Integrated analysis of multimodal single-cell data

Cited by (1,144)

Items 401–500 of 1,144

1. Cell type ontologies of the Human Cell Atlas
   David Osumi-Sutherland, Chuan Xu, Maria Keays, Adam P. Levine, Peter V. Kharchenko, Aviv Regev, Lein Ed S, Sarah Amalia Teichmann · 2021 · Nature Cell Biology
2. Pyramidal neuron subtype diversity governs microglia states in the neocortex
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3. The cycling and aging mouse female reproductive tract at single-cell resolution
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4. Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology
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5. Spatial transcriptomics reveals tryptophan metabolism restricting maturation of intratumoral tertiary lymphoid structures
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6. Towards multimodal foundation models in molecular cell biology
   Haotian Cui, Alejandro Tejada-Lapuerta, Maria Brbić, Julio Sáez-Rodríguez, Simona Cristea, Hani Goodarzi, Mohammad Lotfollahi, Fabian Joachim Theis, Bo Wang · 2025 · Nature
7. Molecular signatures of long-term hepatocellular carcinoma risk in nonalcoholic fatty liver disease
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8. The Human Microglia Atlas (HuMicA) unravels changes in disease-associated microglia subsets across neurodegenerative conditions
   Martins-Ferreira, Ricardo, Calafell-Segura, Josep, Leal, Bárbara, Rodríguez-Ubreva, Javier, Martínez-Saez, Elena, Mereu, Elisabetta, Pinho E Costa, Paulo, Laguna, Ariadna, Ballestar, Esteban · 2025 · Nature Communications
9. A comparison of marker gene selection methods for single-cell RNA sequencing data
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10. Computational solutions for spatial transcriptomics
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11. Annotation of spatially resolved single-cell data with STELLAR
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12. mTORC1 upregulates B7-H3/CD276 to inhibit antitumor T cells and drive tumor immune evasion
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13. Microglia maintain structural integrity during fetal brain morphogenesis
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14. TREM2 protects from atherosclerosis by limiting necrotic core formation
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15. PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors
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16. Behavioural immune landscapes of inflammation
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17. Tumor-associated macrophages are shaped by intratumoral high potassium via Kir2.1
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18. Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development
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19. A new genomic framework to categorize pediatric acute myeloid leukemia
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20. Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission
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21. Identification of a protective microglial state mediated by miR-155 and interferon-γ signaling in a mouse model of Alzheimer’s disease
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22. From bench to bedside: Single-cell analysis for cancer immunotherapy
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23. Sex-Biased T-cell Exhaustion Drives Differential Immune Responses in Glioblastoma
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24. Leveraging deep single-soma RNA sequencing to explore the neural basis of human somatosensation
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25. UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference
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26. nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes
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27. Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity
    Lucy C. Garner, Ali Amini, Michael E. B. FitzPatrick, Martin Joseph Lett, Gabriel Fridolin Hess, Magdalena Filipowicz Sinnreich, Nicholas M. Provine, Paul Klenerman · 2023 · Nature Immunology
28. Molecular classification of hormone receptor-positive HER2-negative breast cancer
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29. Multi-omic profiling of the developing human cerebral cortex at the single-cell level
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30. High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis
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31. From Omics to Multi-Omics: A Review of Advantages and Tradeoffs
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32. Single-cell spatial transcriptomics reveals a dynamic control of metabolic zonation and liver regeneration by endothelial cell Wnt2 and Wnt9b
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33. The APOE-R136S mutation protects against APOE4-driven tau pathology, neurodegeneration, and neuroinflammation
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34. Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
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35. Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis
    Yoshiharu Muto, Eryn E. Dixon, Yasuhiro Yoshimura, Hao Wu, Kohei Omachi, Nicolas Ledru, Parker C. Wilson, Andrew J. King, N. Eric Olson, Marvin G. Gunawan et al. · 2022 · Nature Communications
36. Piezo2 expressing nociceptors mediate mechanical sensitization in experimental osteoarthritis
    Alia M. Obeidat, Matthew J. Wood, Natalie S. Adamczyk, Shingo Ishihara, Jie Li, Lai Wang, Dongjun Ren, David Alan Bennett, Richard J. Miller, Anne‐Marie Malfait et al. · 2023 · Nature Communications
37. Neural basis for fasting activation of the hypothalamic–pituitary–adrenal axis
    Amelia M Douglass, Jon M. Resch, Joseph C. Madara, Hakan Kucukdereli, Ofer Yizhar, Abhinav Grama, Masahito Yamagata, Zongfang Yang, Bradford B. Lowell · 2023 · Nature
38. Metabolic targeting of cancer associated fibroblasts overcomes T-cell exclusion and chemoresistance in soft-tissue sarcomas
    Marina T. Broz, Emily Y. Ko, Kristin Ishaya, Jin-Fen Xiao, Marco Claudio De Simone, Xen Ping Hoi, Roberta Piras, Basia Gala, Fernando Henrique Galvão Tessaro, Anja Karlstaedt et al. · 2024 · Nature Communications
39. Clonal hematopoiesis driven by mutated DNMT3A promotes inflammatory bone loss
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40. Characteristics of blood–brain barrier heterogeneity between brain regions revealed by profiling vascular and perivascular cells
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41. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues
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42. Spatiotemporal single-cell regulatory atlas reveals neural crest lineage diversification and cellular function during tooth morphogenesis
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43. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank
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44. Adaptive sequence divergence forged new neurodevelopmental enhancers in humans
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45. Nasopharyngeal carcinoma cells promote regulatory T cell development and suppressive activity via CD70-CD27 interaction
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46. Obesity-induced dysregulation of skin-resident PPARγ+ Treg cells promotes IL-17A-mediated psoriatic inflammation
    Pulavendran Sivasami, Cody M. Elkins, Pamela P. Diaz-Saldana, Kyndal L. Goss, Amy Chia-Ying Peng, Michael Hamersky, Jennifer Bae, Miaoer Xu, Brian P. Pollack, Edwin M. Horwitz et al. · 2023 · Immunity
47. SOX17 enables immune evasion of early colorectal adenomas and cancers
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48. Gasdermin D-mediated metabolic crosstalk promotes tissue repair
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49. PIEZO-dependent mechanosensing is essential for intestinal stem cell fate decision and maintenance
    Meryem B. Baghdadi, Ronja M. Houtekamer, Louisiane Perrin, Abilasha Rao‐Bhatia, Myles Whelen, Linda Decker, Martin Bergert, Carlos Perez Gonzalez, Réda Bouras, Giacomo Gropplero et al. · 2024 · Science
50. Anatomical structures, cell types and biomarkers of the Human Reference Atlas
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51. Single-cell immunology of SARS-CoV-2 infection
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52. Human circulating and tissue-resident memory CD8+ T cells
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53. Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux
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54. Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling
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55. Conserved and divergent gene regulatory programs of the mammalian neocortex
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56. Mechanisms of action and resistance in histone methylation-targeted therapy
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57. Neoadjuvant PARPi or chemotherapy in ovarian cancer informs targeting effector Treg cells for homologous-recombination-deficient tumors
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58. Alternating high-fat diet enhances atherosclerosis by neutrophil reprogramming
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59. Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s disease
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60. Oligodendrocytes produce amyloid-β and contribute to plaque formation alongside neurons in Alzheimer’s disease model mice
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61. ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells
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62. Single-cell profiling of Arabidopsis leaves to Pseudomonas syringae infection
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63. An oncogenic phenoscape of colonic stem cell polarization
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64. Large Scale Foundation Model on Single-cell Transcriptomics
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65. Spatial Transcriptomic Analysis of a Diverse Patient Cohort Reveals a Conserved Architecture in Triple-Negative Breast Cancer
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66. Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity
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67. A Novel Type of Monocytic Leukemia Stem Cell Revealed by the Clinical Use of Venetoclax-Based Therapy
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68. Pan-cancer proteogenomics connects oncogenic drivers to functional states
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69. Integration of spatial and single-cell data across modalities with weakly linked features
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70. CD4+ T cell activation distinguishes response to anti-PD-L1+anti-CTLA4 therapy from anti-PD-L1 monotherapy
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71. FASN Inhibition Decreases MHC-I Degradation and Synergizes with PD-L1 Checkpoint Blockade in Hepatocellular Carcinoma
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72. conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics
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73. Cell-type profiling in salamanders identifies innovations in vertebrate forebrain evolution
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74. Single-cell transcriptomics reveals cellular heterogeneity and molecular stratification of cervical cancer
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75. Dedifferentiation maintains melanocyte stem cells in a dynamic niche
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76. Integration of Pan-Cancer Single-Cell and Spatial Transcriptomics Reveals Stromal Cell Features and Therapeutic Targets in Tumor Microenvironment
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77. A rare PRIMER cell state in plant immunity
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78. Computational strategies for single-cell multi-omics integration
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79. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data
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80. Single-cell analysis of skeletal muscle macrophages reveals age-associated functional subpopulations
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81. Cytotoxic CD8+ T cells target citrullinated antigens in rheumatoid arthritis
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82. Lineage Tracing and Single-Nucleus Multiomics Reveal Novel Features of Adaptive and Maladaptive Repair after Acute Kidney Injury
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83. Explainable multi-task learning for multi-modality biological data analysis
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84. Fate mapping of Spp1 expression reveals age-dependent plasticity of disease-associated microglia-like cells after brain injury
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85. Brain-wide neuronal circuit connectome of human glioblastoma
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86. Hepatic stellate cells control liver zonation, size and functions via R-spondin 3
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87. Immunological memory diversity in the human upper airway
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88. Synaptic connectome of the Drosophila circadian clock
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89. Benchmarking strategies for cross-species integration of single-cell RNA sequencing data
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90. Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma
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91. Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data
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92. Solid-phase capture and profiling of open chromatin by spatial ATAC
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93. Transferred mitochondria accumulate reactive oxygen species, promoting proliferation
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94. THBS1-producing tumor-infiltrating monocyte-like cells contribute to immunosuppression and metastasis in colorectal cancer
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95. Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response
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96. Fibroblastic reticular cells generate protective intratumoral T cell environments in lung cancer
    Lucas Onder, Chrysa Papadopoulou, Almut Luetge, Hung‐Wei Cheng, Mechthild Lütge, Christian Perez‐Shibayama, Cristina Gil‐Cruz, Angelina De Martin, Lisa Kurz, Nadine Cadosch et al. · 2024 · Cell
97. Spatially organized tumor-stroma boundary determines the efficacy of immunotherapy in colorectal cancer patients
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98. Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data
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