WEHI Special Bioinformatics and Computational Biology Seminar hosted by Professor Rory Bowden, Dr James Fu and Dr Mengbo Li

Dr Tim Stuart

Principal Scientist
Genome Institute of Singapore, A*STAR

Scaling single-cell chromatin analysis with regulatory element modules

Davis Auditorium

Join via ZOOM

Including Q&A session

Single-cell epigenomic assays offer new ways to understand how the activity of DNA regulatory elements may shape cellular states and fates. Recent advances in experimental methods now allow profiling of millions of cells, enabling a much more reliable quantification of these epigenomic states, particularly for rare cells. However, the analysis of such data is still impeded by two computational challenges. First, there is a lack of reusable features for epigenomic analysis, and each dataset requires de novo peak calling. This makes comparison of published datasets difficult as they cannot be directly compared. Second, current analysis methods cannot scale to process large single-cell epigenomic datasets, requiring excessively long runtimes and large memory resources. To address these challenges developed a novel approach for single-cell epigenomic analysis based on feature aggregation. We leveraged epigenomic data from thousands of published datasets to identify groups of co-accessible regulatory elements, which we term Regulatory Element Modules (REMO). We further developed an open-source software toolkit, implemented in Rust, that provides fast and memory-efficient quantification of single-cell epigenomic data. REMO enables accelerated analysis of single-cell epigenomic data with lower memory requirements, and provides reusable features applicable to a broad range of tissue types, offering a robust framework for consistent and scalable analysis of single-cell epigenomic data.

Tim Stuart is a Principal Scientist at the Genome Institute of Singapore, A*STAR. His research focuses on using single-cell genomics and computational biology methods to improve our understanding of the function of noncoding DNA elements, and their impact in human health and disease. Prior to joining A*STAR Dr. Stuart completed his BSc and PhD in Biochemistry at the University of Western Australia with Prof. Ryan Lister, where he studied the impact of transposable elements on epigenetic landscapes. Dr. Stuart later completed a postdoctoral fellowship at the New York Genome Center with Dr. Rahul Satija, where he developed new methods for single-cell data integration and epigenomic analysis.

All Welcome!