Loi, S. et al. Tumor-infiltrating lymphocytes and prognosis: a pooled individual patient analysis of early-stage triple-negative breast cancers. J. Clin. Oncol. 37, 559–569 (2019).
Article PubMed PubMed Central Google Scholar
Abuhadra, N. et al. Prognostic impact of high baseline stromal tumor-infiltrating lymphocytes in the absence of pathologic complete response in early-stage triple-negative breast cancer. Cancers 14, 1323 (2022).
Article CAS PubMed PubMed Central Google Scholar
Berger, M. F. & Mardis, E. R. The emerging clinical relevance of genomics in cancer medicine. Nat. Rev. Clin. Oncol. 15, 353–365 (2018).
Article CAS PubMed PubMed Central Google Scholar
Stuart, T. & Satija, R. Integrative single-cell analysis. Nat. Rev. Genet. 20, 257–272 (2019).
Article CAS PubMed Google Scholar
Lim, J. et al. Transitioning single-cell genomics into the clinic. Nat. Rev. Genet. 24, 573–584 (2023).
Article CAS PubMed Google Scholar
Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377–382 (2009).
Article CAS PubMed Google Scholar
[No authors listed] Method of the year 2013. Nat. Methods 11, 1 (2014).
Blainey, P. C. & Quake, S. R. Dissecting genomic diversity, one cell at a time. Nat. Methods 11, 19–21 (2014).
Article CAS PubMed PubMed Central Google Scholar
Sandberg, R. Entering the era of single-cell transcriptomics in biology and medicine. Nat. Methods 11, 22–24 (2014).
Article CAS PubMed Google Scholar
Eberwine, J., Sul, J. Y., Bartfai, T. & Kim, J. The promise of single-cell sequencing. Nat. Methods 11, 25–27 (2014).
Article CAS PubMed Google Scholar
Chen, W. T. et al. Spatial transcriptomics and in situ sequencing to study Alzheimer’s disease. Cell 182, 976–991.e19 (2020).
Article CAS PubMed Google Scholar
Ratz, M. et al. Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nat. Neurosci. 25, 285–294 (2022).
Article CAS PubMed PubMed Central Google Scholar
Maniatis, S. et al. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science 364, 89–93 (2019).
Article CAS PubMed Google Scholar
Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 185, 1777–1792.e21 (2022).
Article CAS PubMed Google Scholar
Asp, M. et al. A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart. Cell 179, 1647–1660.e19 (2019).
Article CAS PubMed Google Scholar
Fawkner-Corbett, D. et al. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 184, 810–826.e23 (2021).
Article CAS PubMed PubMed Central Google Scholar
Fu, T. et al. Spatial architecture of the immune microenvironment orchestrates tumor immunity and therapeutic response. J. Hematol. Oncol. 14, 98 (2021).
Article PubMed PubMed Central Google Scholar
Larroquette, M. et al. Spatial transcriptomics of macrophage infiltration in non-small cell lung cancer reveals determinants of sensitivity and resistance to anti-PD1/PD-L1 antibodies. J. Immunother. Cancer 10, e003890 (2022).
Article PubMed PubMed Central Google Scholar
Grauel, A. L. et al. TGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts. Nat. Commun. 11, 6315 (2020).
Article CAS PubMed PubMed Central Google Scholar
Coy, S. et al. Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma. Nat. Commun. 13, 4814 (2022).
Article CAS PubMed PubMed Central Google Scholar
Hunter, M. V., Moncada, R., Weiss, J. M., Yanai, I. & White, R. M. Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. Nat. Commun. 12, 6278 (2021).
Article CAS PubMed PubMed Central Google Scholar
[No authors listed] Method of the year 2020: spatially resolved transcriptomics. Nat. Methods 18, 1 (2021).
Zhuang, X. Spatially resolved single-cell genomics and transcriptomics by imaging. Nat. Methods 18, 18–22 (2021).
Article CAS PubMed PubMed Central Google Scholar
Larsson, L., Frisen, J. & Lundeberg, J. Spatially resolved transcriptomics adds a new dimension to genomics. Nat. Methods 18, 15–18 (2021).
Article CAS PubMed Google Scholar
Close, J. L., Long, B. R. & Zeng, H. Spatially resolved transcriptomics in neuroscience. Nat. Methods 18, 23–25 (2021).
Article CAS PubMed Google Scholar
Bressan, D., Battistoni, G. & Hannon, G. J. The dawn of spatial omics. Science 381, eabq4964 (2023).
Article CAS PubMed PubMed Central Google Scholar
Mirzazadeh, R. et al. Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nat. Commun. 14, 509 (2023).
Article CAS PubMed PubMed Central Google Scholar
Petukhov, V. et al. Cell segmentation in imaging-based spatial transcriptomics. Nat. Biotechnol. 40, 345–354 (2022).
Article CAS PubMed Google Scholar
Park, J. et al. Cell segmentation-free inference of cell types from in situ transcriptomics data. Nat. Commun. 12, 3545 (2021).
Article CAS PubMed PubMed Central Google Scholar
Zhang, Y. et al. Deconvolution algorithms for inference of the cell-type composition of the spatial transcriptome. Comput. Struct. Biotechnol. J. 21, 176–184 (2023).
Article CAS PubMed Google Scholar
Li, H. et al. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics. Nat. Commun. 14, 1548 (2023).
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