Modeling intercellular communication in tissues using spatial graphs of cells

Spatial components of molecular tissue biology

(2022) Giovanni Palla et al.   NATURE BIOTECHNOLOGY

Cell2location maps fine-grained cell types in spatial transcriptomics

(2022) Vitalii Kleshchevnikov et al.   NATURE BIOTECHNOLOGY

Squidpy: a scalable framework for spatial omics analysis

(2022) Giovanni Palla et al.   NATURE METHODS

DestVI identifies continuums of cell types in spatial transcriptomics data

(2022) Romain Lopez et al.   NATURE BIOTECHNOLOGY

Multiplexed histology analyses for the phenotypic and spatial characterization of human innate lymphoid cells

(2021) Anna Pascual-Reguant et al.   Nature Communications

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

(2021) T. Lohoff et al.   NATURE BIOTECHNOLOGY

Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture

(2021) Yanfang Lu et al.   Cell Discovery

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

(2021) Luz Garcia-Alonso et al.   NATURE GENETICS

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

(2021) Tommaso Biancalani et al.   NATURE METHODS

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

(2020) Zixuan Cang et al.   Nature Communications

Single-cell metabolic profiling of human cytotoxic T cells

(2020) Felix J. Hartmann et al.   NATURE BIOTECHNOLOGY

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

(2019) Damien Arnol et al.   Cell Reports

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS