Research graph
References from A guidebook of spatial transcriptomic technologies, data resources and analysis approaches. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/nmeth.1315
10.1038/nmeth.1315 · External reference
10.1186/s13073-017-0467-4
10.1186/s13073-017-0467-4 · External reference
10.1038/s41593-020-00787-0
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10.1038/ncomms11022
10.1038/ncomms11022 · External reference
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10.1038/s41592-020-01033-y · External reference
10.15252/msb.20199146
10.15252/msb.20199146 · External reference
10.1016/j.cell.2020.05.039
10.1016/j.cell.2020.05.039 · External reference
10.1016/j.devcel.2022.04.009
10.1016/j.devcel.2022.04.009 · External reference
Clinical and translational values of spatial transcriptomics
10.1038/s41392-022-00960-w · 2022 · External reference
10.1038/s41586-021-03634-9
10.1038/s41586-021-03634-9 · External reference
10.1038/s41592-022-01409-2
10.1038/s41592-022-01409-2 · External reference
Spatially resolved transcriptomes-next generation tools for tissue exploration
10.1002/bies.201900221 · 2020 · External reference
Formation and detection of RNA-DNA hybrid molecules in cytological preparations
10.1073/pnas.63.2.378 · 1969 · External reference
10.1016/0014-4827(80)90087-7
10.1016/0014-4827(80)90087-7 · External reference
10.1126/science.280.5363.585
10.1126/science.280.5363.585 · External reference
10.1038/nmeth.2892
10.1038/nmeth.2892 · External reference
10.1126/science.aaa6090
10.1126/science.aaa6090 · External reference
10.1038/s41586-019-1049-y
10.1038/s41586-019-1049-y · External reference
10.1038/s41587-020-0472-9
10.1038/s41587-020-0472-9 · External reference
10.1038/s41592-020-0858-0
10.1038/s41592-020-0858-0 · External reference
Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH
2022 · External reference
High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging
2022 · External reference
10.1038/nmeth.2563
10.1038/nmeth.2563 · External reference
10.1126/science.1250212
10.1126/science.1250212 · External reference
Three-dimensional intact-tissue sequencing of single-cell transcriptional states
10.1126/science.aat5691 · 2018 · External reference
10.1093/nar/gkaa792
10.1093/nar/gkaa792 · External reference
10.1126/science.1260088
10.1126/science.1260088 · External reference
Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
10.1126/science.aax2656 · 2021 · External reference
10.1093/nar/gkab120
10.1093/nar/gkab120 · External reference
High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue
2022 · External reference
10.1126/science.aaf2403
10.1126/science.aaf2403 · External reference
10.1007/978-3-030-87821-4_7
10.1007/978-3-030-87821-4_7 · 2022 · External reference
10.1126/science.aaw1219
10.1126/science.aaw1219 · External reference
10.1038/s41592-019-0548-y
10.1038/s41592-019-0548-y · External reference
10.1016/j.cell.2020.10.026
10.1016/j.cell.2020.10.026 · External reference
10.1038/s41587-020-0739-1
10.1038/s41587-020-0739-1 · External reference
10.1016/j.cell.2021.05.010
10.1016/j.cell.2021.05.010 · External reference
10.1016/j.cell.2022.04.003
10.1016/j.cell.2022.04.003 · External reference
10.1101/gr.229002
10.1101/gr.229002 · External reference
10.1016/j.cell.2014.09.038
10.1016/j.cell.2014.09.038 · External reference
10.1038/s41587-021-00879-7
10.1038/s41587-021-00879-7 · External reference
10.1016/j.neuron.2016.10.001
10.1016/j.neuron.2016.10.001 · External reference
10.1038/s41592-020-0880-2
10.1038/s41592-020-0880-2 · External reference
10.1016/j.cell.2021.04.048
10.1016/j.cell.2021.04.048 · External reference
Statistical and machine learning methods for spatially resolved transcriptomics data analysis
10.1186/s13059-022-02653-7 · 2022 · External reference
10.1038/s41592-022-01480-9
10.1038/s41592-022-01480-9 · External reference
10.1016/j.devcel.2022.04.006
10.1016/j.devcel.2022.04.006 · External reference
SpatialDB: a database for spatially resolved transcriptomes
2020 · External reference
STOmicsDB: a database of spatial transcriptomic data
2022 · External reference
Unresolved reference
External reference
10.1101/gr.275224.121
10.1101/gr.275224.121 · External reference
10.1186/s13073-022-01075-1
10.1186/s13073-022-01075-1 · External reference
10.15252/msb.20188746
10.15252/msb.20188746 · External reference
Deep learning in spatial transcriptomics: learning from the next next-generation sequencing
2022 · External reference
10.1016/j.csbj.2022.08.043
10.1016/j.csbj.2022.08.043 · External reference
10.1038/s41587-021-01182-1
10.1038/s41587-021-01182-1 · External reference
deepBlink: threshold-independent detection and localization of diffraction-limited spots
10.1093/nar/gkab546 · 2021 · External reference
10.1371/journal.pcbi.1008256
10.1371/journal.pcbi.1008256 · External reference
ISTDECO: in situ transcriptomics decoding by deconvolution
2021 · External reference
Sparcle: assigning transcripts to cells in multiplexed images
2021 · External reference
10.1111/febs.15572
10.1111/febs.15572 · External reference
Joint cell segmentation and cell type annotation for spatial transcriptomics
10.15252/msb.202010108 · 2021 · External reference
Unresolved reference
External reference
10.1016/j.cell.2019.05.031
10.1016/j.cell.2019.05.031 · External reference
10.1038/s41592-019-0619-0
10.1038/s41592-019-0619-0 · External reference
10.1038/s41587-019-0113-3
10.1038/s41587-019-0113-3 · External reference
10.1038/s41592-018-0229-2
10.1038/s41592-018-0229-2 · External reference
10.1186/s13059-019-1850-9
10.1186/s13059-019-1850-9 · External reference
10.1038/s41592-021-01336-8
10.1038/s41592-021-01336-8 · External reference
Optimally weighted PCA for high-dimensional heteroscedastic data
2018 · External reference
Visualizing data using t-SNE
2008 · External reference
UMAP: uniform manifold approximation and projection for dimension reduction
2018 · External reference
Spatially aware dimension reduction for spatial transcriptomics
2022 · External reference
10.1088/1742-5468/2008/10/p10008
10.1088/1742-5468/2008/10/p10008 · External reference
From Louvain to Leiden: guaranteeing well-connected communities
10.1038/s41598-019-41695-z · 2019 · External reference
10.2307/2346830
10.2307/2346830 · External reference
On spectral clustering: analysis and an algorithm
2001 · External reference
10.1198/016214502760047131
10.1198/016214502760047131 · External reference
SC-MEB: spatial clustering with hidden Markov random field using empirical Bayes
2022 · External reference
10.1038/s41587-021-00935-2
10.1038/s41587-021-00935-2 · External reference
10.1038/s41592-021-01255-8
10.1038/s41592-021-01255-8 · External reference
10.1093/nar/gkac219
10.1093/nar/gkac219 · External reference
10.1038/s41576-021-00370-8
10.1038/s41576-021-00370-8 · External reference
Spatial charting of single-cell transcriptomes in tissues
2022 · External reference
10.1038/s41587-021-01139-4
10.1038/s41587-021-01139-4 · External reference
DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence
10.1093/bib/bbaa414 · 2021 · External reference
10.1038/nmeth.4636
10.1038/nmeth.4636 · External reference
10.1038/s41592-019-0701-7
10.1038/s41592-019-0701-7 · External reference
10.1186/s13059-021-02286-2
10.1186/s13059-021-02286-2 · External reference
10.1101/gr.271288.120
10.1101/gr.271288.120 · External reference
10.1016/j.cels.2021.04.008
10.1016/j.cels.2021.04.008 · External reference
Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning
2021 · External reference
10.1101/2020.05.31.125658
10.1101/2020.05.31.125658 · External reference
10.1038/s41467-020-15968-5
10.1038/s41467-020-15968-5 · External reference
10.1101/2020.08.11.245472
10.1101/2020.08.11.245472 · External reference
10.1016/j.celrep.2019.08.077
10.1016/j.celrep.2019.08.077 · External reference
10.1038/s41592-020-0885-x
10.1038/s41592-020-0885-x · External reference
Seamless integration of image and molecular analysis for spatial transcriptomics workflows
10.1186/s12864-020-06832-3 · 2020 · External reference
10.1038/s41592-022-01459-6
10.1038/s41592-022-01459-6 · External reference
3D reconstruction of spatial expression
10.1038/s41592-022-01476-5 · 2022 · External reference
10.1038/s41467-022-29439-6
10.1038/s41467-022-29439-6 · External reference
Seven technologies to watch in 2022
10.1038/d41586-022-00163-x · 2022 · External reference
10.1038/s41592-021-01203-6
10.1038/s41592-021-01203-6 · External reference
Spatial omics: navigating to the golden era of cancer research
10.1002/ctm2.696 · 2022 · External reference
Spatiotemporal Omics-refining the landscape of precision medicine
2022 · External reference
Multi-omics analysis: paving the path toward achieving precision medicine in cancer treatment and immuno-oncology
10.3389/fmolb.2022.962743 · 2022 · External reference
10.1038/s41422-020-00443-z
10.1038/s41422-020-00443-z · External reference
10.1016/j.cell.2022.11.021
10.1016/j.cell.2022.11.021 · External reference
10.1038/s41576-019-0114-6
10.1038/s41576-019-0114-6 · External reference
10.1016/j.cell.2011.02.013
10.1016/j.cell.2011.02.013 · External reference
10.1016/j.crmeth.2022.100340
10.1016/j.crmeth.2022.100340 · External reference
Cancer stem cell niche models and contribution by mesenchymal stroma/stem cells
10.1186/s12943-017-0595-x · 2017 · External reference
10.1038/s41586-022-05435-0
10.1038/s41586-022-05435-0 · External reference
Intratumoral heterogeneity as a predictive biomarker in anti-PD-(L)1 therapies for non-small cell lung cancer
10.1186/s12943-021-01331-9 · 2021 · External reference
10.1158/0008-5472.can-18-3962
10.1158/0008-5472.can-18-3962 · External reference
A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology
10.3389/fimmu.2022.996721 · 2022 · External reference
10.1016/j.kint.2022.08.032
10.1016/j.kint.2022.08.032 · External reference
10.1038/s41588-021-00911-1
10.1038/s41588-021-00911-1 · External reference
10.1038/s41467-021-26271-2
10.1038/s41467-021-26271-2 · External reference
10.1158/0008-5472.can-18-0747
10.1158/0008-5472.can-18-0747 · External reference
10.1016/j.cell.2019.11.025
10.1016/j.cell.2019.11.025 · External reference
10.3390/jcdd9010001
10.3390/jcdd9010001 · External reference
10.1038/s41588-021-00972-2
10.1038/s41588-021-00972-2 · External reference
10.1038/s41593-021-00905-6
10.1038/s41593-021-00905-6 · External reference
The expanding vistas of spatial transcriptomics
2022 · External reference
10.1038/s41467-021-25279-y
10.1038/s41467-021-25279-y · External reference
10.1038/s41586-020-03126-2
10.1038/s41586-020-03126-2 · External reference
Spatial profiling of chromatin accessibility in mouse and human tissues
10.1038/s41586-022-05094-1 · 2022 · External reference
10.1038/s41580-018-0094-y
10.1038/s41580-018-0094-y · External reference
The human cell atlas
10.7554/elife.27041 · 2017 · External reference
10.1016/j.neuron.2017.10.007
10.1016/j.neuron.2017.10.007 · External reference
10.1038/s41556-021-00788-6
10.1038/s41556-021-00788-6 · External reference
Unresolved reference
External reference
10.1152/physiolgenomics.00104.2020
10.1152/physiolgenomics.00104.2020 · External reference
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
10.7554/elife.26726 · 2017 · External reference
10.1016/j.trecan.2018.06.007
10.1016/j.trecan.2018.06.007 · External reference
10.1111/ajt.14757
10.1111/ajt.14757 · External reference
10.1038/550451a
10.1038/550451a · External reference
Unresolved reference
External reference
GUDMAP: the genitourinary developmental molecular anatomy project
10.1681/asn.2007101078 · 2008 · External reference
De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution
10.1038/s41467-022-34271-z · 2022 · External reference
Single-cell and spatial analysis reveal interaction of FAP(+) fibroblasts and SPP1(+) macrophages in colorectal cancer
10.1038/s41467-022-29366-6 · 2022 · External reference
10.1038/s41586-021-03775-x
10.1038/s41586-021-03775-x · External reference
10.1038/nbt.2859
10.1038/nbt.2859 · External reference
10.1186/s13059-019-1663-x
10.1186/s13059-019-1663-x · External reference
10.1016/j.cell.2014.04.005
10.1016/j.cell.2014.04.005 · External reference
10.1038/s41587-020-0591-3
10.1038/s41587-020-0591-3 · External reference
10.1016/j.cell.2021.12.045
10.1016/j.cell.2021.12.045 · External reference
10.1038/s41586-018-0414-6
10.1038/s41586-018-0414-6 · External reference
10.1101/2021.07.26.453774
10.1101/2021.07.26.453774 · External reference
10.1038/s41587-021-01044-w
10.1038/s41587-021-01044-w · External reference
10.1038/s41467-021-23807-4
10.1038/s41467-021-23807-4 · External reference
10.1186/s13059-017-1382-0
10.1186/s13059-017-1382-0 · External reference
Inferring spatially transient gene expression pattern from spatial transcriptomic studies
2020 · External reference
Spaniel: analysis and interactive sharing of Spatial Transcriptomics data
2019 · External reference
SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
10.1186/s12859-020-3489-7 · 2020 · External reference
Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments
2021 · External reference
10.1038/s42003-020-01247-y
10.1038/s42003-020-01247-y · External reference
Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation
2021 · External reference
10.1038/s42003-021-02739-1
10.1038/s42003-021-02739-1 · External reference
10.1038/s41587-021-00830-w
10.1038/s41587-021-00830-w · External reference
10.1038/s41467-022-28020-5
10.1038/s41467-022-28020-5 · External reference
Identifying multicellular spatiotemporal organization of cells with SpaceFlow
10.1038/s41467-022-31739-w · 2022 · External reference
10.1093/nar/gkab043
10.1093/nar/gkab043 · External reference
Clustering spatial transcriptomics data
10.1093/bioinformatics/btab704 · 2021 · External reference
10.1186/s13059-021-02362-7
10.1186/s13059-021-02362-7 · External reference
10.1093/nar/gkac150
10.1093/nar/gkac150 · External reference
10.1038/s41467-022-30033-z
10.1038/s41467-022-30033-z · External reference
10.1038/s41592-021-01264-7
10.1038/s41592-021-01264-7 · External reference
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data
2018 · External reference
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments
10.1093/bioinformatics/btab486 · 2021 · External reference
Bayesian modeling of spatial molecular profiling data via Gaussian process
2021 · External reference
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map
2021 · External reference
10.1371/journal.pcbi.1007509
10.1371/journal.pcbi.1007509 · External reference
10.1038/nmeth.4634
10.1038/nmeth.4634 · External reference
10.1038/s41467-020-17900-3
10.1038/s41467-020-17900-3 · External reference
Identification of spatially variable genes with graph cuts
2018 · External reference
10.1186/s13059-021-02404-0
10.1186/s13059-021-02404-0 · External reference
sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling
10.1093/bioinformatics/btab164 · 2021 · External reference
GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data
10.1186/s13059-020-02214-w · 2020 · External reference
10.1186/s13059-022-02663-5
10.1186/s13059-022-02663-5 · External reference
10.1093/bioinformatics/btaa769
10.1093/bioinformatics/btaa769 · External reference
10.1038/s41592-021-01358-2
10.1038/s41592-021-01358-2 · External reference
Automated identification of the mouse brain’s spatial compartments from in situ sequencing data
10.1186/s12915-020-00874-5 · 2020 · External reference
10.1016/j.cell.2019.05.006
10.1016/j.cell.2019.05.006 · External reference
10.1038/s41592-019-0494-8
10.1038/s41592-019-0494-8 · External reference
Quantitative approaches for investigating the spatial context of gene expression
2017 · External reference
10.1016/j.immuni.2022.02.001
10.1016/j.immuni.2022.02.001 · External reference
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
2020 · External reference
LXMERT: learning cross-modality encoder representations from transformers
2019 · External reference
Multimodal machine learning: a survey and taxonomy
10.1109/tpami.2018.2798607 · 2019 · External reference
