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References from Scalable localization of clustering instability for spatial transcriptomics. Local targets link to admitted publications; unresolved targets remain external evidence.
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High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis
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Unresolved reference
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Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale
10.1038/s41467-023-42237-y · 2023 · External reference
Spatially organized tumor-stroma boundary determines the efficacy of immunotherapy in colorectal cancer patients
10.1038/s41467-024-54710-3 · 2024 · External reference
Complementing muscle regeneration—fibro-adipogenic progenitor and macrophage-mediated repair of elderly human skeletal muscle
10.1038/s41467-025-60627-2 · 2025 · External reference
Graph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for alzheimer’s disease
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Clonal diversity shapes the tumour microenvironment leading to distinct immunotherapy responses in metastatic urothelial carcinoma
10.1038/s41467-025-63309-1 · 2025 · External reference
Charting the spatial transcriptome of the human cerebral cortex at single-cell resolution
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Fast unfolding of communities in large networks
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Cluster-wise assessment of cluster stability
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Identification of cell types from single cell data using stable clustering
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Computational challenges and opportunities in spatially resolved transcriptomic data analysis
10.1038/s41467-021-25557-9 · 2021 · External reference
Spatial transcriptomics reveals distinct and conserved tumor core and leading edge architectures in oral squamous cell carcinoma
2023 · External reference
Spatial transcriptomics technology in cancer research
10.3389/fonc.2022.1019111 · 2022 · External reference
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
2018 · External reference
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Fuzzy C-Means based LSED analysis model of single-cell rna sequencing data for gene expression difference data
2021 · External reference
scHFC: a hybrid fuzzy clustering method for single-cell rna-seq data optimized by natural computation
10.1093/bib/bbab588 · 2022 · External reference
High-order topology for deep single-cell multiview fuzzy clustering
10.1109/tfuzz.2024.3399740 · 2024 · External reference
Soft graph clustering for single-cell rna sequencing data
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Deep soft k-means clustering with self-training for single-cell rna sequence data
2020 · External reference
JOINT for large-scale single-cell rna-sequencing analysis via soft-clustering and parallel computing
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A scalable approach to topic modelling in single-cell data by approximate pseudobulk projection
10.26508/lsa.202402713 · 2024 · External reference
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10.1038/s41587-021-00935-2 · External reference
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10.1186/s13059-022-02734-7 · External reference
BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data
10.1093/bib/bbae524 · 2024 · External reference
Identification of spatial domains, spatially variable genes, and genetic association studies of alzheimer disease with an autoencoder-based fuzzy clustering algorithm
10.2174/0115748936278884240102094058 · 2024 · External reference
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10.1038/nmeth.4236 · 2017 · External reference
10.1093/bioinformatics/bty793
10.1093/bioinformatics/bty793 · External reference
Significance analysis for clustering with single-cell rna-sequencing data
10.1038/s41592-023-01933-9 · 2023 · External reference
10.1038/s41593-020-00787-0
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Unresolved reference
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Unresolved reference
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10.1126/science.aaw1219
10.1126/science.aaw1219 · External reference
Unresolved reference
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Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors
10.1038/s41467-025-64292-3 · 2025 · External reference
From Louvain to Leiden: guaranteeing well-connected communities
2019 · External reference
Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder
10.1038/s41467-022-29439-6 · 2022 · External reference
Unsupervised spatially embedded deep representation of spatial transcriptomics
10.1186/s13073-024-01283-x · 2024 · External reference
Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST
10.1038/s41467-023-36796-3 · 2023 · External reference
10.1038/s41588-022-01256-z
10.1038/s41588-022-01256-z · External reference
10.1201/9781003277965
10.1201/9781003277965 · External reference
10.1186/s13059-024-03183-0
10.1186/s13059-024-03183-0 · External reference
How many markers are needed to robustly determine a cell’s type?
10.1016/j.isci.2021.103292 · 2021 · External reference
Mapping the topography of spatial gene expression with interpretable deep learning
10.1038/s41592-024-02503-3 · 2025 · External reference
Gaston-mix: a unified model of spatial gradients and domains using spatial mixture-of-experts
10.1093/bioinformatics/btaf254 · 2025 · External reference
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
10.1038/s41592-021-01255-8 · 2021 · External reference
10.1101/2020.05.31.125658
10.1101/2020.05.31.125658 · External reference
Spadecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning
10.1038/s42003-023-04761-x · 2023 · External reference
10.1101/gr.271288.120
10.1101/gr.271288.120 · External reference
Intracellular spatial transcriptomic analysis toolkit (InSTAnT)
10.1038/s41467-024-49457-w · 2024 · External reference
Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics
10.1093/bioinformatics/btaf131 · 2025 · External reference
Representation learning for multi-modal spatially resolved transcriptomics data
10.1093/bioinformatics/btag316 · 2026 · External reference
Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
10.1002/cyto.a.24884 · 2024 · External reference
ST-SCSR: identifying spatial domains in spatial transcriptomics data via structure correlation and self-representation
10.1093/bib/bbae437 · 2024 · External reference
10.1038/s41588-024-01664-3
10.1038/s41588-024-01664-3 · External reference
Novae: a graph-based foundation model for spatial transcriptomics data
10.1038/s41592-025-02899-6 · 2025 · External reference
Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding
10.1038/s41467-022-35288-0 · 2022 · External reference
ScType enables fast and accurate cell type identification from spatial transcriptomics data
10.1093/bioinformatics/btae426 · 2024 · External reference
Adjusting the adjusted rand index–a multinomial story
2020 · External reference
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell rna-seq data
10.1186/s13073-023-01168-5 · 2023 · External reference
Spatial transcriptomics in bone mechanomics: Exploring the mechanoregulation of fracture healing in the era of spatial omics
10.1126/sciadv.adp8496 · 2025 · External reference
TAS-Seq is a robust and sensitive amplification method for bead-based scrna-seq
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