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X-WR-CALDESC:Events for Halıcıoğlu Data Science Institute - UC San Diego
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DTSTAMP:20260602T091336
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SUMMARY:The continuum of gene regulation at single cell resolution\, from Drosophila development to human complex traits | Diego Calderon
DESCRIPTION:Single-cell technologies have emerged as powerful tools for studying development\, enabling comprehensive surveys of cellular diversity at profiled timepoints. They shed light on the dynamics of regulatory element activity and gene expression changes during the emergence of each cell type. Despite their potential\, nearly all atlases of embryogenesis are constrained by sampling density\, i.e.\, the number of discrete time points at which individual embryos are harvested. This limitation affects the resolution at which regulatory transitions can be characterized. In this talk\, I present a novel cell collection approach capable of constructing a continuous representation of dynamic regulatory processes. I applied this approach to generate a continuous\, single-cell atlas of chromatin accessibility and gene expression spanning Drosophila embryogenesis. Additionally\, I will discuss my past and future research\, applying new genomic technologies to characterize gene regulation important for human diseases.
URL:https://datascience.ucsd.edu/event/special-seminar-diego-calderon/
LOCATION:Powell-Focht Bioengineering Hall (PFBH)\, FUNG Auditorium
CATEGORIES:Seminar
ATTACH;FMTTYPE=image/png:https://datascience.ucsd.edu/wp-content/uploads/2024/01/HDSI-UCSD-Image_Dark-blue-e1710178042629.png
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DTSTART;TZID=America/Los_Angeles:20240212T140000
DTEND;TZID=America/Los_Angeles:20240212T153000
DTSTAMP:20260602T091336
CREATED:20240126T182854Z
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SUMMARY:Integrating Longitudinal Multimodal Data To Realize Precision Medicine | Samantha Piekos
DESCRIPTION:Abstract: The interplay of biology\, environment\, and lifestyle direct the development and progression of complex diseases and other health outcomes. Therefore\, integration of longitudinal multimodal data is needed to understand the mechanisms underpinning major molecular transitions. Previously during my doctoral work at Stanford\, I integrated multiomics data to elucidate the epigenetic mechanism of human surface ectoderm differentiation. I also built a pipeline to investigate the role of polymorphism\, particularly non-coding genetic variants\, in complex diseases. To address the common pain point of data silos limiting the interpretation of multimodal data integration\, I formed a collaboration with Google Data Commons to build a free\, open-source biomedical knowledge graph with a common schema and API. Currently it is composed of approximately 130 million nodes and 1.7 trillion triples (node-edge-node) from 22 publicly available biomedical datasets. Knowledge graphs are a key tool for hypothesis generation\, data interpretation\, and dimensionality reduction required for systems medicine research. Upon starting my postdoctoral work at the Institute for Systems Biology\, I identified pregnancy as an excellent model system for prototyping precision medicine approaches. I used electronic healthcare records (EHR) from Providence St. Joseph Healthcare to investigate the impact of COVID-19 maternal infection and vaccination on maternal-fetal outcomes. In addition\, I integrated multiomics placental data to investigate molecular network changes (interomics and intraomics) in common obstetric disorders. In a follow-up study (enrollment complete) we have longitudinal deep-phenotyping data of 435 people throughout pregnancy 80 of which have pregnancy complications. This includes multiomics\, survey\, EHR\, and air quality data collected from first prenatal visit through delivery. My lab will use this data to define major molecular transition states throughout pregnancy. I will also investigate the disease mechanisms of common obstetric disorders including identifying for an individual the earliest possible point of deviation from a healthy trajectory. This interdisciplinary approach will identify potential drug targets\, biomarker panels\, and individualized clinical interventions. \n  \nBio: Samantha completed her PhD in Stem Cell Biology and Regenerative Medicine with a PhD minor in Biomedical Informatics at Stanford University under the advisement of Dr. Anthony Oro. Using a multiomics approach\, Samantha demonstrated how transcription factors direct keratinocyte differentiation by changing the epigenetic landscape\, including chromatin looping\, thereby effecting the cell transcriptional program. Samantha has also been collaborating with Google since June 2019 to build Biomedical Data Commons\, a knowledge graph that integrates biomedical data from a wide array of sources into a single searchable database thereby increasing data accessibility. Upon completion of her PhD in 2020\, began her postdoctoral fellowship at the Institute for Systems Biology under the advisement of Drs. Lee Hood and Nathan Price. Using electronic healthcare records (EHR)\, she has provided insight into the impact of maternal COVID-19 and vaccination on maternal-fetal outcomes. In addition to her EHR research\, Samantha is using multidimensional omics placental data to understand the molecular mechanism of common obstetric disorders. Upon transitioning to Assistant Professor\, she intends to perform multimodal data integration of longitudinal deep-phenotyping data to evaluate changes in molecular networks in complex diseases.
URL:https://datascience.ucsd.edu/event/special-seminar-samantha-piekos/
LOCATION:Halıcıoğlu Data Science Institute (HDSI)\, Room 123\, 3234 Matthews Ln\, La Jolla\, CA\, 92093\, United States
CATEGORIES:Seminar
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DTSTART;TZID=America/Los_Angeles:20240205T110000
DTEND;TZID=America/Los_Angeles:20240205T123000
DTSTAMP:20260602T091336
CREATED:20240126T182051Z
LAST-MODIFIED:20240130T224530Z
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SUMMARY:Lessons from the deep: engineering biosensors\, workflows\, and visualizations for communication and collaboration in comparative medicine and climate science | Jessica Kendall-Bar
DESCRIPTION:Abstract: Effective conservation and management relies on an in-depth understanding of the health of marine ecosystems. Dr. Kendall-Bar’s interdisciplinary approach combines engineering\, visualization\, and computation to study ocean resilience in terms of the extreme physiology and behavior of marine animals\, establishing eco-physiological baselines to track over time in the face of climate change. This seminar and chalk talk will review her work to create innovative tools to detect\, visualize\, and analyze the physiology and behavior of animals in extreme environments that showcase their biological resilience to oxygen and sleep deprivation. From individuals to ecosystems\, Kendall-Bar conducts multidisciplinary physiological studies that combine basic and applied science with potential to advance conservation and comparative medicine. This seminar reviews Kendall-Bar’s dissertation research on sleep in seals and presents some current and ongoing projects to combine high-performance computing\, automation\, and visualization to assess diving physiology in human freedivers\, epilepsy in sea lions\, and cardiac performance in some of the largest (blue whales) and smallest (emperor penguins) divers. Kendall-Bar’s newest projects involve novel data visualizations and science communication to inform research as well as international policy in domains ranging from marine mammal conservation to traditional ecological knowledge and coral reef restoration.\n \nBio: Dr. Jessica Kendall-Bar is a Schmidt AI in Science Postdoctoral Fellow at Scripps Institution of Oceanography\, UC San Diego. Her research combines engineering\, data science\, ecology\, and visualization to measure behavior and physiology of marine animals amidst a changing climate. For her dissertation\, she developed a non-invasive system to record and visualize the first recordings of marine mammal sleep at sea published in Science. She is an award-winning scientist\, artist\, and science communicator who designs data visualization courses\, large-scale exhibits\, immersive analytical tools\, and decision support tools. Her data visualizations\, published in local news outlets\, The New York Times and The Atlantic\, have informed international policy in domains ranging from marine mammal conservation to coral reef restoration.\n 
URL:https://datascience.ucsd.edu/event/special-seminar-jessica-kendall-bar/
LOCATION:Powell-Focht Bioengineering Hall (PFBH)\, FUNG Auditorium
CATEGORIES:Seminar
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