Statistical Bioinformatics Seminar: Dr Vipul Singhal (Integrated Biosciences, Inc)

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

Abstract: 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 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.  

About the speaker: Dr.  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.