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References from Cell2Spatial is a computational framework that maps single cells to spatial transcriptomic spots to reconstruct tissue architecture. Local targets link to admitted publications; unresolved targets remain external evidence.
Single-cell sequencing
10.1038/nmeth.2771 · 2014 · External reference
Methods and applications for single-cell and spatial multi-omics
10.1038/s41576-023-00580-2 · 2023 · External reference
Spatial charting of single-cell transcriptomes in tissues
10.1038/s41587-022-01233-1 · 2022 · External reference
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
10.1038/s41576-021-00370-8 · 2021 · External reference
Exploring tissue architecture using spatial transcriptomics
10.1038/s41586-021-03634-9 · 2021 · External reference
Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas
10.1038/s41587-019-0392-8 · 2020 · External reference
Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma
2020 · External reference
A single-cell and spatially resolved atlas of human breast cancers
10.1038/s41588-021-00911-1 · 2021 · External reference
Spatiotemporal analysis of human intestinal development at single-cell resolution
10.1016/j.cell.2020.12.016 · 2021 · External reference
Cell2location maps fine-grained cell types in spatial transcriptomics
10.1038/s41587-021-01139-4 · 2022 · External reference
Spatially informed cell-type deconvolution for spatial transcriptomics
10.1038/s41587-022-01273-7 · 2022 · External reference
Robust decomposition of cell type mixtures in spatial transcriptomics
10.1038/s41587-021-00830-w · 2022 · External reference
SpatialDWLS: accurate deconvolution of spatial transcriptomic data
10.1186/s13059-021-02362-7 · 2021 · External reference
STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing
2022 · External reference
DestVI identifies continuums of cell types in spatial transcriptomics data
10.1038/s41587-022-01272-8 · 2022 · External reference
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography
10.1038/s42003-020-01247-y · 2020 · External reference
Integration of computational analysis and spatial transcriptomics in single-cell studies
10.1016/j.gpb.2022.06.006 · 2023 · External reference
Comprehensive integration of single-cell data
10.1016/j.cell.2019.05.031 · 2019 · External reference
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
10.1038/s41592-021-01264-7 · 2021 · External reference
High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
10.1038/s41587-023-01697-9 · 2023 · External reference
A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples
10.1186/s12864-020-06888-1 · 2020 · External reference
Determining cell type abundance and expression from bulk tissues with digital cytometry
10.1038/s41587-019-0114-2 · 2019 · External reference
On implementing 2D rectangular assignment algorithms
10.1109/taes.2016.140952 · 2016 · External reference
Inferring spatial and signaling relationships between cells from single cell transcriptomic data
10.1038/s41467-020-15968-5 · 2020 · External reference
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport
10.1038/s41596-021-00573-7 · 2021 · External reference
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
10.1093/nar/gkab043 · 2021 · External reference
DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence
10.1093/bib/bbaa414 · 2021 · External reference
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
10.1038/s41592-022-01480-9 · 2022 · External reference
Squidpy: a scalable framework for spatial omics analysis
10.1038/s41592-021-01358-2 · 2022 · External reference
Mapping the developing human immune system across organs
2022 · External reference
A cell atlas of human thymic development defines T cell repertoire formation
2020 · External reference
Journey through the thymus: stromal guides for T-cell development and selection
10.1038/nri1781 · 2006 · External reference
Development of alphabeta T cells in the human thymus
10.1038/nri913 · 2002 · External reference
Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma
10.1038/s41467-022-31951-8 · 2022 · External reference
Integration of spatial and single-cell transcriptomics localizes epithelial cell-immune cross-talk in kidney injury
2021 · External reference
Single-cell profiling reveals sex, lineage, and regional diversity in the mouse kidney
10.1016/j.devcel.2019.10.005 · 2019 · External reference
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
10.1038/s41593-020-00787-0 · 2021 · External reference
Single-cell transcriptomic analysis of Alzheimer’s disease
10.1038/s41586-019-1195-2 · 2019 · External reference
A molecular single-cell lung atlas of lethal COVID-19
10.1038/s41586-021-03569-1 · 2021 · External reference
Human distal lung maps and lineage hierarchies reveal a bipotent progenitor
10.1038/s41586-022-04541-3 · 2022 · External reference
Optimizing xenium in situ data utility by quality assessment and best practice analysis workflows
2023 · External reference
Molecular diversity and specializations among the cells of the adult mouse brain
10.1016/j.cell.2018.07.028 · 2018 · External reference
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
10.1038/nbt.2859 · 2014 · External reference
Using clusterProfiler to characterize multiomics data
10.1038/s41596-024-01020-z · 2024 · External reference
Reversed graph embedding resolves complex single-cell trajectories
10.1038/nmeth.4402 · 2017 · External reference
Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer
10.1016/j.immuni.2022.02.001 · 2022 · External reference
A single-cell tumor immune atlas for precision oncology
10.1101/gr.273300.120 · 2021 · External reference
Using MERSCOPE to generate a cell atlas of the mouse brain that includes lowly expressed genes
10.1017/s1551929521001346 · 2021 · External reference
Full-length RNA-seq from single cells using Smart-seq2
10.1038/nprot.2014.006 · 2014 · External reference
Single-cell RNA sequencing with drop-seq
10.1007/978-1-4939-9240-9_6 · 2019 · External reference
Understanding how dimension reduction tools work: an empirical approach to deciphering t-SNE, UMAP, TriMAP, and PaCMAP for data visualization
2021 · External reference
Getis–ord spatial statistics to identify hot spots by using incident management data
10.3141/2165-05 · 2010 · External reference
Integrated analysis of multimodal single-cell data
2021 · External reference
Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges
10.1093/nar/gkae267 · 2024 · External reference
Mapping the spatial atlas of the human bone tissue integrating spatial and single-cell transcriptomics
2025 · External reference
Modeling zero inflation is not necessary for spatial transcriptomics
10.1186/s13059-022-02684-0 · 2022 · External reference
SciPy 1.0: fundamental algorithms for scientific computing in Python
10.1038/s41592-019-0686-2 · 2020 · External reference
Unresolved reference
2017 · External reference
Adult mouse cortical cell taxonomy revealed by single cell transcriptomics
10.1038/nn.4216 · 2016 · External reference
Single-cell genomics identifies cell type-specific molecular changes in autism
10.1126/science.aav8130 · 2019 · External reference
