600-1787432400@events.ucsc.edu
SUMMARY:BIC 2026 | UC Systemwide Bioengineering Symposium
DESCRIPTION:The 26th Annual UC Systemwide Bioengineering Symposium (BIC 2026) is taking place at UC Santa Cruz on August 22-23\, 2026. The event will bring together faculty\, researchers\, students\, industry representatives\, non-profit organizations\, and other stakeholders to explore bioengineering & AI in the heart of the redwood forest. BIC 2026 will foster new collaborations and showcase the latest advancements in bioengineering research and innovation\, including at the intersection with AI. \nRegister here. \n\nDates & Time\n\n\n\nDay 1 (Saturday\, August 22): August 22 @ 8:00 am – 9:00 pm\nDay 2 (Sunday\, August 23): August 23 @ 8:30 am – 5:00 pm\n\n\n\n\nRegistration Fees & Cost\n\nUndergraduate Student: $215 (Early Bird) / $265 (Standard)\nGraduate Student or Postdoc: $270 (Early Bird) / $320 (Standard)\nFaculty or Staff: $320 (Early Bird) / $370 (Standard)\nIndustry or Guest: $420 (Early Bird) / $470 (Standard)\n\nNote: Late bird/Standard rates apply starting June 16\, 2026\, and a 4.00% processing fee is added at checkout.
URL:https://events.ucsc.edu/event/bic-2026-uc-systemwide-bioengineering-symposium/2026-08-22/
LOCATION:Kresge College\, R-3 Suites\, Santa Cruz\, CA\, 95064
CATEGORIES:Conference,Meetings & Conferences,Reception
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260820T130000
DTEND;TZID=America/Los_Angeles:20260820T150000
DTSTAMP:20260814T163909Z
CREATED:20260814T163815Z
LAST-MODIFIED:20260814T163909Z
UID:10015340-1787230800-1787238000@events.ucsc.edu
SUMMARY:Penunuri\, G. (BMEB) - Genomic\, Proteomic\, and Computational Approaches to the Study of Host-Microbe Systems
DESCRIPTION:Host-microbe systems are core to some of biology’s most consequential interactions\, from the pathogens that drive infectious disease to symbionts affecting agricultural pest control and vector-borne disease transmission. Yet unlike the model organisms that have driven most of modern molecular biology\, the microbes at the center of these interactions are rarely genetically tractable: many cannot be cultured outside a host\, resist standard tools for genetic manipulation\, and are annotated largely by homology to distantly related free-living relatives. This dissertation develops genomic\, proteomic\, and computational methods to work around this lack of infrastructure and contribute techniques and tools to the study and further understanding of host-microbe systems. Using Wolbachia cultured in Drosophila melanogaster cell lines\, I demonstrate that chemical mutagenesis can be used to perturb intracellular genomes leaving a detectable mutational signal. I employ a low error rate sequencing technique to record and model the mutational landscape left by the mutagen ethyl methanesulfonate (EMS) demonstrating its use for mutagenesis screens of intracellular bacteria. I next utilize structural proteome datasets to screen host-microbe proteomes for strong candidates of molecular mimicry\, microbe proteins that have coevolved a eukaryotic like domain or structure and suggest use for host manipulation or microbe survival in the host environment. Building off of this screen for novel effectors through structural alignments I develop and test a distributed computing system for performing large scale systematic literature reviews. Altogether these projects represent generalizable approaches to the study of host-microbe systems reaching from classically studied and thoroughly understood to novel and non-model systems. \nEvent Host: Gabriel Penunuri\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Russell Corbett-Detig \nZoom: https://ucsc.zoom.us/j/98216883331?pwd=uqmUSQba2X6GVNBhOhAGRwgCZyjAyj.1 \nPasscode: 730377
URL:https://events.ucsc.edu/event/penunuri-g-bmeb-genomic-proteomic-and-computational-approaches-to-the-study-of-host-microbe-systems/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260817T130000
DTEND;TZID=America/Los_Angeles:20260817T150000
DTSTAMP:20260813T194341Z
CREATED:20260813T194341Z
LAST-MODIFIED:20260813T194341Z
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SUMMARY:Condon\, C. (BMEB) - Genomic conflict across scales
DESCRIPTION:Genomes are often viewed as cooperative systems in which genes work together to support organismal function. Yet genetic elements can also act in ways that favor their own transmission or persistence\, creating conflict within the genome. In this talk\, I examine the evolutionary and functional consequences of such genomic conflict across three systems. First\, I investigate segregation distortion in Arabidopsis hybrids and its potential role in the early evolution of reproductive isolation. Second\, I characterize the population dynamics and functional effects of introners\, mobile elements that generate new introns in the green alga Micromonas pusilla. Finally\, I explore widespread splicing dysfunction in algal mating-type chromosomes and its consequences for transcript diversity. Together\, these studies highlight how departures from genome cooperation can shape inheritance\, genome evolution\, and gene regulation. \nEvent Host: Chris Condon\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Russell Corbett-Detig
URL:https://events.ucsc.edu/event/condon-c-bmeb-genomic-conflict-across-scales/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260717T113000
DTEND;TZID=America/Los_Angeles:20260717T133000
DTSTAMP:20260715T163613Z
CREATED:20260715T163517Z
LAST-MODIFIED:20260715T163613Z
UID:10015090-1784287800-1784295000@events.ucsc.edu
SUMMARY:Calicchio\, A. (BMEB) - Comparison of long-read sequencing and analysis methods for transcriptome analysis
DESCRIPTION:Alternative splicing\, the process generating different RNA isoforms from a single gene\, is considered one of the main factors driving increased organism complexity in eukaryotes. Variations in isoform and gene expression produce the functional differences that give rise to different cell types and\, in some cases\, result in disease. Long-read RNA sequencing has transformed our ability to characterize isoforms\, since single reads can span full-length transcripts\, but limitations still prevent our identification of all the isoforms in the human transcriptome. Our research proposes to improve both the library preparation and computational analysis steps of the isoform identification process.\nTo do so\, we are updating the isoform identification and quantification tool IG28 (previously called Mandalorion) so that it can analyse both bulk and single-cell long-read sequencing data and. By pairing our analysis with single-cell clustering in Seurat\, we can generate transcriptomes for hundreds of thousands of single cells\, for individual cell types\, and for bulk datasets containing hundreds of millions of reads\, providing a scalable approach to identify isoforms in the largest and most recent datasets.\nFurthermore\, since long reads can carry both the variants defining an allele of origin and the full isoform structure\, we plan to extend IG28 to perform allele-specific transcript usage analysis. We plan to include accurate statistical tests in this module by using beta-binomial and Dirichlet-multinomial models that account for overdispersion\, to provide a tested and integrated pipeline for isoform allelic assignment.\nFinally\, recognizing that isoform detection depends on the quality\, length\, and throughput of the input data\, we are improving library preparation and benchmarking sequencing technologies. We are refining the R2C2 protocol coupled with size selection to overcome the current circularization limit for fragments beyond 6 kb\, and we are generating matched datasets to compare R2C2 to the Kinnex library preparation method\, and ONT against PacBio HiFi sequencing\, to determine which approaches produce the most accurate and longest reads for isoform identification.\nTogether\, these advances will provide a competitive pipeline\, from cDNA preparation to isoform identification and annotation\, enabling accurate isoform annotations that can lead to a deeper understanding of cell differentiation and disease etiology. \nEvent Host: Alessandro Calicchio\, Ph.D. Student\, Biomolecular Engineering & Bioinformatics \nAdvisor: Christopher Vollmers \nZoom: https://ucsc.zoom.us/j/92704819548?pwd=PUqQpq0Soandz8E5DIPCXFdvnFaf00.1 \nPasscode: 760165
URL:https://events.ucsc.edu/event/calicchio-a-bmeb-comparison-of-long-read-sequencing-and-analysis-methods-for-transcriptome-analysis/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260625T130000
DTEND;TZID=America/Los_Angeles:20260625T140000
DTSTAMP:20260622T225613Z
CREATED:20260622T225613Z
LAST-MODIFIED:20260622T225613Z
UID:10014924-1782392400-1782396000@events.ucsc.edu
SUMMARY:BME/Genomics Seminar: Supervised and Unsupervised DeepGene Finding and Genome Foundation Models
DESCRIPTION:Presenter: Mario Stanke\, Professor of Bioinformatics\, University of Greifswald \nDescription: This talk will explore recent machine learning approaches for eukaryotic genome annotation. Our supervised ab initio deep gene finder\, Tiberius\, correctly predicts more than four times as many human protein-coding gene structures as its father\, Augustus\, and in some clades\, it approaches the accuracy of evidence-based pipelines such as BRAKER. Genome foundation models can automatically learn annotation-relevant embeddings from unannotated training genomes. I will also present Vipsania\, the unsupervised wife of Tiberius. Vipsania is a genome foundation model that learns hidden Markov models to find gene structures from naked genomes using a BERT-style masked language model objective. Finally\, I will report on ongoing efforts to use phylogenetic teaching signals from whole-genome vertebrate alignments to train a genome foundation model comparatively. \nKeywords: hidden Markov model layer\, linear recurrent unit\, continuous-time Markov chains on trees \nBio: Mario Stanke studied mathematics and computer science at the University of Göttingen and UCBerkeley\, and received his Dr. rer. nat. from the University of Göttingen. He completed a postdoctoral fellowship in the Haussler lab at UC Santa Cruz in 2006–2007. He has been a Professor of Bioinformatics at the Institute of Mathematics and Computer Science at the University of Greifswald since 2010. \nHosted by: Genomics Institute \nLocation: E2-599 (limited space) \nZoom: https://ucsc.zoom.us/j/95380317295?pwd=0HbwSYKRQqyCtBcPXGfoB0tPOsA16V.1
URL:https://events.ucsc.edu/event/bme-genomics-seminar-supervised-and-unsupervised-deepgene-finding-and-genome-foundation-models/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260605T132000
DTEND;TZID=America/Los_Angeles:20260605T142500
DTSTAMP:20260529T173530Z
CREATED:20260529T173530Z
LAST-MODIFIED:20260529T173530Z
UID:10014890-1780665600-1780669500@events.ucsc.edu
SUMMARY:BME80G Seminar – Sheril Kirshenbaum\, "Science in Policymaking"
DESCRIPTION:Please note: Following this lecture\, the Genomics Institute’s Diversity\, Equity\, and Inclusion Committee will host a reception on the Baskin Engineering Lanai with Dr. Kirshenbaum where we can continue the discussion on how to effectively engage lawmakers and the public to value and support genomic science. \nPresenter: Dr. Sheril Kirshenbaum \nAbstract: Science shapes our world\, but meaningful policy engagement and understanding of research and innovation are critical if new advances are to reach their full potential. Dr. Sheril Kirshenbaum will share her research on science in policymaking and reflect on her experiences serving as a science advisor in Congress. The talk will explore effective strategies for engaging policymakers and staff\, countering misinformation\, promoting evidence-based decision-making\, and strengthening the role of science in the policy process. \nAbout the speaker: Dr. Sheril Kirshenbaum is an Emmy Award-winning scientist and author in the Office of Research and Innovation at Michigan State University\, and an assistant professor in the College of Communication Arts and Sciences. Her research explores how senior policymakers in the U.S. government make decisions about science and she has worked in the U.S. Senate with Senator Gary Peters (MI) and Bill Nelson (FL). She also hosts and writes the PBS series Serving Up Science with WKAR about the global food system and its impact on the environment and our health. Kirshenbaum is the author of The Science of Kissing and Unscientific America: How Scientific Illiteracy Threatens Our Future (with Chris Mooney)\, and co-founded the NGO Science Debate. \nHosted by: Professor Karen Miga\, BME Department
URL:https://events.ucsc.edu/event/bme80g-seminar-sheril-kirshenbaum-science-in-policymaking/
LOCATION:Jack Baskin Auditorium\, 191 Baskin Cir\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260604T114000
DTEND;TZID=America/Los_Angeles:20260604T133000
DTSTAMP:20260601T153627Z
CREATED:20260601T153627Z
LAST-MODIFIED:20260601T153627Z
UID:10014894-1780573200-1780579800@events.ucsc.edu
SUMMARY:BME 280B Seminar: Accelerating the diagnosis of rare diseases using multi-omics
DESCRIPTION:Presenter: Stephen Montgomery\, Endowed Professor of Pathology\, Genetics\, Biomedical Data Science\, Computer Science\, Stanford University \n  \nDescription: N/A \n  \nBio: Stephen Montgomery is an Endowed Professor of Pathology\, Genetics\, Biomedical Data Science and\, by courtesy\, Computer Science at Stanford University. He has trained in multiple countries including Canada\, Germany\, England\, and Switzerland. He is best known for his work mapping the effects of genetic variation to gene expression and authored the first publications that compared whole genomes and transcriptome data within a human population and pioneered the use of molecular outliers to identify impactful rare variants (Montgomery et al\, 2010\, Montgomery et al\, 2011). \nHosted by: Professor Karen Miga\, BME Department
URL:https://events.ucsc.edu/event/bme-280b-seminar-accelerating-the-diagnosis-of-rare-diseases-using-multi-omics/
LOCATION:Biomedical Sciences\, Biomedical Sciences Building Red Hill Road\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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GEO:36.999785;-122.061118
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260604T100000
DTEND;TZID=America/Los_Angeles:20260604T120000
DTSTAMP:20260528T203838Z
CREATED:20260528T203838Z
LAST-MODIFIED:20260528T203838Z
UID:10014885-1780567200-1780574400@events.ucsc.edu
SUMMARY:Okamoto\, F. (BMEB) - Improving read-to-pangenome alignment in complicated genomic regions
DESCRIPTION:Many genetics pipelines start by aligning sequencing reads to a reference genome. Aligners attempt to find the position in the reference sequence which best matches the read sequence\, but this breaks down when the reads come from a sample with variation relative to the reference. A proposed alternative\, pangenome graphs\, is supposed to fix such “reference bias” by including known variation within the reference itself. Yet read alignment is still difficult in graph regions featuring certain complex variation. I will address specific known limitations of pangenome read alignment by developing better methods to align reads to pangenomes (1) in centromeres\, (2) in regions with cycles\, (3) when a “split”/supplementary alignment is required\, and (4) for RNA-seq reads. \nEvent Host: Faith Okamoto\, Ph.D. Student\, Biomolecular Engineering & Bioinformatics \nAdvisor: Benedict Paten \nZoom: https://ucsc.zoom.us/j/3543092299?pwd=5xbPfPhxvoJlx24tusiOwPuLSjzwzb.1 \nPasscode: 767376
URL:https://events.ucsc.edu/event/okamoto-f-bmeb-improving-read-to-pangenome-alignment-in-complicated-genomic-regions/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260603T150000
DTEND;TZID=America/Los_Angeles:20260603T180000
DTSTAMP:20260602T193539Z
CREATED:20260602T193539Z
LAST-MODIFIED:20260602T193539Z
UID:10014898-1780498800-1780509600@events.ucsc.edu
SUMMARY:Xu\, D. (BMEB) - Interplay Between CENP-A\, DNA Methylation\, and H3K9me3 in Defining Centromere Identity
DESCRIPTION:Centromeres ensure proper chromosome segregation during cell division\, yet the organization and regulation of centromeric chromatin within satellite DNA arrays remain incompletely understood. Here\, we leverage the complete diploid human genome benchmark (T2T-HG002) to provide a detailed study of centromeric sequence and chromatin architecture on individual haplotypes. Using adaptive-sampling-enriched\, ultra-long-read DiMeLo-seq\, we achieve single-molecule chromatin profiling across all centromeres\, revealing that along single chromatin fibers\, CENP-A\, the histone variant specifying centromere identity\, forms multiple discrete subdomains within hypomethylated centromere dip regions (CDRs) that are flanked by H3K9me3-enriched heterochromatin. Despite underlying sequence variation\, CDRs localize to sequence-homogeneous domains and maintain relatively balanced CENP-A dosage and aggregate length across all chromosomes and between haplotypes. Further\, we show that bidirectional changes to centromeric and pericentromeric DNA methylation are accompanied by changes to centromeric chromatin architecture. In passaged cells with centromeric hypomethylation\, subdomain boundaries are eroded\, and adjacent CENP-A domains tend to merge and expand. Conversely\, in pluripotent stem cells with centromeric hypermethylation\, CDRs are fundamentally reorganized\, such that discrete hypomethylated domains are frequently consolidated into broader contiguous tracts. These methylation-associated CDR restructuring events suggest that DNA methylation acts as a principal regulator of human centromere organization\, with implications for understanding centromere plasticity\, epigenetic inheritance\, and chromosomal instability in development and disease. \nEvent Host: Daniel Xu\, PhD Candidate\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Karen Miga \nZoom: https://ucsc.zoom.us/j/99197563825?pwd=meEWoi4ffdZ0K4Syo09Jr0ZbpPThMk.1
URL:https://events.ucsc.edu/event/xu-d-bmeb-interplay-between-cenp-a-dna-methylation-and-h3k9me3-in-defining-centromere-identity/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260603T090000
DTEND;TZID=America/Los_Angeles:20260603T110000
DTSTAMP:20260529T161208Z
CREATED:20260529T161208Z
LAST-MODIFIED:20260529T161208Z
UID:10014887-1780477200-1780484400@events.ucsc.edu
SUMMARY:Morey\, C. (BMEB) - Innovations in Interdependence: Genomic and Functional Evolution in Invertebrates and Their Intracellular Symbionts
DESCRIPTION:Intracellular symbionts are microorganisms\, such as bacteria\, that live within host cells. These associations are widespread throughout the invertebrate tree of life\, and can perform a diversity of key metabolic\, immune-response\, or other functions that the host is dependent on for survival or reproduction. Intracellular symbioses allow both the host and the symbiont to occupy new ecological niches\, and thus can have profound impacts on their evolution. Recent and rapid growth of available sequencing data provides new opportunities to investigate the genomic alterations underpinning functional and morphological changes during the evolution of these relationships\, and how they reshape both host and symbiont biology. \nHere\, I propose investigating unique mechanisms of genomic innovation across three levels of host-symbiont evolution: symbiont genome evolution\, host-symbiont regulatory co-evolution\, and host genome evolution. In aim 1\, I will investigate how mobile genetic elements drive episodic genome expansion and functional innovation in obligate chemosynthetic symbionts of deep-sea clams\, further challenging the notion that reductive genome evolution is an inevitable or linear fate for host-restricted lineages. In aim 2\, I will explore the potential for symbiont-derived small-RNA molecules to participate in cross-kingdom gene regulation of their hosts across a diversity of host-symbiont systems using publicly available genome and RNA-sequencing data. In aim 3\, I will explore the convergent evolution of gut loss across independently derived marine bivalve lineages that depend nutritionally on chemosynthetic symbionts\, identifying host genomic changes associated with the transition to a symbiotic lifestyle. Together\, these aims leverage the expanding wealth of genomic data to illuminate how host-symbiont relationships reshape the genomes of both partners and generate novel adaptations across evolutionary time. \nEvent Host: Camryn Morey\, Ph.D. Student\, Biomolecular Engineering & Bioinformatics \nAdvisor: Shelbi Russell and Russ Corbett-Detig \nZoom: https://ucsc.zoom.us/j/92296748824?pwd=kabPBvby5xZbAHBbxBX6IIHNka8sLX.1 \nPasscode: 153631
URL:https://events.ucsc.edu/event/morey-c-bmeb-innovations-in-interdependence-genomic-and-functional-evolution-in-invertebrates-and-their-intracellular-symbionts/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260529T132000
DTEND;TZID=America/Los_Angeles:20260529T142500
DTSTAMP:20260521T182802Z
CREATED:20260521T182802Z
LAST-MODIFIED:20260521T182802Z
UID:10014859-1780060800-1780064700@events.ucsc.edu
SUMMARY:BME80G Seminar – Katherine Bonini\, “Rethinking Familial Risk in Genomic Medicine: Ethical Approaches to Cascade Screening”
DESCRIPTION:Presenter: Katherine Bonini\, Senior Genetic Counselor @ Icahn School of Medicine at Mount Sinai \n  \nDescription: It has long been argued that families are central to genomic medicine. Genomic risk\, diagnosis\, and management are rarely confined to a single individual\, and separating patients’ interests from those of their relatives is often neither straightforward nor desirable. Despite this\, healthcare systems in the United States continue to operationalize care at the level of the individual. This tension is especially evident in cascade screening\, the process of identifying\, notifying\, and offering genetic testing to relatives of a proband with a hereditary condition. Cascade screening can enable earlier diagnosis\, guide preventive care\, and reduce morbidity and mortality\, but its implementation raises important ethical questions.\nIn this talk\, we will examine how current approaches to familial risk communication place responsibility on patients to notify relatives\, often resulting in incomplete reach and missed opportunities for prevention. We will then consider alternative approaches\, including system-led contact models in which health systems directly notify at-risk relatives with proband consent. Drawing on public health ethics frameworks\, we will discuss a proposed framework demonstrating how system-led models may be ethically justified when specific criteria are met\, including considerations of public input\, opt-out mechanisms\, and a focus on actionable conditions. This talk will encourage consideration of how genomic care can be structured to better balance individual rights with broader responsibilities to families and public health. \n  \nBio: Katherine (Kate) Bonini\, MS\, MA\, CGC is a Senior Genetic Counselor and Core Faculty member in the Institute for Genomic Health at the Icahn School of Medicine at Mount Sinai. Her work focuses on the ethical\, legal\, and social implications of integrating emerging genomic technologies into clinical care\, with particular emphasis on implementation science and equitable translation of genomic advances into practice. She has contributed to several major NHGRI-funded initiatives\, including the Clinical Sequencing Evidence-Generating Research (CSER) Consortium\, the Electronic Medical Records and Genomics (eMERGE) Network\, and the Human Pangenome Reference Consortium (HPRC). \nKate is an active leader within the National Society of Genetic Counselors\, where she previously served as Chair of the Research Special Interest Group and Chair of the Public Policy Committee. She is also a member of the Mount Sinai Clinical Ethics Committee\, where she contributes to institutional discussions on complex ethical issues in patient care and research. \nShe received her MS in Genetic Counseling and MA in Medical Humanities and Bioethics from Northwestern University’s Feinberg School of Medicine. \nHosted by: Professor Karen Miga\, BME Department
URL:https://events.ucsc.edu/event/bme80g-seminar-katherine-bonini-rethinking-familial-risk-in-genomic-medicine-ethical-approaches-to-cascade-screening-2/
LOCATION:Jack Baskin Auditorium\, 191 Baskin Cir\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=Jack Baskin Auditorium 191 Baskin Cir Santa Cruz CA 95064;X-APPLE-RADIUS=500;X-TITLE=191 Baskin Cir:geo:-122.0623528,37.0001832
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260528T114000
DTEND;TZID=America/Los_Angeles:20260528T131500
DTSTAMP:20260522T170730Z
CREATED:20260522T170730Z
LAST-MODIFIED:20260522T170730Z
UID:10014864-1779968400-1779974100@events.ucsc.edu
SUMMARY:BME 280B Seminar: 4th Year Grad Talks
DESCRIPTION:Please join us for our BME 280B seminar series Thursday (5/28/26) in person at Biomed 200. The event will run from 11:40 AM to 1:15 PM and feature our 4th year grad talks. \n\n\n11:40AM – 11:50AM: Ivana Pacar\n11:53AM – 12:03PM: Jesus Gonzalez Ferrer\n12:06PM – 12:16PM: Connor Mattingly\n12:19PM – 12:29PM: Samira Vera\n12:32PM – 12:42PM: Nick Chu\n12:45PM – 12:55PM: Julian Menendez\n12:58PM – 1:08PM: Parsa Eskandar
URL:https://events.ucsc.edu/event/bme-280b-seminar-4th-year-grad-talks-2/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260521T114000
DTEND;TZID=America/Los_Angeles:20260521T131500
DTSTAMP:20260507T163056Z
CREATED:20260507T163056Z
LAST-MODIFIED:20260507T163056Z
UID:10014617-1779363600-1779369300@events.ucsc.edu
SUMMARY:BME 280B Seminar: Speaker Dylan Shropshire - "How did Wolbachia become Earth's most pervasive animal symbiont?"
DESCRIPTION:Presenter: Dylan Shropshire\, Assistant Professor in the Department of Biological Sciences\, Lehigh University \nDescription: Maternally transmitted Wolbachia bacteria inhabit roughly half of all arthropod species\, making them likely the most common animal-associated microbe on Earth. Wolbachia alter host reproduction\, persist across deep evolutionary timescales\, and move into new host species in ways that we are only beginning to resolve. Wolbachia‘s biological success now also underpins global biocontrol programs aimed at suppressing arboviral disease\, lending applied urgency to a foundational question: how did a single bacterial lineage come to dominate the animal world? In this seminar\, I will draw on my recent and ongoing work to explore facets of this question\, leveraging Wolbachia‘s evolutionary diversity and wet-lab tools to define the mechanisms driving this microbe’s success across the animal world. Collectively\, this work aims to clarify the determinants of Wolbachia‘s natural prevalence and to sharpen the predictive frameworks underpinning Wolbachia-based biocontrol of vector-borne disease. \nBio: Dylan Shropshire is an Assistant Professor in the Department of Biological Sciences at Lehigh University in Pennsylvania\, where he leads a research group studying mechanisms of Wolbachia-host interactions. He earned his PhD at Vanderbilt University as an NSF Graduate Research Fellow and completed an NSF Postdoctoral Research Fellowship at the University of Montana. He is also a first-generation high school graduate and former Pell Grant recipient\, experiences that motivate his commitment to high-quality mentorship and evidence-based pedagogical practices. His work has been recognized by the Charles E. Kaufman New Investigator Award\, Lehigh’s Pre-Tenure Faculty Award\, and the College of Arts and Sciences Dean’s Award for Teaching Excellence. \nHosted by: Professor Shelbi Russell\, BME Department
URL:https://events.ucsc.edu/event/bme-280b-seminar-speaker-dylan-shropshire-how-did-wolbachia-become-earths-most-pervasive-animal-symbiont/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260521T090000
DTEND;TZID=America/Los_Angeles:20260521T143000
DTSTAMP:20260326T204610Z
CREATED:20260326T204610Z
LAST-MODIFIED:20260326T204610Z
UID:10011802-1779354000-1779373800@events.ucsc.edu
SUMMARY:Annual BE Student Project Showcase
DESCRIPTION:Join Baskin Engineering for our annual Student Project Showcase to celebrate the innovative work and accomplishments of undergraduate engineers in capstone courses and research pathways. The broader campus community\, parents\, and industry partners are invited to view the culmination of student work. \nThe day begins with oral presentations from nominated “best-in-class” teams and those working on industry-sponsored projects. Following this\, all students will participate in a comprehensive Poster Session featuring project outcomes with some teams including table-top demonstrations of functional hardware. \nEvent Details: \n\nDate: May 21\, 2026\nOral Presentations (Nominated/Industry Teams): 9:00 AM to 11:00 AM\, Engineering 2\, Room 180\nPoster Session (All Student Teams): 11:30 AM to 2:30 PM\, Engineering Courtyard
URL:https://events.ucsc.edu/event/be-student-project-showcase-2026/
CATEGORIES:Lectures & Presentations,Undergraduate
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260520T132000
DTEND;TZID=America/Los_Angeles:20260520T142500
DTSTAMP:20260513T212109Z
CREATED:20260513T211954Z
LAST-MODIFIED:20260513T212109Z
UID:10014632-1779283200-1779287100@events.ucsc.edu
SUMMARY:BME80G Seminar – Ann Mc Cartney\, "The Why\, What and How of Indigenous Data Sovereignty"
DESCRIPTION:Presenter: Dr. Ann Mc Cartney\n\n\nLocation: Virtual. Please register here: https://ucsc.zoom.us/meeting/register/ciShTZsyRViYxMDjCc_cAQ#/registration \nAbstract: In 2007 the General Assembly of the United Nations adopted the United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP) that supports Indigenous Peoples’ inherent rights to self-determination and governance over Indigenous Peoples\, territories and resources. This codification in an international treaty led to the conceptualization of Indigenous Data Sovereignty in 2016. Indigenous Data Sovereignty is defined as the right of Indigenous Peoples to own\, control\, access and possess data that derive from them\, and which pertain to Nation membership\, knowledge systems\, customs or territories and is not an internationally recognized concept. Practically\, Indigenous Data Sovereignty gives decision-making authority to Indigenous Peoples and allows them to decide how best data should be collected\, accessed\, and used for nation-building. For this reason\, Indigenous Data Sovereignty is inextricably linked to Indigenous Data Governance. \nThis lecture will dive into the why\, what\, and how of Indigenous Data Sovereignty. Beginning with dive into the history of genomics research and Indigenous Peoples. Then moving into a more in-depth description of both Indigenous Data Sovereignty and Indigenous Data Governance. The lecture will close with highlighting three real world case-studies of genomics projects operationalising Indigenous Data Sovereignty. \nAbout the speaker: Dr. Mc Cartney is a Full Researcher at the University of California\, Irvine and a Consultant for the Secretariat of the Convention on Biological Diversity\, where she works at the intersection of bioinformatics\, bioethics and policy across human and non-human species. Dr. Mc Cartney completed her PhD in Bioinformatics and Molecular Evolution from Dublin City University. After this she carried out a Genomics Aotearoa Postdoctoral Research Fellowship where she created culturally respectful genomic informatics pipelines for the project that were responsive to the needs and rights of Māori. She then moved Stateside and carried out a second Visiting Postdoctoral Fellowship in the Genome Informatics Section at the NHGRI. During this time\, she also conducted a detail in the NIH Office of Science Policy. Dr. Mc Cartney then transitioned to the University of California\, Santa Cruz’s Genomics Institute as an Assistant Researcher where she worked at the forefront of genomic sequencing technologies to develop more just genomic data infrastructures\, policies and frameworks for engagement. She became an elected member of the Executive Council of the Earth BioGenome Project\, the Vice-chair of the European Reference Genome Atlas\, and the Director of International Partnerships for the Human Pangenome Reference Consortium. She also acted as a “technical expert” for many international science policy initiatives including the DSI Scientific Network\, Native Biodata Consortium and the Informal Advisory Group on DSI for the Convention on Biological Diversity. Additionally\, Dr. Mc Cartney was part of the team to build the first NIH-funded Tribal Data Repository for American Indian and Alaska Natives.
URL:https://events.ucsc.edu/event/bme80g-seminar-ann-mc-cartney-the-why-what-and-how-of-indigenous-data-sovereignty/
CATEGORIES:Lectures & Presentations,Seminars
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LOCATION:https://events.ucsc.edu/event/bme80g-seminar-ann-mc-cartney-the-why-what-and-how-of-indigenous-data-sovereignty/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260520T090000
DTEND;TZID=America/Los_Angeles:20260520T110000
DTSTAMP:20260507T160500Z
CREATED:20260507T160500Z
LAST-MODIFIED:20260507T160500Z
UID:10014616-1779267600-1779274800@events.ucsc.edu
SUMMARY:Lucas\, J. (BMEB) - Enabling Population-Scale Analysis of Human Centromere Diversity
DESCRIPTION:Centromeric DNA is critical for accurate chromosome segregation and genome stability\, but due to its repetitive nature\, it was only recently fully included in a human reference. Rapid evolution and sequence diversity in these regions limit the utility of one reference sequence\, however. Integrating centromeric and pericentromeric satellite DNA – which together constitute over 5% of the human genome – into genetic research requires access to diverse sequences and the variation between them. The HPRC’s Release 2 dataset\, together with recent advancements in long-read assembly algorithms and new tools for sequence alignment and annotation\, now make characterization of centromeric variation possible. In this proposal\, I outline my work as part of the Human Pangenome Reference Consortium (HPRC) to create a diverse set of reference assemblies that accurately represent centromeric variation (aim 1)\, use novel tooling to characterize variation in centromeric regions (aim 2)\, and define the mutational processes that drive centromere evolution (aim 3). Completion of these aims will create a resource to enable the analysis and interpretation of centromeric variation data\, bringing these historically inaccessible regions into mainstream studies of human genetics\, evolution\, and disease. \nEvent Host: Julian Lucas\, Ph.D. Student\, Biomolecular Engineering & Bioinformatics \nAdvisor: Karen Miga \nZoom: https://ucsc.zoom.us/j/94129246296?pwd=QAs2hW8QZRNgpfaGJXvmaVfo52tIh7.1 \nPasscode: 669318
URL:https://events.ucsc.edu/event/lucas-j-bmeb-enabling-population-scale-analysis-of-human-centromere-diversity/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260519T133000
DTEND;TZID=America/Los_Angeles:20260519T153000
DTSTAMP:20260512T163246Z
CREATED:20260512T161808Z
LAST-MODIFIED:20260512T163246Z
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SUMMARY:Bai\, G. (BMEB) - Long-read single-molecule chromatin architecture and its role in transcriptome regulation
DESCRIPTION:Sequencing technologies have revolutionized our understanding of biology\, yet many existing methods require fragmentation of DNA or RNA\, fundamentally limiting our ability to study these molecules in their native\, intact forms. Long-read sequencing overcomes this constraint by enabling the sequencing of long\, single-molecule native DNA and RNA\, providing simultaneous access to both sequence and base modifications that reflect epigenetic state. This capability has already yielded landmark achievements\, including the first complete\, gapless human genome assembly. Yet while our ability to decode genomic sequence has advanced dramatically\, how chromatin structure shapes a cell’s transcriptome remains poorly understood. My thesis addresses this gap through three aims. First\, I co-developed a novel long-read approach for profiling chromatin accessibility at single-molecule resolution using the small molecule angelicin. Second\, I characterized how long-range chromatin states are associated with RNA processing and transcription\, leveraging multi-omic long-read data in yeast. Third\, I incorporate chromatin data into sequence-to-function deep learning models to interpret the mechanistic contribution of chromatin state to RNA processing. Together\, these aims establish a new framework for studying the relationship between epigenetic state and transcriptome regulation at a resolution not previously possible. \nEvent Host: Gali Bai\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics \nAdvisor: Angela Brooks \nZoom Meeting ID: 940 6201 8397 \nPasscode: 700963
URL:https://events.ucsc.edu/event/bai-g-bmeb-long-read-single-molecule-chromatin-architecture-and-its-role-in-transcriptome-regulation/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260515T180000
DTEND;TZID=America/Los_Angeles:20260516T180000
DTSTAMP:20260508T194542Z
CREATED:20260428T221013Z
LAST-MODIFIED:20260508T194542Z
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SUMMARY:NemoClaw NVIDIA x ASUS Hackathon @ UC Santa Cruz
DESCRIPTION:Welcome to the premier physical AI hackathon on the West Coast. We are bringing together the top 200 AI\, infrastructure\, and hardware engineers to build autonomous\, agentic applications on the NVIDIA NemoClaw stack. \n​You aren’t just calling APIs\, you are building on enterprise-grade hardware. \n​The Tracks: \n\nThe Edge Track: 40 exclusive teams will be granted physical\, on-site access to an ASUS DGX Spark unit to build and deploy locally.\n​The Cloud Track: Teams will build the exact same stack utilizing fully sponsored cloud compute instances via Brev.dev.\n\n​The Arsenal & Prizes: Every team builds on a unified playing field. The top projects will take home heavy enterprise hardware\, including: \n\n​NVIDIA Jetson Orin Nanos\n​The ASUS Ascent (DGX Spark)\n​Jensen Huang signed NVIDIA hats & premium swag\n​High-value Brev.dev compute credits\n​Monitors\n​Internship Opportunities\n\n​The Details: \n\n​Who: Open to the top engineers at UC Santa Cruz and local feeder universities.\n​Food: Fully catered for 24 hours. Energy\, caffeine\, and meals are on us.\n​Special Guests*: Opening and closing ceremonies featuring VIP industry leaders (to be announced).\n​Title Sponsors: Nvidia\, ASUS\, Baskin School of Engineering\n\nRegister today!  \n​Space is strictly capped at 200 builders. Registration requires application approval. \n*May subject to change \n 
URL:https://events.ucsc.edu/event/nvidia-hackathon-2026/
LOCATION:Kresge College\, R-3 Suites\, Santa Cruz\, CA\, 95064
CATEGORIES:Competition,Meetings & Conferences
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260515T130000
DTEND;TZID=America/Los_Angeles:20260515T160000
DTSTAMP:20260429T224549Z
CREATED:20260306T005653Z
LAST-MODIFIED:20260429T224549Z
UID:10009405-1778850000-1778860800@events.ucsc.edu
SUMMARY:STEM Culture Festival
DESCRIPTION:The STEM Culture Festival is returning to UC Santa Cruz on Friday\, May 15 from 1-4pm in the Baskin Engineering Courtyard. Join us! \nThis year\, we’re expanding with even more performances\, activities\, and creative ways to celebrate UCSC’s vibrant\, diverse\, and excellent STEM culture!  \nWhat to expect: \n\nCuban Dance Master Susana Arenas and her troupe of Orisha dancers led by Cuban Drum Master Toribio Garcia return for a rousing\, communal dance\n\nStudent performers: Los Mejicas and their traditional baile folklórico followed by an open dance lesson/performance by Slug N’ Boots\n\nSTEM-themed drag performances and spoken word poetry by student creatives \n\nAssociate Vice Chancellor for Student Success and Equity Dr. Ebonee Williams (Chemical Engineering\, University of Washington ‘04) will share an inspirational talk on “Bringing our whole selves to STEM!”\n\nEl Buen Taco and Falafel Santa Cruz will be serving delicious food\, completely FREE for all attendees who engage with the student orgs and their activities\n\nMore than just your standard student organization tabling: Games\, interactive demos\, culturally themed activities\, and opportunities to learn more about clubs from all over campus \n\nRaffle for gift cards to be awarded every hour from 1-4pm – must be present to win! \n\nThis event will take place in the Baskin Engineering Courtyard and will be open to all UCSC students\, staff\, and faculty. \nThe STEM Culture Festival celebrates and elevates the many backgrounds\, cultures\, and identities that intersect with our work as scientists\, engineers\, educators\, and members of the UCSC community. It is a rare opportunity when all of UCSC is invited to meet at the engineering school for a time of joy and togetherness. We enthusiastically invite you to attend and be in community with us – especially now in these tumultuous times of division and disunity.  \nThis event represents a collaboration between Baskin Engineering\, the Women’s Center\, the Lionel Cantú Queer Resource Center\, El Centro Latinx and Chicanx Resource Center\, the Asian American and Pacific Islander Resource Center\, the Physical and Biological Sciences Division\, and the Genomics Institute.
URL:https://events.ucsc.edu/event/stem-culture-festival-2026/
LOCATION:Jack Baskin Engineering\, Baskin Engineering 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Concerts,Performances,Social Gathering,Undergraduate
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260514T114000
DTEND;TZID=America/Los_Angeles:20260514T131500
DTSTAMP:20260506T210719Z
CREATED:20260506T202824Z
LAST-MODIFIED:20260506T210719Z
UID:10014614-1778758800-1778764500@events.ucsc.edu
SUMMARY:BME 280B Seminar: Speaker Dr. Magdalena Zernicka-Goetz - "How Embryos Build Themselves: Rules of Self-Organization"
DESCRIPTION:Presenter: Dr. Magdalena Zernicka-Goetz\, Bren Professor of Biology and Biological Engineering\, California Institute of Technology \nDescription: N/A \nBio: Magdalena Zernicka-Goetz is a Bren Professor of Biology and Biological Engineering at the California Institute of Technology. Over the past 25 years\, the Zernicka-Goetz Lab has pioneered key discoveries in early mammalian development\, including the first studies of post-implantation human embryo development in vitro\, insights into the origins of cell fate specification in mouse and human embryos\, and the creation of the first stem cell-derived embryo models using multiple stem cell types. By uncovering fundamental principles that regulate cell identity\, pluripotency\, and self-organization\, the lab continues to advance our understanding of embryo development with broad implications for fertility\, regenerative medicine\, and stem cell biology. \nHosted by: Professor Ali Shariati\, BME Department \nhttps://zernickagoetzlab.com/
URL:https://events.ucsc.edu/event/bme-280b-seminar-speaker-dr-magdalena-zernicka-goetz-how-embryos-build-themselves-rules-of-self-organization/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260513T132000
DTEND;TZID=America/Los_Angeles:20260513T142500
DTSTAMP:20260507T203232Z
CREATED:20260507T203136Z
LAST-MODIFIED:20260507T203232Z
UID:10014620-1778678400-1778682300@events.ucsc.edu
SUMMARY:BME80G Seminar – Susanne Haga\, "Ethics of AI in Genomic Medicine"
DESCRIPTION:Presenter: Dr. Susanne Haga\, Professor in Medicine @ Duke University\n\n\nAbout the speaker: Dr. Haga’s research focuses on the translation of genomics into clinical practice. A central theme across her work is education\, spanning professional\, public\, and patient audiences. Her projects have encompassed the development of educational materials on genomic research\, pharmacogenetic testing\, and the communication of genetic test results. She also teaches at the undergraduate level\, with courses covering genetics and genomics\, ethics\, and policy.\n\nLocation: Jack Baskin Auditorium 101 @ 1:20 – 2:25 PM\n\nHosted by: Professor Karen Miga\, BME Department
URL:https://events.ucsc.edu/event/bme80g-seminar-susanne-haga-ethics-of-ai-in-genomic-medicine/
LOCATION:Jack Baskin Auditorium\, 191 Baskin Cir\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260508T132000
DTEND;TZID=America/Los_Angeles:20260508T142500
DTSTAMP:20260504T172423Z
CREATED:20260504T172423Z
LAST-MODIFIED:20260504T172423Z
UID:10014544-1778246400-1778250300@events.ucsc.edu
SUMMARY:BME80G Seminar - Aubrey Streit Krug\, "Living Roots: Perennial Grain Agriculture and Ethics of Care & Repair"
DESCRIPTION:Presenter: Aubrey Streit Krug; Director of the Perennial Cultures Lab at The Land Institute \n  \nAbout the speaker: Aubrey Streit Krug is a writer and researcher who investigates relationships among humans\, plants\, and places. She is the Director of the Perennial Cultures Lab at The Land Institute. She leads a team devoted to collaboratively advancing social and cultural research and educational efforts like civic science that feature transdisciplinary learning with communities to help realize more just\, diverse\, and perennial agricultures. Aubrey loves rocky prairie hillsides and holds a PhD in English & Great Plains Studies. Her most recent project\, co-edited with Liz Carlisle\, is the collection Living Roots: The Promise of Perennial Foods. \n  \nHosted by: Professor Karen Miga\, BME Department
URL:https://events.ucsc.edu/event/bme80g-seminar-aubrey-streit-krug-living-roots-perennial-grain-agriculture-and-ethics-of-care-repair/
LOCATION:Jack Baskin Auditorium\, 191 Baskin Cir\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
END:VCALENDAR