Vaswani, A. et al. Attention is all you need. Preprint at https://doi.org/10.48550/arXiv.1706.03762 (2017).
Devlin, J., Chang, M. W., Lee, K. & Toutanova, K. BERT: pre-training of deep bidirectional transformers for language understanding. In Proc. 2019 Conference North American Chapter of the Association for Computational Linguistics: Human Language Technologies Vol. 1 (eds Burstein, J. et al.) 4174–4186 (Association for Computational Linguistics, 2019).
He, K., Zhang, X., Ren, S. & Sun, J. Deep residual learning for image recognition. In Proc. IEEE Computer Society Conference on Computer Vision and Pattern Recognition 770–778 (IEEE, 2016).
Theodoris, C. V. et al. Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Cell 160, 1072–1086 (2015).
Google Scholar
Theodoris, C. V. et al. Network-based screen in iPSC-derived cells reveals therapeutic candidate for heart valve disease. Science 371, eabd0724 (2021).
Google Scholar
Shao, X. et al. ScDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network. Nucleic Acids Res. 49, e122 (2021).
Google Scholar
Lieberman, Y., Rokach, L. & Shay, T. CaSTLe—classification of single cells by transfer learning: harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments. PLoS ONE 13, e0205499 (2018).
Google Scholar
Lin, T., Wang, Y., Liu, X. & Qiu, X. A survey of transformers. Preprint at https://doi.org/10.48550/arXiv.2106.04554 (2021).
Ren, J. et al. ZeRO-offload: democratizing billion-scale model training. In Proc. 2021 USENIX Annual Technical Conference 551–564 (USENIX, 2021).
Rajbhandari, S., Rasley, J., Ruwase, O. & He, Y. Zero: memory optimizations toward training trillion parameter models. In International Conference for High Performance Computing, Networking, Storage and Analysis 1–16 (IEEE, 2020).
Selewa, A. et al. Systematic comparison of high-throughput single-cell and single-nucleus transcriptomes during cardiomyocyte differentiation. Sci. Rep. 10, 1535 (2020).
Google Scholar
10x Genomics Datasets https://www.10xgenomics.com/resources/datasets/frozen-pbm-cs-donor-a-1-standard-1-1-0.
10X Genomics Datasets https://www.10xgenomics.com/resources/datasets/fresh-68-k-pbm-cs-donor-a-1-standard-1-1-0.
Li, Y. et al. Single-cell transcriptome analysis reveals dynamic cell populations and differential gene expression patterns in control and aneurysmal human aortic tissue. Circulation 142, 1374–1388 (2020).
Google Scholar
Xing, Q. R. et al. Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing. Sci. Adv. 6, 463–474 (2020).
Google Scholar
Guo, D. et al. iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling. eLife 11, e70341 (2022).
Google Scholar
Zhang, Y., Parmigiani, G. & Johnson, W. E. ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genom. Bioinform. 2, lqaa078 (2020).
Google Scholar
Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
Google Scholar
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).
Google Scholar
Shihab, H. A., Rogers, M. F., Campbell, C. & Gaunt, T. R. HIPred: an integrative approach to predicting haploinsufficient genes. Bioinformatics 33, 1751–1757 (2017).
Google Scholar
Ni, Z., Zhou, X. Y., Aslam, S. & Niu, D. K. Characterization of human dosage-sensitive transcription factor genes. Front. Genet. 10, 1208 (2019).
Google Scholar
Collins, R. L. et al. A cross-disorder dosage sensitivity map of the human genome. Cell 185, 3041–3055 (2022).
Google Scholar
Cao, J. et al. A human cell atlas of fetal gene expression. Science 370, 808 (2020).
Google Scholar
Pirruccello, J. P. et al. Analysis of cardiac magnetic resonance imaging in 36,000 individuals yields genetic insights into dilated cardiomyopathy. Nat. Commun. 11, 2254 (2020).
Google Scholar
Bolte, C. et al. Expression of Foxm1 transcription factor in cardiomyocytes is required for myocardial development. PLoS ONE 6, e22217 (2011).
Google Scholar
Bolte, C. et al. Postnatal ablation of Foxm1 from cardiomyocytes causes late onset cardiac hypertrophy and fibrosis without exacerbating pressure overload-induced cardiac remodeling. PLoS ONE 7, e48713 (2012).
Google Scholar
Currey, L., Thor, S. & Piper, M. TEAD family transcription factors in development and disease. Development 148, dev196675 (2021).
Google Scholar
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–356 (2006).
Google Scholar
Franzén, O., Gan, L.-M. & Björkegren, J. L. M. PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database 2019, baz406 (2019).
Google Scholar
Pan, G. et al. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1, 299–312 (2007).
Google Scholar
Chen, C. H. et al. Determinants of transcription factor regulatory range. Nat. Commun. 11, 2472 (2020).
Google Scholar
Litviňuková, M. et al. Cells of the adult human heart. Nature 588, 455–472 (2020).
Google Scholar
Ang, Y. S. et al. Disease model of GATA4 mutation reveals transcription factor cooperativity in human cardiogenesis. Cell 167, 1734–1749 (2016).
Google Scholar
Kathiriya, I. S. et al. Modeling human TBX5 haploinsufficiency predicts regulatory networks for congenital heart disease. Dev. Cell 56, 292–309 (2021).
Google Scholar
Chaffin, M. et al. Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy. Nature 608, 174–180 (2022).
Google Scholar
Hinson, J. T. et al. Titin mutations in iPS cells define sarcomere insufficiency as a cause of dilated cardiomyopathy. Science 349, 982–986 (2015).
Google Scholar
Seidman, C. E. & Seidman, J. G. Identifying sarcomere gene mutations in hypertrophic cardiomyopathy: a personal history. Circ. Res. 108, 743–750 (2011).
Google Scholar
Kamisago, M. et al. Mutations in sarcomere protein genes as a cause of dilated cardiomyopathy. New Engl. J. Med. 343, 1688–1696 (2000).
Google Scholar
Ramaccini, D. et al. Mitochondrial function and dysfunction in dilated cardiomyopathy. Front. Cell Dev. Biol. https://doi.org/10.3389/fcell.2020.624216 (2021).
Ho, D., Yan, L., Iwatsubo, K., Vatner, D. E. & Vatner, S. F. Modulation of β-adrenergic receptor signaling in heart failure and longevity: targeting adenylyl cyclase type 5. Heart Fail. Rev. 15, 495–512 (2010).
Google Scholar
Wagner, A. H. et al. DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Res. 44, D1036–D1044 (2016).
Google Scholar
Nakagawa, O. et al. Centronuclear myopathy in mice lacking a novel muscle-specific protein kinase transcriptionally regulated by MEF2. Genes Dev. 19, 2066–2077 (2005).
Google Scholar
Akazawa, H. & Komuro, I. Roles of cardiac transcription factors in cardiac hypertrophy. Circ. Res. 92, 1079–1088 (2003).
Henighan, T. et al. Scaling laws for autoregressive generative modeling. Preprint at https://doi.org/10.48550/arXiv.2010.14701 (2020).
Madissoon, E. et al. ScRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation. Genome Biol. 21, 1 (2019).
Google Scholar
Anderson, D. J. et al. NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network. Nat. Commun. 9, 1373 (2018).
Google Scholar
Smillie, C. S. et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178, 714–730 (2019).
Google Scholar
Lee, J. S. et al. Immunophenotyping of Covid-19 and influenza highlights the role of type I interferons in development of severe Covid-19. Sci. Immunol. 5, eabd1554 (2020).
Google Scholar
Baron, M. et al. A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Cell Syst. 3, 346–360 (2016).
Google Scholar
Fang, Z. et al. Single-cell heterogeneity analysis and CRISPR screen identify key β-cell-specific disease genes. Cell Rep. 26, 3132–3144 (2019).
Google Scholar
Agarwal, D. et al. A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders. Nat. Commun. 11, 4183 (2020).
Google Scholar
Rasouli, J. et al. A distinct GM-CSF+ T helper cell subset requires T-bet to adopt a TH1 phenotype and promote neuroinflammation. Sci. Immunol. 5, eaba9953 (2020).
Google Scholar
Park, J.-E. et al. A cell atlas of human thymic development defines T cell repertoire formation. Science 367, eaay3224 (2020).
Google Scholar
Mende, N. et al. Quantitative and molecular differences distinguish adult human medullary and extramedullary haematopoietic stem and progenitor cell landscapes. Preprint at BioRxiv https://doi.org/10.1101/2020.01.26.919753 (2020).
Setty, M. et al. Characterization of cell fate probabilities in single-cell data with Palantir. Nat. Biotechnol. 37, 451–460 (2019).
Google Scholar
Popescu, D.-M. et al. Decoding human fetal liver haematopoiesis. Nature 574, 365–371 (2019).
Google Scholar
Vento-Tormo, R. et al. Single-cell reconstruction of the early maternal-fetal interface in humans. Nature 563, 347–353 (2018).
Google Scholar
Ramachandran, P. et al. Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature 575, 512–518 (2019).
Google Scholar
Kinchen, J. et al. Structural remodeling of the human colonic mesenchyme in inflammatory bowel disease. Cell 175, 372–386 (2018).
Google Scholar
James, K. R. et al. Distinct microbial and immune niches of the human colon. Nat. Immunol. 21, 343–353 (2020).
Google Scholar
Zhou, L. et al. Single-cell RNA-seq analysis uncovers distinct functional human NKT cell sub-populations in peripheral blood. Front. Cell Dev. Biol. 8, 384 (2020).
Google Scholar
Liao, J. et al. Single-cell RNA sequencing of human kidney. Sci. Data 7, 4 (2020).
Google Scholar
Jäkel, S. et al. Altered human oligodendrocyte heterogeneity in multiple sclerosis. Nature 566, 543–547 (2019).
Google Scholar
Merrick, D. et al. Identification of a mesenchymal progenitor cell hierarchy in adipose tissue. Science 364, eaav2501 (2019).
Google Scholar
Habermann, A. C. et al. Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis. Sci. Adv. 6, eaba1972 (2020).
Google Scholar
Rosa, F. F. et al. Direct reprogramming of fibroblasts into antigen-presenting dendritic cells. Sci. Immunol. 3, eaau4292 (2018).
Google Scholar
Stewart, B. J. et al. Spatiotemporal immune zonation of the human kidney. Science 365, 1461–1466 (2019).
Google Scholar
MacParland, S. A. et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat. Commun. 9, 4383 (2018).
Google Scholar
Welch, J. et al. Integrative inference of brain cell similarities and differences from single-cell genomics. Preprint at BioRxiv https://doi.org/10.1101/459891 (2018).
Ledergor, G. et al. Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma. Nat. Med. 24, 1867–1876 (2018).
Google Scholar
Lukowski, S. W. et al. A single-cell transcriptome atlas of the adult human retina. EMBO J. 38, e100811 (2019).
Google Scholar
Kang, H. M. et al. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat. Biotechnol. 36, 89–94 (2018).
Google Scholar
Zirkel, A. et al. HMGB2 loss upon senescence entry disrupts genomic organization and induces CTCF clustering across cell types. Mol. Cell 70, 730–744 (2018).
Google Scholar
Goudot, C. et al. Aryl hydrocarbon receptor controls monocyte differentiation into dendritic cells versus macrophages. Immunity 47, 582–596 (2017).
Google Scholar
McCauley, K. B. et al. Single-cell transcriptomic profiling of pluripotent stem cell-derived SCGB3A2+ airway epithelium. Stem Cell Rep. 10, 1579–1595 (2018).
Google Scholar
Das, R. et al. Early B cell changes predict autoimmunity following combination immune checkpoint blockade. J. Clin. Invest. 128, 715–720 (2018).
Google Scholar
Kini Bailur, J. et al. Changes in bone marrow innate lymphoid cell subsets in monoclonal gammopathy: target for IMiD therapy. Blood Adv. 1, 2343–2347 (2017).
Google Scholar
Patil, V. S. et al. Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis. Sci. Immunol. 3, eaan8664 (2018).
Google Scholar
Wang, C. et al. Expansion of hedgehog disrupts mesenchymal identity and induces emphysema phenotype. J. Clin. Invest. 128, 4343–4358 (2018).
Google Scholar
Hermann, B. P. et al. The mammalian spermatogenesis single-cell transcriptome, from spermatogonial stem cells to spermatids. Cell Rep. 25, 1650–1667 (2018).
Google Scholar
Menon, R. et al. Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Development 145, dev164038 (2018).
Google Scholar
Czerniecki, S. M. et al. High-throughput screening enhances kidney organoid differentiation from human pluripotent stem cells and enables automated multidimensional phenotyping. Cell Stem Cell 22, 929–940 (2018).
Google Scholar
Papa, L. et al. Ex vivo human HSC expansion requires coordination of cellular reprogramming with mitochondrial remodeling and p53 activation. Blood Adv. 2, 2766–2779 (2018).
Google Scholar
Schulthess, J. et al. The short chain fatty acid butyrate imprints an antimicrobial program in macrophages. Immunity 50, 432–445 (2019).
Google Scholar
Guo, J. et al. The adult human testis transcriptional cell atlas. Cell Res. 28, 1141–1157 (2018).
Google Scholar
Karow, M. et al. Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. Nat. Neurosci. 21, 932–940 (2018).
Google Scholar
Xin, Y. et al. Pseudotime ordering of single human β-cells reveals states of insulin production and unfolded protein response. Diabetes 67, 1783–1794 (2018).
Google Scholar
Phipson, B. et al. Evaluation of variability in human kidney organoids. Nat. Methods 16, 79–87 (2019).
Google Scholar
Balan, S. et al. Large-scale human dendritic cell differentiation revealing notch-dependent lineage bifurcation and heterogeneity. Cell Rep. 24, 1902–1915 (2018).
Google Scholar
Milpied, P. et al. Human germinal center transcriptional programs are de-synchronized in B cell lymphoma. Nat. Immunol. 19, 1013–1024 (2018).
Google Scholar
Parikh, K. et al. Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature 567, 49–55 (2019).
Google Scholar
Habiel, D. M. et al. CCR10+ epithelial cells from idiopathic pulmonary fibrosis lungs drive remodeling. JCI Insight 3, e122211 (2018).
Google Scholar
Paik, D. T. et al. Large-scale single-cell RNA-seq reveals molecular signatures of heterogeneous populations of human induced pluripotent stem cell-derived endothelial cells. Circ. Res. 123, 443–450 (2018).
Google Scholar
Martin, J. C. et al. Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy. Cell 178, 1493–1508 (2019).
Google Scholar
Zheng, Y. et al. A human circulating immune cell landscape in aging and COVID-19. Protein Cell 11, 740–770 (2020).
Google Scholar
Hochane, M. et al. Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development. PLoS Biol. 17, e3000152 (2019).
Google Scholar
Sohni, A. et al. The neonatal and adult human testis defined at the single-cell level. Cell Rep. 26, 1501–1517 (2019).
Google Scholar
Tran, T. et al. In vivo developmental trajectories of human podocyte inform in vitro differentiation of pluripotent stem cell-derived podocytes. Dev. Cell 50, 102–116 (2019).
Google Scholar
Wang, Y. et al. Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J. Exp. Med. 217, e20191130 (2020).
Google Scholar
Vieira Braga, F. A. et al. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153–1163 (2019).
Google Scholar
Guo, J. et al. The dynamic transcriptional cell atlas of testis development during human puberty. Cell Stem Cell 26, 262–276 (2020).
Google Scholar
Voigt, A. P. et al. Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration. Proc. Natl Acad. Sci. USA 116, 24100–24107 (2019).
Google Scholar
Menon, M. et al. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat. Commun. 10, 4902 (2019).
Google Scholar
Wilk, A. J. et al. A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat. Med. 26, 1070–1076 (2020).
Google Scholar
Li, B. et al. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Nat. Methods 17, 793–798 (2020).
Google Scholar
Daniszewski, M. et al. Single cell RNA sequencing of stem cell-derived retinal ganglion cells. Sci. Data 5, 180013 (2018).
Google Scholar
Goveia, J. et al. An integrated gene expression landscape profiling approach to identify lung tumor endothelial cell heterogeneity and angiogenic candidates. Cancer Cell 37, 21–36 (2020).
Google Scholar
Norelli, M. et al. Monocyte-derived IL-1 and IL-6 are differentially required for cytokine-release syndrome and neurotoxicity due to CAR T cells. Nat. Med. 24, 739–748 (2018).
Google Scholar
Daniszewski, M. et al. Single-cell profiling identifies key pathways expressed by iPSCs cultured in different commercial media. iScience 7, 30–39 (2018).
Google Scholar
Miller, A. J. et al. In vitro and in vivo development of the human airway at single-cell resolution. Dev. Cell 53, 117–128 (2020).
Google Scholar
Silvin, A. et al. Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19. Cell 182, 1401–1418 (2020).
Google Scholar
Deprez, M. et al. A single-cell atlas of the human healthy airways. Am. J. Resp. Crit. Care Med. 202, 1636–1645 (2020).
Google Scholar
Sridhar, A. et al. Single-cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures. Cell Rep. 30, 1644–1659 (2020).
Google Scholar
Wu, H. et al. Comparative analysis and refinement of human PSC-derived kidney organoid differentiation with single-cell transcriptomics. Cell Stem Cell 23, 869–881 (2018).
Google Scholar
Vijay, J. et al. Single-cell analysis of human adipose tissue identifies depot and disease specific cell types. Nat. Metab. 2, 97–109 (2020).
Google Scholar
Solé-Boldo, L. et al. Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun. Biol. 3, 188 (2020).
Google Scholar
Adams, T. S. et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci. Adv. 6, eaba1983 (2020).
Google Scholar
Moreira, L. M. et al. Paracrine signalling by cardiac calcitonin controls atrial fibrogenesis and arrhythmia. Nature 587, 460–465 (2020).
Google Scholar
Ren, X. et al. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell 184, 1895–1913 (2021).
Google Scholar
Bunis, D. G. et al. Single-cell mapping of progressive fetal-to-adult transition in human naive T cells. Cell Rep. 34, 108573 (2021).
Google Scholar
Plasschaert, L. W. et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377–381 (2018).
Google Scholar
Takeda, A. et al. Single-cell survey of human lymphatics unveils marked endothelial cell heterogeneity and mechanisms of homing for neutrophils. Immunity 51, 561–572 (2019).
Google Scholar
Frumm, S. M. et al. A hierarchy of proliferative and migratory keratinocytes maintains the tympanic membrane. Cell Stem Cell 28, 315–330 (2021).
Google Scholar
Yu, Z. et al. Single-cell transcriptomic map of the human and mouse bladders. J. Am. Soc. Nephrol. 30, 2159–2176 (2019).
Google Scholar
Rubenstein, A. B. et al. Single-cell transcriptional profiles in human skeletal muscle. Sci. Rep. 10, 229 (2020).
Google Scholar
McCracken, I. R. et al. Transcriptional dynamics of pluripotent stem cell-derived endothelial cell differentiation revealed by single-cell RNA sequencing. Eur. Heart J. 41, 1024–1036 (2020).
Google Scholar
Hua, P. et al. Single-cell analysis of bone marrow-derived CD34+ cells from children with sickle cell disease and thalassemia. Blood 134, 2111–2115 (2019).
Google Scholar
Orozco, L. D. et al. Integration of eQTL and a single-cell atlas in the human eye identifies causal genes for age-related macular degeneration. Cell Rep. 30, 1246–1259 (2020).
Google Scholar
Hurley, K. et al. Reconstructed single-cell fate trajectories define lineage plasticity windows during differentiation of human PSC-derived distal lung progenitors. Cell Stem Cell 26, 593–608 (2020).
Google Scholar
Schafflick, D. et al. Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis. Nat. Commun. 11, 247 (2020).
Google Scholar
Su, C. et al. Single-cell RNA sequencing in multiple pathologic types of renal cell carcinoma revealed novel potential tumor-specific markers. Front. Oncol. 11, 719564 (2021).
Google Scholar
He, J. et al. Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses. Cell Res. 31, 742–757 (2021).
Google Scholar
Liao, M. et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat. Med. 26, 842–844 (2020).
Google Scholar
Liu, X. et al. Reprogramming roadmap reveals route to human induced trophoblast stem cells. Nature 586, 101–107 (2020).
Google Scholar
He, S. et al. Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs. Genome Biol. 21, 294 (2020).
Google Scholar
Wu, C.-L. et al. Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesis. Nat. Commun. 12, 362 (2021).
Google Scholar
Cowan, C. S. et al. Cell types of the human retina and its organoids at single-cell resolution. Cell 182, 1623–1640 (2020).
Google Scholar
Savas, P. et al. Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis. Nat. Med. 24, 986–993 (2018).
Google Scholar
Wang, L. et al. Single-cell map of diverse immune phenotypes in the metastatic brain tumor microenvironment of non small cell lung cancer. Preprint at BioRxiv https://doi.org/10.1101/2019.12.30.890517 (2019).
Lu, Y.-C. et al. Single-cell transcriptome analysis reveals gene signatures associated with T-cell persistence following adoptive cell therapy. Cancer Immunol. Res. 7, 1824–1836 (2019).
Google Scholar
Wang, L. et al. The phenotypes of proliferating glioblastoma cells reside on a single axis of variation. Cancer Discov. 9, 1708–1719 (2019).
Google Scholar
Wang, R. et al. Adult human glioblastomas harbor radial glia-like cells. Stem Cell Rep. 14, 338–350 (2020).
Google Scholar
Wang, L., Catalan, F., Shamardani, K., Babikir, H. & Diaz, A. Ensemble learning for classifying single-cell data and projection across reference atlases. Bioinformatics 36, 3585–3587 (2020).
Google Scholar
Ruffin, A. T. et al. B cell signatures and tertiary lymphoid structures contribute to outcome in head and neck squamous cell carcinoma. Nat. Commun. 12, 3349 (2021).
Google Scholar
Zhang, Q. et al. Landscape and dynamics of single immune cells in hepatocellular carcinoma. Cell 179, 829–845 (2019).
Google Scholar
Song, Q. et al. Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq. Cancer Med. 8, 3072–3085 (2019).
Google Scholar
Kim, N. et al. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nat. Commun. 11, 2285 (2020).
Google Scholar
Tang-Huau, T.-L. et al. Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway. Nat. Commun. 9, 2570 (2018).
Google Scholar
Peng, J. et al. Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Res. 29, 725–738 (2019).
Google Scholar
10x Genomics Datasets: Single Cell Gene Expression. 10x Genomics https://www.10xgenomics.com/resources/datasets?menu%5Bproducts.name%5D=Single%20Cell%20Gene%20Expression&query=&page=1&configure%5Bfacets%5D%5B0%5D=chemistryVersionAndThroughput&configure%5Bfacets%5D%5B1%5D=pipeline.version&configure%5BhitsPerPage%5D=500.
de Andrade, L. F. et al. Discovery of specialized NK cell populations infiltrating human melanoma metastases. JCI Insight 4, e133103 (2019).
Google Scholar
Zhang, P. et al. Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer. Cell Rep. 27, 1934–1947 (2019).
Google Scholar
Durante, M. A. et al. Single-cell analysis reveals new evolutionary complexity in uveal melanoma. Nat. Commun. 11, 496 (2020).
Google Scholar
Svensson, V., da Veiga Beltrame, E. & Pachter, L. A curated database reveals trends in single-cell transcriptomics. Database 2020, baaa073 (2020).
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
Google Scholar
Xin, J. et al. High-performance web services for querying gene and variant annotation. Genome Biol. 17, 91 (2016).
Google Scholar
Dunning, T. The t-digest: efficient estimates of distributions. Softw. Impacts 7, 100049 (2021).
Google Scholar
Lhoest, Q. et al. Datasets: a community library for natural language processing. Preprint at https://doi.org/10.48550/arXiv.2109.02846 (2021).
Wolf, T. et al. HuggingFace’s transformers: state-of-the-art natural language processing. Preprint at https://doi.org/10.48550/arXiv.1910.03771 (2019).
Loshchilov, I. & Hutter, F. Decoupled weight decay regularization. Preprint at https://doi.org/10.48550/arXiv.1711.05101 (2017).