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DTSTART;TZID=America/Los_Angeles:20250808T140000
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DTSTAMP:20260512T053628
CREATED:20250801T070000Z
LAST-MODIFIED:20250925T231427Z
UID:10000087-1754661600-1754661600@events.ucsc.edu
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://events.ucsc.edu/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
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DTSTART;TZID=America/Los_Angeles:20250808T150000
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CREATED:20250805T070000Z
LAST-MODIFIED:20250925T231428Z
UID:10000090-1754665200-1754665200@events.ucsc.edu
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://events.ucsc.edu/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/
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