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DTSTART;TZID=America/Los_Angeles:20260519T100000
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DTSTAMP: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:20260512T163246Z
CREATED:20260512T161808Z
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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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