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X-WR-CALDESC:Events for Sydney Precision Data Science Centre
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DTSTART;TZID=Australia/Sydney:20250804T130000
DTEND;TZID=Australia/Sydney:20250804T140000
DTSTAMP:20260407T060230
CREATED:20250721T065026Z
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UID:3984-1754312400-1754316000@spds.sydney.edu.au
SUMMARY:Spatial and Functional Analysis of the Mammalian Brain
DESCRIPTION:Statistical Bioinformatics SeminarDr Rongxin Fang\, Stanford University\n\n\n\nThis is an online event held via Zoom: https://uni-sydney.zoom.us/j/85114748391 \n\n\n\n\n\n\n\n\n\nThe mammalian brain is composed of an extraordinarily diverse cell types\, yet how these cells are spatially organized in the human brain—and how this organization differs across species or in disease—remains poorly understood. In this talk\, I will present two innovations in spatial transcriptomics aimed at addressing this gap. In the first part\, I will introduce genome-scale MERFISH\, a transcriptome imaging method capable of profiling over 4\,000 genes in situ at single-cell resolution. Applying this approach to the human cerebral cortex\, we identified more than 100 transcriptionally distinct cell populations and constructed a spatially resolved\, molecularly defined cell atlas. Comparative analysis with mouse cortex revealed conserved laminar organization\, but also species-specific differences—particularly in somatic interactions between neurons and non-neuronal cells—highlighting unique aspects of human brain organization. While MERFISH has primarily been applied to thin tissue sections (~10 µm)\, many biological questions require volumetric analysis of thicker tissue samples. In the second part of the talk\, I will present 3D MERFISH\, a method that combines MERFISH with confocal microscopy for optical sectioning and deep learning for enhanced image reconstruction. We applied this technique to mouse brain tissue up to 200 µm thick\, achieving high detection sensitivity and spatial fidelity. Together\, these genome-scale and volumetric transcriptome imaging methods expand the capabilities of spatial genomics\, enabling unprecedented insight into brain organization\, species evolution\, and disease mechanisms. \n\n\n\n\n\n\nSubscribe to our seminar mailing list\n\n\n\n\n→\n\n\n\n\n\n\n\nFind out more about the Statistical Bioinformatics seminar series\n\n\n\n\n\n→\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nDr Rongxin Fang\n\n\n\nDr Rongxin Fang is an Assistant Professor at Stanford University in the Departments of Neurosurgery and Genetics (by courtesy) and a member of the Wu Tsai Neuroscience Institute. Rongxin received his Ph.D. in Bioinformatics and Systems Biology in the Department of Molecular and Cellular Medicine at UC San Diego\, where he was advised by Bing Ren (2015-2019). Rongxin has also received multiple fellowships and awards\, including the HHMI/Damon Runyon Postdoctoral Fellowship\, Rising Star in Health and Engineering – Johns Hopkins and Columbia University\, Next Generation Leader – Allen Institute\, Damon Runyon-Dale F. Frey Award for Breakthrough Scientists.
URL:https://spds.sydney.edu.au/event/spatial-and-functional-analysis-of-the-mammalian-brain/
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BEGIN:VEVENT
DTSTART;TZID=Australia/Sydney:20250811T130000
DTEND;TZID=Australia/Sydney:20250811T140000
DTSTAMP:20260407T060230
CREATED:20250725T033046Z
LAST-MODIFIED:20250922T065408Z
UID:4024-1754917200-1754920800@spds.sydney.edu.au
SUMMARY:TenK10K multiome initiative: Genetic regulation of cell-type–specific chromatin accessibility shapes immune function and disease risk
DESCRIPTION:Statistical Bioinformatics SeminarDr Angli Xue\, Garvan Institute of Medical Research\n\n\n\nThis was an online event held via Zoom. \n\n\n\n\n\n\n\n\n\n\n\nUnderstanding how genetic variation influences gene regulation at the single-cell level is crucial for elucidating the mechanisms underlying complex diseases. However\, limited large-scale single-cell multi-omics data have constrained our understanding of the regulatory pathways that link variants to gene expression. Here\, we present the TenK10K multiome initiative as part of the TenK10K phase 1 projects: chromatin accessibility profiles from 3.5 million peripheral blood mononuclear cells (PBMCs) across 1\,013 donors\, generated using single-cell ATAC-seq and multiome (RNA+ATAC) sequencing\, with matched whole-genome sequencing. We characterised ~441\,000 chromatin peaks across 28 immune cell types and mapped ~243\,000 chromatin accessibility QTLs (caQTLs)\, 60% of which are cell-type-specific. Integration with TenK10K scRNA-seq (5.4 million PBMCs) identified 31\,688 candidate cis-regulatory elements colocalised with eQTLs; over half (52.5%) show evidence of causal effects mediated via chromatin accessibility. Combining caQTLs with GWAS loci for 17 diseases and 44 blood traits uncovered 10–41% more colocalised signals compared to eQTLs alone. For example\, incorporating caQTLs increased the number of candidate inflammatory bowel disease (IBD) genes in CD8 effector memory T cells from 39 to 55. We demonstrate cell-type-specific mechanisms\, such as a regulatory effect on IRGM acting through altered chromatin accessibility in CD8 effector memory T cells but not in naïve cells. Using a graphical neural network\, we link peaks to genes in unpaired multiome data with up to 80% higher accuracy than with paired data lacking QTLs\, improving gene regulatory network inference by identifying 128 additional TF–target pairs (a 22% increase). These findings provide an unprecedented single-cell map of chromatin accessibility and genetic variation in human circulating immune cells\, establishing a powerful resource for dissecting cell-type-specific regulation and advancing our understanding of genetic risk for complex diseases. \n\n\n\n\n\n\nSubscribe to our seminar mailing list\n\n\n\n\n→\n\n\n\n\n\n\n\nFind out more about the Statistical Bioinformatics seminar series\n\n\n\n\n\n→\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nDr Angli Xue\n\n\n\nDr Angli Xue is an NHMRC Investigator Fellow (EL1) and a postdoctoral researcher with Prof Joseph Powell at the Garvan Institute of Medical Research. He currently leads the multiome stream of the TenK10K project — a population cohort study aiming to map 50 million human cells from 10\,000 individuals. His research focuses on leveraging large-scale multi-omics data to uncover cell type–specific genetic regulatory mechanisms and identify novel drug targets. Dr Xue earned his BSc from Zhejiang University and completed a PhD in Statistical Genetics at The University of Queensland under the supervision of Prof Jian Yang. He is the recipient of an NHMRC Investigator Grant (2025–2029) and a Ramaciotti Health Investment Grant as Chief Investigator.
URL:https://spds.sydney.edu.au/event/tenk10k-multiome-initiative-genetic-regulation-of-cell-type-specific-chromatin-accessibility-shapes-immune-function-and-disease-risk/
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DTSTART;TZID=Australia/Sydney:20250818T130000
DTEND;TZID=Australia/Sydney:20250818T140000
DTSTAMP:20260407T060230
CREATED:20250728T015038Z
LAST-MODIFIED:20250922T065421Z
UID:4051-1755522000-1755525600@spds.sydney.edu.au
SUMMARY:The lazy way of pathological images analysis in the era of large models
DESCRIPTION:Statistical Bioinformatics SeminarDr Yimin Zheng\, CeMM Research Center for Molecular Medicine\n\n\n\nThis was an online event held via Zoom. \n\n\n\n\n\n\n\n\n\n\n\nHistopathological slides remain the gold standard for disease diagnosis and the study of tissue architecture and pathology\, offering an exceptionally rich yet often underutilized source of biomedical information. Unlike single-cell datasets\, pathology slides are readily available in clinical workflows and comparatively inexpensive to generate. \n\n\n\nRecent advances in foundation models have transformed our ability to extract meaningful insights from image data\, leading to a surge of high-impact studies leveraging pathology images for survival prediction\, subtyping\, spatial integration\, and more. However\, for many bioinformaticians and systems biologists\, the field of image analysis still feels inaccessible because of steep technical barriers: diverse file formats\, fragmented tools\, and a lack of intuitive frameworks for exploration and analysis. \n\n\n\nIs there a way to analyze pathology images as intuitively as we analyze single-cell data? The answer is yes! \n\n\n\nIn this talk\, I will introduce LazySlide\, an open-source platform for pathology image analysis specifically designed for users scientists already comfortable with tools like Scanpy and AnnData. LazySlide supports multiple image formats and enables interaction with large models. This talk will demonstrate how LazySlide empowers scientists to “analyze images with text” and incorporate rich histopathological information into multi-omics workflows\, without needing to become image processing experts. Whether you’re studying cancer progression\, tissue aging\, or immune landscapes\, LazySlide unlocks a new dimension of spatial and morphological context at scale. \n\n\n\nGet started with LazySlide in no time: https://github.com/rendeirolab/LazySlide \n\n\n\n\n\n\nSubscribe to our seminar mailing list\n\n\n\n\n→\n\n\n\n\n\n\n\nFind out more about the Statistical Bioinformatics seminar series\n\n\n\n\n\n→\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nDr Yimin Zheng\n\n\n\nDr Yimin Zheng is Postdoctoral Fellow at CeMM Research Center for Molecular Medicine at Vienna\, Austria. He comes from a spatial biology background. His current research focuses on understanding cancer metastasis and aging from a multimodel pathological imaging perspective. He is also an open source contributor to multiple scientific software projects and a big-fan on visualization who has developed the composable visualization package of Marsilea.
URL:https://spds.sydney.edu.au/event/the-lazy-way-of-pathological-images-analysis-in-the-era-of-large-models/
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DTSTART;TZID=Australia/Sydney:20250825T130000
DTEND;TZID=Australia/Sydney:20250825T140000
DTSTAMP:20260407T060230
CREATED:20250806T002331Z
LAST-MODIFIED:20250922T065544Z
UID:4078-1756126800-1756130400@spds.sydney.edu.au
SUMMARY:The secret sauce - building insights from integrated atlas of human biology
DESCRIPTION:Judith and David Coffey SeminarProf Christine Wells\, University of Melbourne\n\n\n\nThis event was held in-person and online. \n\n\n\n\n\n\n\n\n\n\n\nThe human cell atlas is a global consortium seeking to build a detailed map of cell types through developmental time\, health and disease states. Molecular snapshots of individual cells can be taken at many measurement levels\, and the expectation is that integrating multiple modalities will lead to new discoveries about human cell development and behaviour. Data integration at this scale requires two main considerations – the first is statistical models to remove experimental artefacts and harmonise informative signals ; the second is curation of the metadata to identify possible technical\, experimental or even biological confounders. We often pay a lot of attention to the first challenge\, at the expense of minimizing or ignoring the second\, simply because data curation is difficult\, and often requires biological expertise that sits outside of our own groups. \n\n\n\nIn this talk\, I’ll introduce generative AI driven tools developed by my own team for stem cell curation\, as well as provide a preview of the community-driven curation platforms being lead out of the Human Cell Atlas consortium and provide some examples of how these tools are supporting high quality data integration and the creation of new cell atlases. \n\n\n\n\n\n\nSubscribe to our seminar mailing list\n\n\n\n\n→\n\n\n\n\n\n\n\nFind out more about the Statistical Bioinformatics seminar series\n\n\n\n\n\n→\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nProf Christine Wells\n\n\n\nProfessor Christine Wells is chair of stem cell systems at the University of Melbourne. She uses computational models to understand human stem cell behaviour\, and pluripotent stem cell models to test these computational predictions. Christine graduated with a PhD from UQ in 2004\, and established her first laboratory at Griffith University in 2005. Over the past 20 years\, her team has built several human cell atlases describing immune cell subsets\, then uses these atlases to benchmark lab grown immune cells\, and have invented new protocols to make specialist immune cells in the laboratory. Christine has authored over 150 papers\, collectively cited >30\,000 times. She is a member of several international consortia including the Functional Annotation of the Mammalian genome (FANTOM)\, the Human Cell Atlas (HCA) and the equity working group for the International Society for Stem Cell Research. Christine is the architect of the Stemformatics data collaboration platform and academic lead of the Australian stem cell registry.
URL:https://spds.sydney.edu.au/event/the-secret-sauce-building-insights-from-integrated-atlas-of-human-biology/
LOCATION:Mackenzie Room\, Level 6\, Charles Perkins Centre\, University of Sydney\, Johns Hopkins Drive\, University of Sydney\, Sydney\, 2006\, Australia
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