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X-WR-CALDESC:Events for Sydney Precision Data Science Centre
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DTSTART;TZID=Australia/Sydney:20250505T130000
DTEND;TZID=Australia/Sydney:20250505T140000
DTSTAMP:20260407T131649
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SUMMARY:Vitessce framework for interactive visualization of single-cell data and its applications
DESCRIPTION:Statistical Bioinformatics SeminarMark Keller\, PhD student at Harvard Medical School\n\n\n\n\n\n\n\n\n\n\n\nWe introduce Vitessce to address the need for a scalable\, interactive\, and extensible framework that supports visualization of spatial and multimodal single-cell data. Its modular architecture\, compatibility with multiple file formats\, and support for coordinated multiple views enable researchers to integrate previously disconnected data modalities and view them with a single tool. The adoption of Vitessce by multiple data portals\, publication-associated websites\, and commercial products underscores its utility. This framework also supports multiple projects in which we have applied Vitessce for comparative\, spatial\, and epigenomic data visualization\, which will be highlighted in this presentation. \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\nMark Keller\n\n\n\nMark Keller is a PhD student in the Bioinformatics and Integrative Genomics program at Harvard Medical School\, advised by Professor Nils Gehlenborg. His research interests include developing visualization tools for single-cell data.
URL:https://spds.sydney.edu.au/event/vitessce-framework-for-interactive-visualization-of-single-cell-data-and-its-applications/
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BEGIN:VEVENT
DTSTART;TZID=Australia/Sydney:20250512T130000
DTEND;TZID=Australia/Sydney:20250512T140000
DTSTAMP:20260407T131649
CREATED:20250324T010319Z
LAST-MODIFIED:20250630T032541Z
UID:3055-1747054800-1747058400@spds.sydney.edu.au
SUMMARY:BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis
DESCRIPTION:Statistical Bioinformatics SeminarDr Vipul Singhal\, Head of Computational Biology\, Integrated Biosciences\, Inc\n\n\n\n\n\n\n\n\n\n\n\n\n\nA core property of solid tissue is the spatial arrangement of cell types into stereotypical spatial patterns. These cells can be investigated with spatial omics technologies to reveal both their omics features (transcriptomes\, proteomes\, etc)\, and their spatial coordinates. Because a cell’s state can be influenced by interactions with other cells\, it is informative to cluster cells using their omics signatures as well as their spatial relationships. We present BANKSY (Singhal et al.\, Nat. Genetics\, 2024)\, an algorithm with R and Python implementations that identifies both cell types and tissue domains from spatially-resolved -omics data. It does so by embedding cells in a product space of their own and neighbourhood omics features. BANKSY revealed niche-dependent cell states in the mouse brain\, and outperformed competing methods on domain segmentation and cell-typing benchmarks. BANKSY can also be used for quality control of spatial transcriptomics data and for spatially aware batch correction. Critically\, it is substantially faster and more scalable than existing methods\, enabling the processing of datasets with millions of cells. BANKSY comes in both Python and R implementations\, and works with major single cell frameworks like SingleCellExperiment\, Seurat\, and Scanpy. \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\n\n\n\n\nDr Vipul Singhal\n\n\n\nDr. Singhal is a computational biologist at Integrated Biosciences in Redwood City\, CA\, where he uses systems biology and machine learning to explore cellular responses to drugs and other perturbations. Previously\, he worked at the Genome Institute of Singapore\, developing algorithms to analyze spatial gene expression data in Dr. Kok Hao Chen’s lab. He earned his PhD in Bioengineering from Caltech\, focusing on tools for designing genetic circuits\, and his undergraduate degree in Electrical Engineering from Imperial College London. Outside work\, he enjoys snowboarding and climbing.
URL:https://spds.sydney.edu.au/event/banksy-unifies-cell-typing-and-tissue-domain-segmentation-for-scalable-spatial-omics-data-analysis/
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DTSTART;TZID=Australia/Sydney:20250519T130000
DTEND;TZID=Australia/Sydney:20250519T140000
DTSTAMP:20260407T131649
CREATED:20250507T041753Z
LAST-MODIFIED:20250630T032526Z
UID:3688-1747659600-1747663200@spds.sydney.edu.au
SUMMARY:The 7TM family: are template-based models better than AlphaFold models?
DESCRIPTION:Judith and David Coffey SeminarProf Shoba Ranganathan\, Macquarie University\n\n\n\nThis event was held in person and online. \n\n\n\n\n\n\n\n\n\n\n\nInsect odorant and gustatory receptors (ORs/GRs) are 7-transmembrane-domain (7TM) ion channels essential for the survival of insects. ORs play a key role in many insect behaviours\, including foraging\, pollination\, social interactions\, and recognizing prey and enemies. ORs are also the target of biocontrol of insect pests and disease vectors. Ors are therefore highly specialized and bear very little sequence similarity\, even within the same species. These receptors are “upside-down” compared to G-protein coupled receptors (GPCRs)\, and function without any accessory G proteins to let calcium ions in upon ligand binding. To design or identify novel volatile attractant or repellent chemicals\, a knowledge of the 3D structure of these inverted topology 7TM receptors is essential. With the rise of AlphaFold\, currently in its third avatar\, we explored if detailed template-based modelling (TBM) using the few experimental insect OR structures available is still required\, instead of a quick AI-generated AlphaFold3 (AF3) model. Using all Ors from the genomes of two economically important Australian fruit fly pest species\, we show that 7TM receptors still need step-by-step TBM rather than AF3 models. \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 Shoba Ranganathan\n\n\n\nShoba Ranganathan is an Honorary Professor of Bioinformatics in Applied Biosciences\, Macquarie University. She was the first Chair of Bioinformatics in Australia (2004-22). She has held research and academic positions in India\, USA\, Singapore and Australia as well as a consultancy in industry. Shoba’s research addresses several key areas of bioinformatics to understand biological systems using computational approaches. Her group has achieved both experience and expertise in different aspects of computational biology\, ranging from metabolites and small molecules to biochemical networks\, pathway analysis and computational systems biology. She has authored as well as edited several books in as well as contributed several articles to the 1st edition of this Encyclopedia. She was awarded the 2023 Outstanding Contributions to the International Society for Computational Biology (ISCB) Award. She is an Honorary Senior Fellow of the Australian Society for Bioinformatics and Computational Biology since 2018\, an ISCB Fellow since 2023 and an Asia Association for Artificial Intelligence Fellow since 2024.
URL:https://spds.sydney.edu.au/event/the-7tm-family-are-template-based-models-better-than-alphafold-models/
LOCATION:Mackenzie Room\, Level 6\, Charles Perkins Centre\, University of Sydney\, Johns Hopkins Drive\, University of Sydney\, Sydney\, 2006\, Australia
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DTSTART;TZID=Australia/Sydney:20250526T130000
DTEND;TZID=Australia/Sydney:20250526T140000
DTSTAMP:20260407T131649
CREATED:20250514T042721Z
LAST-MODIFIED:20250630T032509Z
UID:3759-1748264400-1748268000@spds.sydney.edu.au
SUMMARY:Systems or sub-systems biology? Which can best help us understand the cell?
DESCRIPTION:Judith and David Coffey SeminarProf Marc Wilkins\, UNSW\n\n\n\nThis event was held in person and online. \n\n\n\n\n\n\n\n\n\n\n\nThe promise of systems biology is that the study of a cell\, via its components and their interactions\, will define and reveal emergent properties of that system. The use of large-scale ‘omics techniques is essential for this\, however many such techniques still cannot measure all relevant biomolecules and their interactions. This leaves us with an incomplete and sometimes shallow understanding. This talk will describe our research into two\, tractable sub-systems of the cell where we have sought to fully define their components\, interactions and aspects of function. \n\n\n\nFirst\, I will describe our work to fully define the ‘protein methylation network’ of a eukaryotic cell. Here\, we asked is it possible to identify all instances of a post-translational modification in a eukaryote? We also asked\, can we prove it? We then asked can we define all enzymes\, in this case methytransferases\, that are responsible for this modification – and in doing so construct a complete sub-system in the cell. We have been successful in addressing the above\, which has allowed a range of emergent properties of this network to be discovered. \n\n\n\nSecondly\, I will describe our work to understand how two regulatory subsystems in the cell – the signalling system and the histone methylation system – actually connect. In yeast\, four enzymes methylate histones and four can demethylate histones. They do so with remarkable precision and dynamism\, helping define regions of the genome to be transcribed. We asked are these enzymes phosphorylated\, and to what degree? We also asked are phosphosites associated with specific cellular responses; in effect do certain phosphorylation events on the histone methylating enzymes direct them to change chromatin in certain parts of the genome? We additionally asked can we find which kinases are responsible; thus connecting the sensing / signalling system with that of chromatin regulation? This story is less complete than that above\, but is compelling! \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 Marc Wilkins\n\n\n\nMarc is a professor of systems biology and is deputy dean (research and enterprise) in the faculty of science at UNSW. He has had a longstanding interest in understanding cells at a systems level\, and finding ways to do that. He defined the concept of the proteome\, coined the term\, and has directed entities such as the Systems Biology Initiative (SBI) and the Ramaciotti Centre for Genomics (2011-2022). He is currently the UNSW node leader in the MACSYS ARC Centre of Excellence\, which has the goal of building mathematical and computational models of whole cells. \n\n\n\nMarc has a career output of >280 publications in proteomics\, especially concerning protein post-translational modifications\, and in genomics\, transcriptomics and biological networks. In industry\, Prof. Wilkins co-founded two biotechnology companies\, both which took products to market and which were ASX-listed. Proteome Systems had a focus on proteomic technology development and its application to biodiscovery. Regeneus (now Cambium Bio) developed cell-based therapies for the treatment of inflammatory conditions.
URL:https://spds.sydney.edu.au/event/systems-or-sub-systems-biology-which-can-best-help-us-understand-the-cell/
LOCATION:Mackenzie Room\, Level 6\, Charles Perkins Centre\, University of Sydney\, Johns Hopkins Drive\, University of Sydney\, NSW\, 2006\, Australia
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