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DTSTART;TZID=America/Los_Angeles:20250806T170000
DTEND;TZID=America/Los_Angeles:20250806T170000
DTSTAMP:20250925T231316Z
CREATED:20250703T070000Z
LAST-MODIFIED:20250925T231316Z
UID:10000060-1754499600-1754499600@live-events-ucsc.pantheonsite.io
SUMMARY:Exploring your science major
DESCRIPTION:Choosing a major can feel overwhelming\, but many science students share a common academic path in their first year. This session breaks down the similarities in core coursework\, introduces the range of science majors available\, and helps you begin thinking about where your interests align. To receive a Zoom link\, register HERE.
URL:https://live-events-ucsc.pantheonsite.io/event/exploring-your-science-major/
LOCATION:CA
CATEGORIES:Lectures & Presentations,Meetings & Conferences
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20250807T103000
DTEND;TZID=America/Los_Angeles:20250807T103000
DTSTAMP:20250925T231625Z
CREATED:20250805T070000Z
LAST-MODIFIED:20250925T231625Z
UID:10000091-1754562600-1754562600@live-events-ucsc.pantheonsite.io
SUMMARY:Rose\, N. (BMEB) - MACHINE LEARNING MODELS FOR T CELL RECEPTOR TARGET DISCOVERY AND AFFINITY ENGINEERING
DESCRIPTION:T cell receptors (TCRs) mediate antigen-specific immune responses through recognition of peptides presented by major histocompatibility complex (pMHC) molecules. Accurately predicting TCR–pMHC interactions remains a major barrier to TCR-based immunotherapy\, due to limitations in current models that fail to generalize beyond common viral epitopes and well-characterized HLA alleles. In this PhD proposal\, I outline a computational framework that integrates deep learning\, structural modeling\, and molecular simulation to improve TCR–pMHC prediction and discovery. I first introduce TRIOPS\, a convolutional neural network trained on harmonized\, experimentally validated data to predict MHC restriction from TCR sequence alone. TRIOPS outperforms state-of-the-art models in both held-out evaluation and independent patient datasets\, demonstrating improved accuracy in assigning TCRs to their correct restricting MHC alleles. I then propose TRILOBITE\, a two-part structure-based model combining atomic-resolution graph representations and dynamics-derived biophysical features to classify TCR–pMHC binding and estimate affinity. Finally\, I propose an end-to-end pipeline to identify tumor-reactive TCRs from patient-derived sequencing data by integrating HLA typing\, antigen prediction\, structure generation\, and binding assessment. Applied to a pan-cancer atlas of over 1.2 million T cells\, this framework will enable high-throughput\, structure-informed TCR discovery across diverse HLA backgrounds. Together\, these aims address a critical need for scalable\, mechanistically grounded methods for mapping T cell specificity to accelerate cancer immunotherapy discovery. \nEvent Host: Nicholas Rose\, PhD student\, Biomolecular Engineering & Bioinformatics \nAdvisor: Vanessa Jonsson
URL:https://live-events-ucsc.pantheonsite.io/event/rose-n-bmeb-machine-learning-models-for-t-cell-receptor-target-discovery-and-affinity-engineering/
LOCATION:Jack Baskin Engineering\, Baskin Engineering 1156 High Street\, Santa Cruz\, CA\, 95064
GEO:37.000369;-122.0632371
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=Jack Baskin Engineering Baskin Engineering 1156 High Street Santa Cruz CA 95064;X-APPLE-RADIUS=500;X-TITLE=Baskin Engineering 1156 High Street:geo:-122.0632371,37.000369
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DTSTART;TZID=America/Los_Angeles:20250807T173000
DTEND;TZID=America/Los_Angeles:20250807T173000
DTSTAMP:20250925T231620Z
CREATED:20250702T070000Z
LAST-MODIFIED:20250925T231620Z
UID:10000055-1754587800-1754587800@live-events-ucsc.pantheonsite.io
SUMMARY:Slugs at Sundown - The Art of the Career Pivot
DESCRIPTION:Thinking about making a career change? Join fellow Banana Slugs for an evening of connection and guidance from professional career coaches. Learn how to navigate transitions with confidence\, gain practical strategies\, and get inspired to take the next step in your journey—whether you’re pivoting by choice or by chance. \nBonus: Come early for a 15-minute\, one-on-one resume review—available from 4:30 to 5:30 PM.
URL:https://live-events-ucsc.pantheonsite.io/event/slugs-at-sundown-the-art-of-the-career-pivot/
LOCATION:Silicon Valley Campus\, 3175 Bowers Avenue\, Santa Clara\, CA\, 95054\, United States
CATEGORIES:Meetings & Conferences
GEO:37.3796975;-121.9765484
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=Silicon Valley Campus 3175 Bowers Avenue Santa Clara CA 95054 United States;X-APPLE-RADIUS=500;X-TITLE=3175 Bowers Avenue:geo:-121.9765484,37.3796975
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20250808T140000
DTEND;TZID=America/Los_Angeles:20250808T140000
DTSTAMP:20250925T231427Z
CREATED:20250801T070000Z
LAST-MODIFIED:20250925T231427Z
UID:10000087-1754661600-1754661600@live-events-ucsc.pantheonsite.io
SUMMARY:Katte\, P. (BMEB) - Interactive and Scalable Frameworks for Pathogen Surveillance and Ancestral Recombination Graph
DESCRIPTION:The explosive growth of genomic data\, driven by advances in sequencing and inference technologies\, presents both an opportunity and a challenge for evolutionary biology and public health. Existing visualization and analysis tools often fall short in handling the scale\, complexity\, and uncertainty of modern genomic datasets—especially in the areas of pathogen surveillance and ancestral recombination inference. This thesis introduces new tools that provide scalable visualization and analysis to bridge these gaps and enable more interpretable and actionable genomic insights. \nFirst\, I develop an interactive dashboard within a tool called WEPP for wastewater-based pathogen surveillance. It combines phylogenetic placement with intuitive web-based visualization\, allowing public health officials to track variant spread at high resolution. Second\, I build Lorax\, a browser-based platform for visualizing Ancestral Recombination Graphs (ARGs) at biobank scale. Lorax incorporates a multi-agent system that supports natural language querying\, code generation\, and interactive tree exploration. Finally\, I introduce a novel inference framework based on Generative Flow Networks to sample from posterior distributions over ARGs\, addressing key limitations in uncertainty quantification and scalability found in existing methods. Together\, these tools aim to make the study of evolution and disease more accessible and effective\, helping researchers and public health teams draw clearer conclusions from complex genetic data. \nEvent Host: Pratik Katte\, PhD Student\, Biomolecular Engineering & Bioinformatics \nAdvisor: Russ Corbett-Detig
URL:https://live-events-ucsc.pantheonsite.io/event/katte-p-bmeb-interactive-and-scalable-frameworks-for-pathogen-surveillance-and-ancestral-recombination-graph/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
GEO:46.1226939;-64.7891251
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=Biomedical Sciences Building 575 McLaughlin Drive;X-APPLE-RADIUS=500;X-TITLE=575 McLaughlin Drive:geo:-64.7891251,46.1226939
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20250808T150000
DTEND;TZID=America/Los_Angeles:20250808T150000
DTSTAMP:20250925T231428Z
CREATED:20250805T070000Z
LAST-MODIFIED:20250925T231428Z
UID:10000090-1754665200-1754665200@live-events-ucsc.pantheonsite.io
SUMMARY:Vera-Choqqueccota\, S. (BMEB) - A CRISPRi-Based platform for multimodal functional analysis of neurodevelopmental and neuropsychiatric disorders risk genes in engineered mouse cortical neurons
DESCRIPTION:Neurodevelopmental and neuropsychiatric disorders (NPDs)\, such as autism spectrum disorder and schizophrenia\, are among the most heritable yet mechanistically complex conditions. While large-scale genomic studies have identified hundreds of high-confidence risk genes\, the lack of scalable and integrative platforms has limited our ability to functionally characterize these genes. To address this\, I am developing a CRISPR interference (CRISPRi)-based screening platform using mouse embryonic stem cells (mESCs) engineered to express Ngn2 for rapid and standardized neuronal differentiation and dCas9-KRAB for gene repression. In Aim 1\, I will generate and validate this cell line\, enabling reproducible and scalable perturbation of disease-relevant genes. In Aim 2\, I will apply this system to characterize the effects of knocking down ten NPD-risk genes using multimodal analysis of morphology\, transcriptomics\, and electrophysiology. In Aim 3\, I will build a framework to crowdsource functional analysis of NPD risk genes to design gRNAs\, access experiments remotely\, and analyze data using simplified\, accessible tools. Together\, this project advances both scientific understanding of NPD mechanisms and equitable access to functional analysis. \nEvent Host: Samira Vera-Choqqueccota\, PhD Student\, Biomolecular Engineering & Bioinformatics \nAdvisor: David Haussler
URL:https://live-events-ucsc.pantheonsite.io/event/vera-choqqueccota-s-bmeb-a-crispri-based-platform-for-multimodal-functional-analysis-of-neurodevelopmental-and-neuropsychiatric-disorders-risk-genes-in-engineered-mouse-cortical-neurons/
LOCATION:CA
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