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DTSTART;TZID=America/Los_Angeles:20260312T114000
DTEND;TZID=America/Los_Angeles:20260312T131500
DTSTAMP:20260423T170907
CREATED:20260303T000204Z
LAST-MODIFIED:20260303T000204Z
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SUMMARY:BME 280B Seminar: Modulating Insulin Receptor Through New Ligands
DESCRIPTION:Presenter: Danny Chou\, Associate Professor of Pediatrics\, Stanford University \nDescription: Since its discovery in 1921\, insulin has been at the forefront of scientific breakthroughs. From its amino acid sequencing to the revelation of its three‐dimensional structure\, the progress in insulin research has spurred significant therapeutic breakthroughs. In recent years\, protein engineering has introduced innovative chemical and enzymatic methods for insulin modification\, fostering the development of therapeutics with tailored pharmacological profiles. In this seminar\, I will highlight the use of new ligands to modulate insulin receptors and discuss how they continue to shape the future trajectory of insulin research. \nBio: Danny Chou is an Associate Professor of Pediatrics and by courtesy\, of Chemical & Systems Biology at Stanford University. He is an affinity group leader at Stanford Diabetes Research Center. His research interests lie in the intersection of peptide therapeutics and metabolic diseases. He started his independent career as an assistant professor of biochemistry at University of Utah in 2014. He moved his lab to Stanford University in 2020 and continued their pursuit of using peptide and protein chemistry to develop therapeutics to address unmet needs.  \nHosted by: Professor Andy Yeh\, BME Department
URL:https://events.ucsc.edu/event/bme-280b-seminar-modulating-insulin-receptor-through-new-ligands/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260226T114000
DTEND;TZID=America/Los_Angeles:20260226T131500
DTSTAMP:20260423T170907
CREATED:20260212T231636Z
LAST-MODIFIED:20260212T231636Z
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SUMMARY:BME 280B Seminar: The evolution of structural variation across vertebrate genomes
DESCRIPTION:Presenter: Peter Sudmant\, Assistant Professor of Integrative Biology\, University of California\, Berkeley \nDescription: Structural variants (SVs) contribute substantially to genetic variation and play vital roles in adaptation and disease. However\, SVs are poorly captured by short read sequencing and thus are understudied\, particularly in non-model organisms. Here\, taking advantage of recently generated haplotype-resolved genome assemblies from >600 vertebrate species\, we present the most comprehensive survey of the diversity of SVs and single nucleotide variants (SNVs) across the vertebrate tree of life to date. \nBio: Peter Sudmant is an Assistant Professor of Integrative Biology at the University of California Berkeley. Prior to joining UC Berkeley\, Dr Sudmant completed his PhD at the University of Washington in the Lab of Dr Evan Eichler as HHMI International Fellow. Dr Sudmant went on to complete a postdoc with Christopher Burge at MIT as a Genentech fellow of the Life Sciences Research Foundation. Dr Sudmant is a recipient of the American Foundation for Aging Research Junior Faculty Award and a Hellman Fellow. \nHosted by: Professor Russ Corbett-Detig\, BME Department
URL:https://events.ucsc.edu/event/bme-280b-seminar-the-evolution-of-structural-variation-across-vertebrate-genomes/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260212T114000
DTEND;TZID=America/Los_Angeles:20260212T133000
DTSTAMP:20260423T170907
CREATED:20260211T234225Z
LAST-MODIFIED:20260211T234252Z
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SUMMARY:BME Seminar: Population Genetics in an Era of Genomic Health
DESCRIPTION:Presenter: Dr. Eimear Kenny\, Founding Director of the Institute for Genomic Health and a Endowed Chair and Professor for Genomic Health at the Icahn School of Medicine at Mount Sinai \nDescription: The overarching goal of my work is to advance genomics in medicine and research through diversity and innovation. The work of my group seeks to enrich our understanding of human genomic diversity by focusing on populations underrepresented in genomics\, developing and disseminating computational genomic tools to enhance precision and accuracy in diverse populations\, unveiling genetic architectures of diseases that can track with demographic history\, and advancing diversity large-scale genomic databases. We also work to integrate new paradigms of genomic medicine into routine clinical practice\, ensuring genomic insights are appropriately applied in real-world healthcare settings and lead to improved patient care and health equity. I will discuss aspects of this work with emphasis on why we should promote inclusivity\, innovate methodologies\, and harness the potential of diverse populations in genomic health.  \nBio: Eimear Kenny\, PhD\, is the Founding Director of the Institute for Genomic Health\, building resources for integrating genomic information and AI in routine clinical care\, and supporting the sequencing and return of results to a diverse patients in the Mount Sinai Health System. She also the Founding Director of the Center for Translational Genomics and a Endowed Chair and Professor of Genomic Health\, at the Icahn School of Medicine at Mount Sinai\, working on computational and translational genomic research. She is Principal Investigator in many large NIH-funded international consortium focused on computational genomics and genomic medicine\, including eMERGE\, PRIMED\, CSER\, GSP\, TOPMed\, PAGE\, and HPRC. She is a strong advocate for the importance of diversity in genomic research\, is improving the accessibility of genetics to global populations\, and has led multiple genetics-based clinical trials. Her exceptional contributions to the field earned her the prestigious Early Career Award from the American Society of Human Genetics in 2022. In addition to her academic and research roles\, Dr. Kenny serves as a scientific advisor to various genomic medicine initiatives in government\, non-profit\, and industry sectors. \nHosted by: Professor Karen Miga\, BME Department
URL:https://events.ucsc.edu/event/8123/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260129T114000
DTEND;TZID=America/Los_Angeles:20260129T131500
DTSTAMP:20260423T170907
CREATED:20260122T232352Z
LAST-MODIFIED:20260122T232352Z
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SUMMARY:BME 280B Seminar: Satellite repeats encode megabase-scale transcription factor hubs
DESCRIPTION:Presenter: Matt Franklin\, Postdoctoral Researcher\, Stanford University \nDescription: Eukaryotic genomes contain large stretches of repetitive DNA called satellite DNA\, often found near centromeres and ribosomal DNA regions. In humans\, alpha satellite has well-established roles in centromere biology\, however the functions of other human satellite DNAs remain largely unexplored. \nWe recently identified the Hippo pathway effector TEAD as a novel Human Satellite 3 (HSat3) binding TF. Because HSat3 is highly enriched near ribosomal DNA (rDNA) genes\, we examined whether the Hippo pathway regulates rDNA via HSat3. Our work demonstrates that HSat3 localizes the Hippo factors YAP and TEAD inside the nucleolus\, where YAP directly activates ribosomal RNA (rRNA) transcription. These findings present the first evidence that the Hippo pathway factor YAP directly regulates RNA Polymerase I activity. \nDisparate studies have identified examples of transcription factors that bind repetitive DNA elements through motif recognition. However\, a systematic search for such factors has not been conducted. Using Telomere-to-telomere genome assemblies\, we predicted and validated dozens of new satellite-binding TFs\, many of which are part of highly conserved signaling pathways. Beyond revealing a direct relationship between the Hippo pathway and ribosomal DNA regulation\, this work demonstrates that satellite DNA can encode a broad range of functional motifs\, hinting at new roles for these enormous genomic elements. \nBio: Following his undergraduate studies\, Matt conducted a 1-year research fellowship at EMBL Hamburg\, where he worked on X-ray scattering methods for structural biology. He then earned his PhD in chemical engineering at Stanford University\, where he investigated mechanotransduction and Hippo pathway signaling. Matt continued this research as a postdoc under Kun-Liang Guan at UC San Diego\, where he discovered that Hippo pathway effectors bind repetitive DNA elements. To expand on his newfound interest in repetitive DNA\, Matt returned to Stanford as a postdoctoral researcher under Nicolas Altemose\, where he is studying the functions of satellite repeats as hubs for transcription factor binding. \nHosted by: Professor Karen Miga\, BME Department
URL:https://events.ucsc.edu/event/bme-280b-seminar-satellite-repeats-encode-megabase-scale-transcription-factor-hubs/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260122T114000
DTEND;TZID=America/Los_Angeles:20260122T131500
DTSTAMP:20260423T170907
CREATED:20260115T232014Z
LAST-MODIFIED:20260115T232014Z
UID:10008410-1769082000-1769087700@events.ucsc.edu
SUMMARY:BME Seminar: Rotation Talks
DESCRIPTION:Presenter: Grad Students \nDescription: Rotation Talks \nBio: N/A \nHosted by: Professor Rebecca DuBois\, BME Department
URL:https://events.ucsc.edu/event/bme-seminar-rotation-talks/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260108T114000
DTEND;TZID=America/Los_Angeles:20260108T131500
DTSTAMP:20260423T170907
CREATED:20251216T231619Z
LAST-MODIFIED:20251216T231619Z
UID:10005856-1767872400-1767878100@events.ucsc.edu
SUMMARY:BME 280B Seminar: Nature’s Miniature Masterpieces - Nanobodies as Small but Mighty Antibodies for the next Pandemic
DESCRIPTION:Presenter: Katja Hanack\, Founder and CEO\, New/Era/Mabs \nDescription: Nanobodies combine remarkable simplicity with surprising power. Their small size allows them to reach targets that remain inaccessible to conventional antibodies\, while maintaining high specificity and stability. Their compact architecture allows them to access targets that conventional antibodies cannot reach\, yet they preserve the specificity and power that make antibody therapeutics so transformative. In this talk I will introduce the science behind selma\, a cell based discovery platform developed over more than a decade to rapidly identify high quality antibodies and nanobodies. I will explore why these tiny binders matter\, how they differ from classical antibodies\, and what their unique biology enables for diagnostics and therapeutics. \nThe presentation will conclude with my current project on immune infrastructure and how pre validated nanobody archives can shift the pandemic response from a reactive model to proactive preparedness for future outbreaks. \nBio: Katja Hanack\, PhD\, MBA\, is the Founder and CEO of new/era/mabs and a leading expert in antibody discovery for diagnostic and therapeutic applications\, with a particular focus on nanobody technologies. With more than 20 years of experience\, she has developed pioneering platforms that enable the efficient generation and selection of next-generation monoclonal antibodies and nanobodies. She holds a Biology degree from Humboldt University of Berlin and a PhD in Biotechnology from the University of Potsdam. As a former Professor of Biochemistry and Biology at the University of Potsdam\, she built and led a research group of 25 scientists\, secured over €16 million in external funding\, and authored more than 40 peer-reviewed publications. Since 2017\, Dr. Hanack has contributed to translational innovation as an industrial advisor for SPARK Stanford and SPARK Berlin\, supporting academic teams in bringing biomedical discoveries to patients. \nHosted by: Professor Rebecca Dubois\, BME Department
URL:https://events.ucsc.edu/event/bme-280b-seminar-natures-miniature-masterpieces-nanobodies-as-small-but-mighty-antibodies-for-the-next-pandemic/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20251204T114000
DTEND;TZID=America/Los_Angeles:20251204T131500
DTSTAMP:20260423T170907
CREATED:20251203T194937Z
LAST-MODIFIED:20251203T195447Z
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SUMMARY:BME 280B Seminar: Gali Bai & David Haussler
DESCRIPTION:Presenter 1: Gali Bai\, BME/PBSE Doctoral Candidate\, Brooks Lab\, UC Santa Cruz \nTitle 1: Dissecting the contribution of chromatin accessibility to RNA transcription and processing with long-read sequencing \nDescription: Although all cells in an organism share the same genomic sequence\, transcriptional programs vary dramatically across cell types. This diversity is governed by epigenetic regulation involving the coordinated activities of chromatin remodelers\, histone modifiers\, and histone chaperones that precisely modulate chromatin accessibility. While previous studies have shown that chromatin accessibility at DNase I–hypersensitive sites such as promoters and enhancers is closely associated with gene expression\, much less is known about how chromatin influences transcription and RNA processing. To study how chromatin regulates RNA processing\, we perturbed yeast chromatin accessibility by deleting two highly conserved chromatin remodelers ISW1 and CHD1. With Oxford Nanopore long-read sequencing\, we profiled nascent RNA\, full-length mRNA\, and chromatin fibers in wild-type and chd1 isw1 double-mutant yeast cells. Loss of ISW1 and CHD1 led to increased chromatin accessibility within intragenic regions\, accompanied by aberrant transcription initiation. Leveraging long-read data\, we associated distinct chromatin states with specific RNA processing events and isoform expression outcomes. Despite a similar level of chromatin perturbations across the genome\, genes with low baseline expression showed extensive transcriptional reprogramming\, whereas highly expressed genes remained largely unaffected. These discrepancies can be partially explained by differences in the enrichment of transcription initiation motifs. In intron-containing genes\, loss of ISW1 and CHD1 reduced splicing efficiency and increased intron retention\, likely due to disrupted RNAPII elongation in the double mutant. Together\, our findings highlight the crucial role of ATP-dependent chromatin remodelers in maintaining nucleosome organization and coordinating co-transcriptional RNA processing. \nPresenter 2: David Haussler\, Distinguished Professor\, UC Santa Cruz \nTitle 2: Brain Organoids \nBio: Haussler received his PhD in computer science from the University of Colorado at Boulder. He is a member of the National Academy of Sciences\, the National Academy of Engineering\, the American Academy of Arts and Sciences and a fellow of AAAS and AAAI. He has won a number of awards\, including the 2015 Dan David Prize\, the 2011 Weldon Memorial Prize from University of Oxford\, the 2009 ASHG Curt Stern Award in Human Genetics\, the 2008 Senior Scientist Accomplishment Award from the International Society for Computational Biology\, the 2005 Dickson Prize for Science from Carnegie Mellon University\, and the 2003 ACM/AAAI Allen Newell Award in Artificial Intelligence. \nHosted by: Professor Josh Stuart\, BME Department
URL:https://events.ucsc.edu/event/bme-280b-seminar-gali-bai-david-haussler/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20251106T114000
DTEND;TZID=America/Los_Angeles:20251106T131500
DTSTAMP:20260423T170907
CREATED:20251106T012339Z
LAST-MODIFIED:20251106T012339Z
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SUMMARY:BME 280B Seminar: Anne Nakamoto\, Alan Zhang\, Shelbi Russell
DESCRIPTION:Presenter 1: Anne Nakamoto\, BME PhD Candidate\, Corbett-Detig Lab\, UC Santa Cruz \nTalk: Investigating deleterious mutation burden across populations and landscapes in the California Conservation Genomics Project \nDescription: Biodiversity is being lost at an accelerated rate due in part to anthropogenic forces\, posing a threat to the sustainability of Earth’s ecosystems as well as to human health. A major goal of conservation genomics is to use genomic data to understand population health\, which can inform management decisions for the preservation of biodiversity. The California Conservation Genomics Project (CCGP) is an extensive dataset containing species of conservation interest sampled across California\, allowing a landscape genomics approach to conservation. Among the many metrics that can be used to assess population health is genetic load\, which refers to the reduction in fitness imposed by deleterious mutations. In this work\, we construct a bioinformatic analysis framework to identify deleterious genomic variants in CCGP species based on evolutionary constraint. This allows us to investigate patterns in genetic burden across populations and the landscape of California. \nPresenter 2: Alan Zhang\, BME PhD Candidate\, Corbett-Detig Lab\, UC Santa Cruz \nTalk: Scalable Strain-Level Metagenomic Deconvolution and Assembly Using Pangenome Mutation-Annotated Networks \nDescription: Strain-level deconvolution of metagenomic samples is essential for pathogen surveillance\, mixed infection diagnosis\, and evolutionary genomics\, yet remains computationally challenging as genomic databases expand. Existing methods scale poorly with database size or rely exclusively on single nucleotide polymorphism (SNP) information. SNP-based approaches rely on mutation-annotated trees and thus require well-established reference genomes\, limiting their applicability to divergent species that lack alignable root references. We present panMAMA (panMAN Metagenomic Assignment and Metagenomic Assembly)\, a method that leverages the pangenome Mutation-Annotated Network (panMAN) data structure to enable accurate strain-level quantification across both closely related and divergent genomes. By employing k-min-mer-based pseudo-chaining with a seed-annotated tree index\, panMAMA achieves substantial computational speedup compared to existing k-mer-based tools while maintaining high accuracy. We demonstrate that panMAMA accurately deconvolves both closely related SARS-CoV-2 genomes and divergent HIV and respiratory syncytial virus (RSV) genomes\, outperforming existing tools including Freyja on simulated wastewater samples. Through a hybrid heuristic and maximum likelihood approach for read assignment and consensus calling\, panMAMA effectively recovers variant genomes from low-heterogeneity samples of divergent species. These results establish panMAMA as a scalable and accurate platform that extends strain-level metagenomic analysis to previously intractable highly divergent species. \nPresenter 3: Shelbi Russell\, PhD\, UC Santa Cruz\, Ph.D.\, Organismic & Evol Bio\, Harvard\, PostDoc MCDB\, UC Santa Cruz \nDescription: Many animals harbor bacterial symbionts that manipulate host reproduction to enhance bacterial survival and transmission. Obligate intracellular symbionts\, such as Wolbachia pipientis\, are particularly adept at host manipulation\, influencing reproductive biology and even blocking viral replication. These bacterially induced traits have been harnessed in field studies to control mosquito populations and limit the spread of human pathogens like Dengue and Zika viruses. Despite these promising applications\, the molecular mechanisms underlying Wolbachia’s interactions with host cells remain poorly understood. Furthermore\, even less is known about the implications of these symbionts spreading to non-target hosts in the ecosystem. Previous work from my lab tackled these questions in vivo: we discovered that the wMel strain of Wolbachia can enhance host fertility and we discovered that even extremely low rates of horizontal symbiont transmission among hosts can influence bacterial genome evolution. However\, in vivo systems offer limited resolution to identify the precise cellular mechanisms of fertility enhancement and the real-time genomic impacts of horizontal transmission. Here\, we use an in vitro Drosophila system to 1) identify the cell type-specific impacts of Wolbachia infection on host-microbe interactions and 2) characterize how strains interact within host tissues during mixed infections. This simplified\, easy to sample system enabled us to concentrate the effects of host cell type on Wolbachia gene expression and to control de novo strain infections and mixtures. Through these experiments\, we discovered that different host cell types induce differential Wolbachia gene expression that feeds back to alter host gene expression and epigenetic silencing. These findings have motivated on-going single cell RNAseq work to resolve the process at the single cell level\, during de novo infections. Results from the experimental mixed infections revealed highly reproducible strain and cell type-specific dynamics. We will leverage these discoveries to understand strain-specific tissue tropisms and how multiple strains can co-exist as superinfections in nature\, which will inform future biocontrol strategies. \nBio: Shelbi is an Assistant Professor in the Department of Biomolecular Engineering at UCSC. She started her lab in 2022\, after completing her PhD at Harvard University in 2016 and performing her postdoctoral work at UCSC. Her passion for studying symbiotic systems began as an undergraduate researcher at the University of Kansas describing new tapeworm species. She transitioned to studying the evolutionary genomics of bacterial-animal mutualisms in her PhD and was awarded the UC Chancellor’s Postdoctoral Fellowship and the NIH Career Development Award (K99) to test genomic hypotheses in the Wolbachia-Drosophila model system during her postdoc. As faculty\, she is working to learn how hosts and microbes function and evolve so we can engineer associations for biological control. She has authored 24 papers and obtained $2.75 million in funding. Her interdisciplinary training makes her uniquely qualified to lead these investigations and has enabled novel breakthroughs in our understanding of symbiont evolution and microbe-induced host phenotypes. \nHosted by: Professor Josh Stuart\, BME Department \nRoom: PSB-240
URL:https://events.ucsc.edu/event/bme-280b-seminar-anne-nakamoto-alan-zhang-shelbi-russell/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20251030T114000
DTEND;TZID=America/Los_Angeles:20251030T131500
DTSTAMP:20260423T170907
CREATED:20251028T222750Z
LAST-MODIFIED:20251028T222750Z
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SUMMARY:BME 280B Seminar: Preconfigured neuronal firing sequences in human brain organoids
DESCRIPTION:Presenter: Tjitse (TJ) van der Molen\, Ph.D. (Postdoc\, Sharf Lab\, UC Santa Cruz and PhD Kosik Lab\, UC Santa Barbara) \nDescription: Neuronal firing sequences are thought to be the building blocks of information and broadcasting within the brain. Yet\, it remains unclear when these sequences emerge during neurodevelopment. Here we demonstrate that structured firing sequences appear in spontaneous activity of human and murine brain organoids\, both unguided and forebrain identity directed\, as well as ex vivo neonatal murine cortical slices. We observed temporally rigid and flexible firing patterns in human and murine brain organoids and early postnatal murine somatosensory cortex\, but not in dissociated primary cortical cultures. These results suggest that temporal sequences do not arise in an experience-dependent manner\, but are rather constrained by a preconfigured architecture established during neurodevelopment. By demonstrating the developmental recapitulation of neural firing patterns\, these findings highlight the potential of brain organoids as a model for neuronal circuit assembly. \nBio: Tjitse van der Molen studies spontaneous and evoked neural circuit activity in human and mouse stem cell derived brain organoids using dense multi electrode arrays. His main goal is to gain a better understanding of how healthy neural circuits process information and how possible malfunctions in neural circuit activity may result in disease\, in order to develop appropriate treatments. Tjitse recently completed his PhD in the Kosik lab at UC Santa Barbara and is now continuing his research as a postdoc in the Sharf lab at UC Santa Cruz. \nIn this talk\, Tjitse will present his latest manuscript that is currently in press with Nature Neuroscience\, focused on spontaneously occurring repeated sequential firing patterns that are present in the intrinsic activity of both brain organoids and neonatal mouse brain slices but not in 2D primary cultures. Similar sequential firing patterns have recently been shown to be important for information encoding and learning in the human cortex. The presence of these sequential firing patterns in the spontaneous activity of brain organoids that have never received external stimuli supports the notion that they develop in an experience-independent manner. \nHosted by: Professor Josh Stuart\, BME Department \nZoom Link: https://ucsc.zoom.us/j/99970819390?pwd=8sl5pd5TTBA5f6nqyCzo5mFpaqcEJG.1 \nFull Schedule: https://docs.google.com/document/d/1xD09vITwd_Pj9Ge6hHEuBFa5zBUYu2O-bjpSibt7VHE/edit?tab=t.0 \nRoom: PSB-240
URL:https://events.ucsc.edu/event/bme-280b-seminar-preconfigured-neuronal-firing-sequences-in-human-brain-organoids/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20251023T114000
DTEND;TZID=America/Los_Angeles:20251023T131500
DTSTAMP:20260423T170907
CREATED:20251020T204418Z
LAST-MODIFIED:20251022T183840Z
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SUMMARY:BME 280B Seminar: Computational Models of Biological Systems
DESCRIPTION:Presenter: Chen-Hsiang Yeang\, Associate Research Fellow\, Institute of Statistical Science of Academia Sinica \nDescription: Computational models are roughly categorized into two types: describing the patterns of the phenomenon or data (description-driven models) and explaining the phenomenon or data with simpler\, comprehensible rules (explanation-driven models). When building a model\, the choice of the mixture ingredients of these two classes depends on the nature of the problem\, availability of the knowledge and data of the underlying system. In this talk\, I will give an overview of five models with varying combinations of descriptive and explanatory elements on different biological problems. First\, I will introduce a joint model to capture irreversible and reversible drug resistance mechanisms of cancers and a dynamic treatment strategy to tackle drug resistance. Second\, I will introduce a backward deconvolution algorithm based on probabilistic graphical models to unravel the cell type heterogeneity of the RNASeq data. Third\, I will introduce a deep neural network model to integrate direct and indirect associations of genotypes and images with phenotypes. Fourth\, I will introduce an experimental and computational framework to predict protein stability and discover motifs at C-terminals. Fifth\, I will introduce three algorithms to demarcate independent holes of specified dimensions in large networks. These works illustrate how “model selection” should be tailored for specific biological problems. \nBio: Chen-Hsiang Yeang is currently an associate research fellow at the Institute of Statistical Science of Academia Sinica. His research interests focus on several areas in computational biology and data science: 1) cancer genomics\, 2) cancer treatment\, 3) molecular evolution\, 4) network topology\, and 5) machine learning. \nHosted by: Professor Josh Stuart\, BME Department \nRoom: PSB-240
URL:https://events.ucsc.edu/event/bme-280b-seminar-computational-models-of-biological-systems/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations
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DTSTART;TZID=America/Los_Angeles:20251002T114000
DTEND;TZID=America/Los_Angeles:20251002T131500
DTSTAMP:20260423T170907
CREATED:20251001T230805Z
LAST-MODIFIED:20251001T230805Z
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SUMMARY:BME 280B Seminar: Computational Precision Health & Genomic Diversity
DESCRIPTION:Presenter: Dr. Alex Ioannidis\, BME Assistant Professor\, UCSC \nDescription: N/A \nBio: Alex Ioannidis graduated summa cum laude in Chemistry and Physics from Harvard and completed an M.Phil in Computational Biology in the Dept. of Applied Math & Theoretical Physics at Cambridge. He earned his Ph.D. in Computational & Mathematical Engineering at Stanford and M.S. in Mgt. Science & Engineering (Numerical Optimization concentration). Prior to this\, he worked on novel superconducting computing logic and quantum computing at Northrop Grumman (Advanced Technology Lab).\n\nAlex’s teachings has included machine learning algorithms and data science courses in the Institute for Computational & Mathematical Engineering (ICME) at Stanford\, AI in healthcare at Stanford Medical School\, and computational biology in the Dept. of Biomolecular Engineering (BME) at the University of California\, Santa Cruz. His research group focuses on computational techniques and deep learning methods for genomics & precision health with a particular focus on populations in Oceania and Latin America (spotlight article). \nHosted by: Professor Josh Stuart\, BME Department\n\nLocation: PSB-240
URL:https://events.ucsc.edu/event/bme-280b-seminar-computational-precision-health-genomic-diversity/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations
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DTSTART;TZID=America/Los_Angeles:20250925T114000
DTEND;TZID=America/Los_Angeles:20250925T114000
DTSTAMP:20260423T170907
CREATED:20250919T070000Z
LAST-MODIFIED:20250925T231705Z
UID:10000209-1758800400-1758800400@events.ucsc.edu
SUMMARY:BME 280B Seminar: Applying a translational research framework to understand PFAS exposures and health risks
DESCRIPTION:Presenter: Dr. Max Aung\, Assistant Professor of Environmental Health\, USC Keck School of Medicine \nDescription: Per and poly-fluoroalkyl substances (PFAS) are a group of industrial chemicals that are ubiquitous in the environment and in humans. The National Academies of Science\, Engineering\, and Medicine\, have identified PFAS as an important environmental risk factor for various chronic health conditions\, including cancer and metabolic disorders. Contaminated drinking water is one source of human PFAS exposure\, specifically for communities within East and South Los Angeles (LA) that have multiple point sources of PFAS (e.g. metal plating facilities and textile industries). Importantly\, the CalEnviroScreen 4.0 indicates that many neighborhoods in East and South LA have high pollution burden overlapping with high PFAS contamination in public water systems. \nThis presentation will highlight key translational environmental health projects in our USC ShARP Superfund Research Center that have been instrumental for increasing knowledge of PFAS exposures and health risks and strengthening community engagement for science and policy translation. I will outline how our team has utilized basic experimental models to complement epidemiologic studies\, leveraging multi-omics data integration to uncover biological mechanisms. Building on this\, I will illustrate how we have developed community and multi-sector partnerships to inform exposure assessment and science translation to address local PFAS contamination. \nBio: Max Aung is an Assistant Professor of Environmental Health at the USC Keck School of Medicine. He holds leadership roles as Director of the Translational Research Core in the USC Southern California Environmental Health Sciences Center and as Director of Community Engagement in the USC ShARP Superfund Research Center and the USC Center for Translational Exposomics Research. He is also a current Harvard JPB Environmental Health Fellow. Max’s research program focuses on investigating biological mechanisms linking environmental exposures to maternal and child health outcomes. He uses translational approaches to advance environmental health research\, including experimental models\, epidemiological studies\, community-engagement\, and science communication and policy translation. \nHosted by: Marina Ramon\, Director of Genomics Training Programs for the Genomics Institute
URL:https://events.ucsc.edu/event/bme-280b-seminar-applying-a-translational-research-framework-to-understand-pfas-exposures-and-health-risks/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations
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