BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

Statistical Bioinformatics SeminarDr Vipul Singhal, Head of Computational Biology, Integrated Biosciences, Inc A 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 […]

Spatially resolved mapping of cells associated with human complex traits

Liyang Song, PhD student, Westlake University This is an online event held via Zoom: https://uni-sydney.zoom.us/j/85114748391 Depicting spatial distributions of disease-relevant cells is crucial for understanding disease pathology. In our recent work, we developed a method, gsMap, that integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including […]

RNA polymerase II at histone genes predicts outcome in human cancer

Dr Ye Zheng, University of Texas MD Anderson Cancer Center This is an online event held via Zoom: https://uni-sydney.zoom.us/j/85114748391 Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how hypertranscription might drive cancer, we applied our formalin-fixed paraffin-embedded (FFPE)–cleavage under targeted accessible chromatin method for mapping RNA polymerase II (RNAPII) genome-wide in FFPE […]

Revisiting quality control, normalisation, and spatially variable gene calling in CosMx WTx

Dr Dharmesh D Bhuva, NHMRC Emerging Leadership Fellow (EL1), Frazer Institute, The University of Queensland This is an online event held via Zoom: https://uni-sydney.zoom.us/j/85114748391 Spatially resolved molecular measurements have revolutionised the study of disease systems, providing an unprecedented resolution and throughput of molecular measurements. The opportunity posed by such data requires a new set of tools […]

Incorporating experimental medicine into single-cell multi-omics

Mackenzie Room, Level 6, Charles Perkins Centre, University of Sydney Johns Hopkins Drive, University of Sydney, NSW, Australia

Special Statistical Bioinformatics Seminar Dr Jacqueline Siu, Kennedy Institute of Rheumatology, University of Oxford About the seminar: Coordinated global efforts to create a comprehensive map of the human body using single-cell technologies has opened up avenues in computational biology and AI. However, there remains a pressing need to increase the data diversity from the ancestral […]

Veridical data science and alignment in medical AI

Lecture Theatre 173, Carslaw Building (F07.01.173)

Professor Bin Yu, Statistics, EECS, Center for Computational Biology, Simons Institute for the Theory of Computing, UC Berkeley About the seminar Alignment and trust are crucial for the successful integration of AI in healthcare including digital twin projects, a field involving diverse stakeholders such as medical personnel, patients, administrators, public health officials, and taxpayers, all […]