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DTSTART;TZID=America/Los_Angeles:20260603T130000
DTEND;TZID=America/Los_Angeles:20260603T170000
DTSTAMP:20260529T164521Z
CREATED:20260529T164521Z
LAST-MODIFIED:20260529T164521Z
UID:10014860-1780491600-1780506000@live-events-ucsc.pantheonsite.io
SUMMARY:22nd Annual Graduate Research Symposium
DESCRIPTION:This event celebrates and highlights the work of UCSC graduate students in all academic divisions. Enrolled graduate students will present either a poster\, talk\, or mixed media presentation. Judges will select and award a top prize for each academic division. This event is free and open to the public. \nLocation : Science Hill\nResearch talks will be scheduled in BioMed 200\, BioMed 300 and PSB 240 from 1:00 – 2:30 PM\nThe poster session will be outside on the Plaza between PSB and the Science & Engineering Library\, 2:30 – 4:00 PM
URL:https://live-events-ucsc.pantheonsite.io/event/22nd-annual-graduate-research-symposium/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260603T090000
DTEND;TZID=America/Los_Angeles:20260603T110000
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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://live-events-ucsc.pantheonsite.io/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:20260528T114000
DTEND;TZID=America/Los_Angeles:20260528T131500
DTSTAMP:20260522T170730Z
CREATED:20260522T170730Z
LAST-MODIFIED:20260522T170730Z
UID:10014864-1779968400-1779974100@live-events-ucsc.pantheonsite.io
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://live-events-ucsc.pantheonsite.io/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@live-events-ucsc.pantheonsite.io
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://live-events-ucsc.pantheonsite.io/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:20260519T133000
DTEND;TZID=America/Los_Angeles:20260519T153000
DTSTAMP:20260512T163246Z
CREATED:20260512T161808Z
LAST-MODIFIED:20260512T163246Z
UID:10014626-1779197400-1779204600@live-events-ucsc.pantheonsite.io
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://live-events-ucsc.pantheonsite.io/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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END:VEVENT
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@live-events-ucsc.pantheonsite.io
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://live-events-ucsc.pantheonsite.io/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
ATTACH;FMTTYPE=image/jpeg:https://live-events-ucsc.pantheonsite.io/wp-content/uploads/2026/05/BME-280B-Seminar-1.jpg
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260507T114000
DTEND;TZID=America/Los_Angeles:20260507T131500
DTSTAMP:20260506T220532Z
CREATED:20260506T220532Z
LAST-MODIFIED:20260506T220532Z
UID:10014615-1778154000-1778159700@live-events-ucsc.pantheonsite.io
SUMMARY:BME 280B Seminar: 4th Year Grad Talks
DESCRIPTION:Please join us for our BME 280B seminar series Thursday (5/7/26) 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\n11:40AM – 11:50AM: Jodie Jacobs\n\nTopic/Title: Impact of Wolbachia infection on host gene expression in pseudotime\n\n\n11:53AM – 12:03PM: Ariana Cisneros\n\nTopic/Title: Engineering tunable interregional inter-regional neural circuits in vitro\n\n\n12:06PM – 12:16PM: Liam Tran\n\nTopic/Title: Polysome Shadowing: A Long-Read Sequencing Approach to Study Translation\n\n\n12:19PM – 12:29PM: Samira Vera\n\nTopic/Title: TBD\n\n\n12:32PM – 12:42PM: Seungho Lee\n\nTopic/Title: TBD
URL:https://live-events-ucsc.pantheonsite.io/event/bme-280b-seminar-4th-year-grad-talks/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260423T114000
DTEND;TZID=America/Los_Angeles:20260423T131500
DTSTAMP:20260423T163021Z
CREATED:20260423T150019Z
LAST-MODIFIED:20260423T163021Z
UID:10013983-1776944400-1776950100@live-events-ucsc.pantheonsite.io
SUMMARY:BME 280B Seminar: Speaker Dr. Aaron Newman - Molecular and spatial determinants of single-cell developmental states in cancer
DESCRIPTION:Presenter: Dr. Newman\, Associate Professor in the Department of Biomedical Data Science\, Stanford University \n  \nDescription: Determining the factors that shape cell potency—the ability of a cell to differentiate into other cell types—is essential for understanding tissue biology in health and disease\, including cancer. In previous work\, we found that single-cell transcriptional diversity decreases across developmental time\, from the fertilized egg to the most mature cells in the body\, and in multiple organisms. More recently\, we developed CytoTRACE 2\, an interpretable AI framework trained on millions of data points from single-cell RNA sequencing data\, to determine cell potency on an absolute scale and reveal molecular hallmarks of developmental potential. We are now leveraging this method along with advances in spatial transcriptomics\, to identify multicellular ecosystems linked to cancer cell differentiation states and clinical outcomes. I will highlight these tools along with our ongoing work to decode cell plasticity and clinically relevant spatial microenvironments in human malignancies. \n  \nBio: Dr. Newman is an Associate Professor in the Department of Biomedical Data Science at Stanford University and a Chan Zuckerberg Biohub Investigator. He is also a member of the Stanford Cancer Institute and the Stanford Institute for Stem Cell Biology and Regenerative Medicine. Dr. Newman has made significant contributions to computational biology with applications to liquid biopsy\, cancer genomics\, and tumor immunology. Key contributions include CAPP-Seq for ultrasensitive detection of circulating tumor DNA; CIBERSORT/x for decoding cellular composition from bulk genomic data; CytoTRACE/2 for inferring cellular differentiation states from scRNA-seq data; and EcoTyper for delineating context-dependent cellular ecosystems from bulk\, single-cell\, and spatial expression data. His research program focuses on developing innovative data science tools to study the phenotypic diversity\, differentiation hierarchies\, and clinical significance of tumor cells and their surrounding microenvironments. Key results are further explored experimentally\, both in the lab and through collaboration\, with the goal of translating promising findings into the clinic.  \nHosted by: Professor Camilla Forsberg\, BME Department
URL:https://live-events-ucsc.pantheonsite.io/event/molecular-and-spatial-determinants-of-single-cell-developmental-states-in-cancer/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Lectures & Presentations,Seminars
ATTACH;FMTTYPE=image/jpeg:https://live-events-ucsc.pantheonsite.io/wp-content/uploads/2026/04/BME-280B-Seminar-04232026.jpg
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260402T114000
DTEND;TZID=America/Los_Angeles:20260402T131500
DTSTAMP:20260401T004313Z
CREATED:20260401T004313Z
LAST-MODIFIED:20260401T004313Z
UID:10011828-1775130000-1775135700@live-events-ucsc.pantheonsite.io
SUMMARY:BME 280B Seminar: Small changes\, Big consequences: Modulators of Alphavirus Assembly
DESCRIPTION:Presenter: Dr. Suchetana (Tuli) Mukhopadhyay\, Professor\, Indiana University \nDescription: N/A \nBio: Suchetana “Tuli” Mukhopadhyay\, Ph.D.\, is a professor in the Department of Biology at Indiana University\, Bloomington. She received her B.A. in chemistry from DePauw University and her Ph.D. in chemistry from the University of Illinois at Chicago. Following her doctoral studies\, Mukhopadhyay conducted postdoctoral research at the University of Texas Southwestern Medical Center\, focusing on G-protein mediated signaling. She continued her postdoctoral work at Purdue University in structural virology\, where she developed a strong interest in arboviruses. Mukhopadhyay joined Indiana University in 2005\, where she established her research program on the assembly and spread of alphaviruses. \nHosted by: Professor Rebecca Dubois\, BME Department
URL:https://live-events-ucsc.pantheonsite.io/event/bme-280b-seminar-small-changes-big-consequences-modulators-of-alphavirus-assembly/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Lectures & Presentations,Seminars
ATTACH;FMTTYPE=image/jpeg:https://live-events-ucsc.pantheonsite.io/wp-content/uploads/2026/03/mukhopadhyay-tuli-mar28-2017.jpg
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20251211T090000
DTEND;TZID=America/Los_Angeles:20251211T110000
DTSTAMP:20251209T161343Z
CREATED:20251202T162054Z
LAST-MODIFIED:20251209T161343Z
UID:10005717-1765443600-1765450800@live-events-ucsc.pantheonsite.io
SUMMARY:Tran\, L. (BMEB) -  Polysome Shadowing: A Long-Read Sequencing Approach to Study Translation
DESCRIPTION:Translation is a central and highly regulated step of gene expression\, yet there are few quantitative\, high-throughput tools to study translation. Existing methods such as sucrose gradients provide only bulk ribosome counts\, while Ribo-Seq offers positional information in the genome but destroys long-range structure and transcript expression information. Because of these limitations\, many fundamental questions about mRNA translation into protein remain difficult to assay. In this proposal\, I outline my plans to develop a novel technology\, deemed Polysome Shadowing\, that covalently marks ribosome-unprotected regions of RNA with hyperactive base editors. Because ribosomes protect ~21–30 nt regions of mRNAs\, ribosome “shadows” appear as tracts of unedited bases in long-read sequencing. In Aim 1\, I will identify ribosome shadows on single molecules by increasing editing efficiency through optimization of dual cytosine and adenosine base editors and statistical modeling. In Aim 2\, I will maximize the accuracy of information recovered from highly-edited RNAs by developing a multipass library preparation protocol to generate high-confidence reads. In Aim 3\, I will apply the tools I have already developed to examine previously difficult-to-assay paradigms of translational control in the form of viral frameshifting mechanisms. Together\, completion of these aims will build an information-rich sequencing technology capable of positioning ribosomes on intact mRNAs while preserving long-range information and establish feasibility to study nascent paradigms. \nHost: Liam Tran\, Ph.D. Student\, Biomolecular Engineering and Bioinformatics  \nAdvisor: Joshua Arribere 
URL:https://live-events-ucsc.pantheonsite.io/event/tran-l-bmeb-polysome-shadowing-a-long-read-sequencing-approach-to-study-translation/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20250828T110000
DTEND;TZID=America/Los_Angeles:20250828T110000
DTSTAMP:20250925T231433Z
CREATED:20250821T070000Z
LAST-MODIFIED:20250925T231433Z
UID:10000119-1756378800-1756378800@live-events-ucsc.pantheonsite.io
SUMMARY:Shanks\, C. (BMEB) -  Development and Application of Local Ancestry Methods for Population Genomics
DESCRIPTION:Local ancestry methods classify the segments of DNA inherited from a specific ancestry (e.g.\, African\, East Asian\, European)\, improving analyses of admixed populations. Aim 1 applies ancestry-specific analysis to more than 1000 whole genome sequences across Polynesia\, revealing strong bottlenecks in the voyagers who settled both Hawaiʻi and Rapa Nui\, and confirming frequencies of Mendelian disease–causing variants in French Polynesia not found even in large-scale biobanks. Conventional local ancestry methods are only accurate for deeply diverged populations and recent admixture events. In aim 2 I present ARGMix\, a new deep-learning approach incorporating ancestral recombination graphs (ARGs)\, which contains the inferred history of coalescent events with recombination. This method classifies the local ancestry of present day Europeans as originating from early European farmers and hunter gather ancestries. As an application I find evidence of continuity between Ötzi the Iceman and present-day Europeans of similar geography. I further propose to apply ARGMix to trace the TCC/TTC mutational pulse strongest in Europeans across geography and time. In aim 3 I present a method incorporating these ancient local ancestries to improve polygenic risk scores in the UK biobank. \nEvent Host: Cole Shanks\, Ph.D Student\, Biomolecular Engineering & Bioinformatics
URL:https://live-events-ucsc.pantheonsite.io/event/shanks-c-bmeb-development-and-application-of-local-ancestry-methods-for-population-genomics/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20250827T120000
DTEND;TZID=America/Los_Angeles:20250827T120000
DTSTAMP:20250925T231630Z
CREATED:20250819T070000Z
LAST-MODIFIED:20250925T231630Z
UID:10000116-1756296000-1756296000@live-events-ucsc.pantheonsite.io
SUMMARY:Leavitt\, J. (BMEB) - Evolutionary Dynamics\, Functional Adaptations in Stress Response\, and Direct Detection of tRNA modifications in Archaea
DESCRIPTION:Transfer RNA (tRNA) modifications are essential for structural integrity\, decoding fidelity\, and stress adaptation\, yet their dynamics across phylogenetically distinct archaeal species and their functional roles during stress remain incompletely understood. This dissertation aims to address some of these gaps through a multi-scale investigation that spans the evolutionary dynamics\, stress-responsive functions\, and direct detection of archaeal tRNA modifications. The first chapter maps this unexplored landscape by applying Ordered Two-Template Relay sequencing (OTTR-seq) across nine archaeal species from diverse and extreme environments. This comparative analysis revealed previously unrecognized\, coordinated modification patterns\, including mutually exclusive methylation patterns in the acceptor stem of hyperthermophiles. Additional comparisons revealed co-evolution of tRNA modifying enzymes\, demonstrating how their domain architectures and substrate specificities have diverged to shape lineage-specific adaptations. Building on these evolutionary observations\, the second chapter investigates the functional role of tRNA modifications in the stress responses of the model halophile Haloferax volcanii. This work reveals how tRNA modification dynamics might balance structural stability against flexibility to manage stress\, focusing on N2\,N2-dimethylguanosine (m22G) at position 26. By integrating tRNA sequencing\, proteomics\, and codon usage data within a linear mixed-effects model\, this work quantifies how the m22G modification status fine-tunes the translation of specific\, codon-biased genes\, establishing it as a modulator of the adaptive stress response. Addressing limitations of reverse-transcription (RT)-based sequencing methods for detecting modifications\, the final chapter explores the use of direct RNA nanopore sequencing. The focus is on archaeosine (G+)\, a modification unique to Archaea that is inaccessible to RT-based sequencing methods. The resulting custom model accurately detects archaeosine in its native species. However\, cross-species comparisons reveal significant challenges with species-specific overfitting\, providing insights into development of universally applicable modification callers. \nEvent Host: Jesse Leavitt\, Ph.D Candidate\, Biomolecular Engineering & Bioinformatics
URL:https://live-events-ucsc.pantheonsite.io/event/leavitt-j-bmeb-evolutionary-dynamics-functional-adaptations-in-stress-response-and-direct-detection-of-trna-modifications-in-archaea/
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
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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
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