Integrating single-cell transcriptomic data across different conditions, technologies, and species

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2. Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity
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3. hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data
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4. Tryptophan-derived microbial metabolites activate the aryl hydrocarbon receptor in tumor-associated macrophages to suppress anti-tumor immunity
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5. A lymphocyte–microglia–astrocyte axis in chronic active multiple sclerosis
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6. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
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7. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
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8. Homeostatic mini-intestines through scaffold-guided organoid morphogenesis
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9. Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis
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10. Single-cell transcriptomic profiling of the aging mouse brain
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11. scmap: projection of single-cell RNA-seq data across data sets
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12. Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease
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13. A comparison of automatic cell identification methods for single-cell RNA sequencing data
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14. Machine learning for integrating data in biology and medicine: principles, practice, and opportunities
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15. Single-cell RNA sequencing highlights the role of inflammatory cancer-associated fibroblasts in bladder urothelial carcinoma
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16. Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
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17. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
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18. Functional characterization of the dural sinuses as a neuroimmune interface
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19. Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK+ CD8+ T Cells as Conserved Hallmark of Inflammaging
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20. Single-cell RNA landscape of intratumoral heterogeneity and immunosuppressive microenvironment in advanced osteosarcoma
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21. Ageing hallmarks exhibit organ-specific temporal signatures
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22. Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer
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23. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data
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24. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
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25. scGen predicts single-cell perturbation responses
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26. Proteogenomic and metabolomic characterization of human glioblastoma
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27. TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy
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28. TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment
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29. Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease
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30. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids
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31. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
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32. Locally renewing resident synovial macrophages provide a protective barrier for the joint
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33. Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets
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34. Single-cell landscape of immunological responses in patients with COVID-19
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35. Cell stress in cortical organoids impairs molecular subtype specification
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36. Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report
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37. Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human
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38. Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma
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39. Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single Cell RNA Sequencing
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40. Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
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41. Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity
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42. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens
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44. Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics
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45. Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics
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46. Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment
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47. Characteristics of anti-CD19 CAR T cell infusion products associated with efficacy and toxicity in patients with large B cell lymphomas
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48. Allergic inflammatory memory in human respiratory epithelial progenitor cells
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49. Generation of Functional Human 3D Cortico-Motor Assembloids
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50. Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration
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51. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
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52. The Mammalian Spermatogenesis Single-Cell Transcriptome, from Spermatogonial Stem Cells to Spermatids
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53. Tissue-resident FOLR2+ macrophages associate with CD8+ T cell infiltration in human breast cancer.
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54. Impaired mitochondrial oxidative phosphorylation limits the self-renewal of T cells exposed to persistent antigen
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55. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation
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56. Neuroinflammatory astrocyte subtypes in the mouse brain
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57. The Human and Mouse Enteric Nervous System at Single-Cell Resolution
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58. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
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59. Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell
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60. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells
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61. Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function
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62. Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy
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63. Single-cell atlas of lineage states, tumor microenvironment, and subtype-specific expression programs in gastric cancer
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64. Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx
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65. Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart
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66. Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles
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67. Transcriptional and Cellular Diversity of the Human Heart
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68. Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury
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69. Stem-like CD8 T cells mediate response of adoptive cell immunotherapy against human cancer
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70. Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease
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71. Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells
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72. Anti-human TREM2 induces microglia proliferation and reduces pathology in an Alzheimer’s disease model
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73. Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection
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74. Mesothelial cell-derived antigen-presenting cancer-associated fibroblasts induce expansion of regulatory T cells in pancreatic cancer
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75. Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics
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76. Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes
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77. Single-Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis
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78. Spatiotemporal analysis of human intestinal development at single-cell resolution
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79. Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons
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81. Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells
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82. Microscopic examination of spatial transcriptome using Seq-Scope
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83. A noninflammatory mRNA vaccine for treatment of experimental autoimmune encephalomyelitis
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84. muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data
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85. Capillary cell-type specialization in the alveolus
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86. MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate
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87. Auto-aggressive CXCR6+ CD8 T cells cause liver immune pathology in NASH
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88. A test metric for assessing single-cell RNA-seq batch correction
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89. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma
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90. Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data
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91. Co-option of Neutrophil Fates by Tissue Environments
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92. Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
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93. Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression
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