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DTSTART;TZID=America/Los_Angeles:20260519T100000
DTEND;TZID=America/Los_Angeles:20260519T120000
DTSTAMP:20260623T082047
CREATED:20260512T163057Z
LAST-MODIFIED:20260512T163057Z
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SUMMARY:Paul Pena\, D. (CSE) - Efficient Pattern Counting in Sparse Graphs and Hypergraphs
DESCRIPTION:Pattern counting is a fundamental problem in computer science with applications in many domains. For a fixed small pattern H\, we are given a large graph G and we are asked to count the number of subgraphs or homomorphisms (edge-preserving maps) of H in G. For practical applications where the input graph can be very large\, we are interested in finding efficient algorithms\, that is\, algorithms that run in linear or subquadratic time with respect to the size of the input. \nFinding such algorithms in general (when G can be any graph) is not possible. Instead\, we restrict our input to sparse classes of graphs. One family of graph classes that has been widely studied in the context of subgraph and homomorphism counting is bounded-degeneracy graph classes. Real-world graphs in many domains have bounded degeneracy\, so studying these classes in theory can lead to practical algorithms. \nA series of advances in the study of homomorphism counting led to a dichotomy theorem that exactly characterized which patterns were linear-time computable for bounded-degeneracy inputs. This dissertation builds on this result\, extending it to other variants of this problem\, and generalizing it to other different settings\, like counting hypergraphs and notions of sparsity beyond degeneracy. \nOur results help develop the theory of subgraph counting in sparse graphs and hypergraphs\, and showcase how sparsity can be used both in theory and practice to develop faster algorithms. \n  \nEvent Host: Daniel Paul Pena\, Ph.D. Candidate\, Computer Science & Engineering  \nAdvisor: C. Sheshadhri \nZoom: https://ucsc.zoom.us/j/97685906168?pwd=O35brsWilyn2m8AgMn0dKgALBe6wi1.1
URL:https://events.ucsc.edu/event/paul-pena-d-cse-efficient-pattern-counting-in-sparse-graphs-and-hypergraphs/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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DTSTART;TZID=America/Los_Angeles:20260519T133000
DTEND;TZID=America/Los_Angeles:20260519T153000
DTSTAMP:20260623T082047
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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DTSTART;TZID=America/Los_Angeles:20260520T080000
DTEND;TZID=America/Los_Angeles:20260520T100000
DTSTAMP:20260623T082047
CREATED:20260422T160446Z
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SUMMARY:Maram\, S. (CM) - Scripture To Console: The Nexus between Religion and Digital Play
DESCRIPTION:Religion has historically been a profound force for global mobilization\, shaping geopolitics\, economies\, and geography. Similarly\, contemporary interactive media\, with video games at the forefront\, has moved beyond mere entertainment to become a powerful vehicle for communication\, narrative\, and inspiration\, reaching millions worldwide. This dissertation investigates the intersection of these two influential forces: religion and video games\, demonstrating the influence of religion on video games\, the influence of video games on religion\, and finally\, how these two powerful mobilization forces can come together to solve global challenges. \nFirst\, I examine the current landscape of religious representation in commercial video games (e.g.\, Assassin’s Creed\, SMITE). I analyze how key stakeholders i.e. players\, game designers\, and development studios\, interpret and engage with embedded religious elements\, drawing on existing critical reception and player discourse. This analysis identifies common narrative pitfalls and successful strategies for incorporating complex religious themes in digital spaces\, culminating in proposed design frameworks for sensitive and effective representation. \nBuilding on this foundational work\, the thesis culminates in defining and validating a new interaction paradigm where learning meets religion through play. This paradigm focuses on intentionally leveraging religious content i.e. specifically its rituals and narratives as mechanics in serious games to drive motivation and learning toward collective action. I validate this paradigm through a comprehensive case study focused on climate change\, arguably the most pressing issue of the modern era. This involves the design and empirical discussion of a serious game that incorporates specific religious mechanics\, ethics\, and narratives (e.g.\, stewardship\, ritual) to effectively communicate the severity of the climate crisis and motivate stakeholders toward a collective solution. \n  \nEvent Host: Sai Siddartha Maram\, Ph.D. Candidate\, Computational Media \nAdvisor: Magy Seif El-Nasr \nZoom: https://ucsc.zoom.us/j/91946426300?pwd=wxe1x3YCRsXrtcvOSy2kmfC9dZ3inW.1 \nPasscode: 558570
URL:https://events.ucsc.edu/event/maram-s-cm-scripture-to-console-the-nexus-between-religion-and-digital-play/
LOCATION:
CATEGORIES:Ph.D. Presentations
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260520T090000
DTEND;TZID=America/Los_Angeles:20260520T110000
DTSTAMP:20260623T082047
CREATED:20260507T160500Z
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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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