Computational principles and challenges in single-cell data integration

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Best practices for single-cell analysis across modalities (2023, background): “Whereas BCRs directly recognize soluble or membrane-bound epitopes , TCRs interact with linear peptides bound to cell-surface major histocompatibility complex (MHC) molecules.”
Gene regulatory network inference in the era of single-cell multi-omics (2023, background): “In these ‘simultaneous’ methods, unpaired data can still be modelled if both modalities are matched using integration approaches 61 .”
Spatial components of molecular tissue biology (2022, positive): “These methods transfer cell-type labels from scRNA-seq to spot transcriptomics by manifold alignment techniques 142 .”
Methods and applications for single-cell and spatial multi-omics (2023, result): “Recently, Argelaguet et al. 130 defined three categories of data integration strategies depending on the anchor used to link the different data modalities.”