Mapping cells through time and space with moscot
Single-cell genomics technologies enable multimodal profiling of millions of cells across
temporal and spatial dimensions. Experimental limitations prevent the measurement of all …
temporal and spatial dimensions. Experimental limitations prevent the measurement of all …
Embryo-scale, single-cell spatial transcriptomics
Spatial patterns of gene expression manifest at scales ranging from local (eg, cell-cell
interactions) to global (eg, body axis patterning). However, current spatial transcriptomics …
interactions) to global (eg, body axis patterning). However, current spatial transcriptomics …
Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming
Understanding the molecular programs that guide cellular differentiation during
development is a major goal of modern biology. Here, we introduce an approach …
development is a major goal of modern biology. Here, we introduce an approach …
Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis
Transcriptional and epigenetic profiling of single-cells has advanced our knowledge of the
molecular bases of gastrulation and early organogenesis. However, current approaches rely …
molecular bases of gastrulation and early organogenesis. However, current approaches rely …
Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics
Cells do not live in a vacuum, but in a milieu defined by cell–cell communication that can be
measured via emerging high-resolution spatial transcriptomics approaches. However …
measured via emerging high-resolution spatial transcriptomics approaches. However …
SpiceMix enables integrative single-cell spatial modeling of cell identity
Spatial transcriptomics can reveal spatially resolved gene expression of diverse cells in
complex tissues. However, the development of computational methods that can use the …
complex tissues. However, the development of computational methods that can use the …
Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope
The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our
understanding of tissue spatial architecture and biology. Although current ST methods …
understanding of tissue spatial architecture and biology. Although current ST methods …
Cell2location maps fine-grained cell types in spatial transcriptomics
Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in
health and disease, but comprehensive mapping of cell types in situ remains a challenge …
health and disease, but comprehensive mapping of cell types in situ remains a challenge …
Revealing spatial multimodal heterogeneity in tissues with SpaTrio
Capturing and depicting the multimodal tissue information of tissues at the spatial scale
remains a significant challenge owing to technical limitations in single-cell multi-omics and …
remains a significant challenge owing to technical limitations in single-cell multi-omics and …
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
Charting an organs' biological atlas requires us to spatially resolve the entire single-cell
transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and …
transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and …