Integrated analysis of multimodal single-cell data

Cited by (1,144)

Items 801–900 of 1,144

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2. Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation
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3. The future of rapid and automated single-cell data analysis using reference mapping
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6. FLASH radiation reprograms lipid metabolism and macrophage immunity and sensitizes medulloblastoma to CAR-T cell therapy
   Haiwei Ni, Zachary J. Reitman, Wei Zou, Md. Naushad Akhtar, Ritama Paul, Menggui Huang, Duo Zhang, Hao Zheng, Ruitao Zhang, Ruiying Ma et al. · 2025 · Nature Cancer
7. Autoantigen-specific CD4+ T cells acquire an exhausted phenotype and persist in human antigen-specific autoimmune diseases
   Saggau, Carina, Bacher, Petra, Esser, Daniela, Rasa, Mahdi, Meise, Silja, Mohr, Nicola, Kohlstedt, Nora, Hutloff, Andreas, Schacht, Sarah-Sophie, Dargvainiene, Justina et al. · 2024 · Immunity
8. Human T follicular helper clones seed the germinal center-resident regulatory pool
   Le Coz, Carole, Oldridge, Derek A., Herati, Ramin S., De Luna, Nina, Garifallou, James, Cruz Cabrera, Emylette, Belman, Jonathan P., Pueschl, Dana, Silva, Luisa V., Knox, Ainsley V. C. et al. · 2023 · Science Immunology
9. A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing
   Lengyel, Ernst, Li, Yan, Weigert, Melanie, Zhu, Lisha, Eckart, Heather, Javellana, Melissa, Ackroyd, Sarah, Xiao, Jason, Olalekan, Susan, Glass, Dianne et al. · 2022 · Cell Reports
10. Deciphering endothelial heterogeneity in health and disease at single-cell resolution: progress and perspectives
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11. Big data: Historic advances and emerging trends in biomedical research
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12. A single-cell liver atlas of Plasmodium vivax infection
    Liliana Mâncio-Silva, Nil Gural, Eliana Real, Marc H. Wadsworth, Vincent L. Butty, Sandra March, Niketa Nerurkar, Travis K. Hughes, Wanlapa Roobsoong, Heather E. Fleming et al. · 2022 · Cell Host & Microbe
13. Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters
    Geraldine Nouailles, Julia Maria Adler, Peter Pennitz, Stefan Peidli, Luiz Gustavo Teixeira Alves, Morris Baumgardt, Judith Bushe, Anne Voß, Alina Katharina Langenhagen, Christine Langner et al. · 2023 · Nature Microbiology
14. Wnt signaling preserves progenitor cell multipotency during adipose tissue development
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15. Spatially resolved transcriptomic analysis of the germinating barley grain
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16. Zeb2 drives the formation of CD11c + atypical B cells to sustain germinal centers that control persistent infection
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17. Th17 Cells Secrete TWEAK to Trigger Epithelial–Mesenchymal Transition and Promote Colorectal Cancer Liver Metastasis
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18. Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities
    Tobias Roider, Marc‐Andrea Baertsch, Donnacha Fitzgerald, Harald S. Vöhringer, Berit J. Brinkmann, Felix Czernilofsky, Mareike Knoll, Laura Llaó Cid, Anna Mathioudaki, Bianca Faßbender et al. · 2024 · Nature Cell Biology
19. CD200+ fibroblasts form a pro-resolving mesenchymal network in arthritis
    Simon Rauber, Hashem Mohammadian, Christian Schmidkonz, Armin Atzinger, Alina Soare, Christoph Treutlein, Samuel Kemble, Christopher B. Mahony, Manuel Geisthoff, Mario Raphael Angeli et al. · 2024 · Nature Immunology
20. Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer
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21. Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome
    Minghui Jia, Senlin Zhu, Ming‐Yuan Xue, Hongyi Chen, Jinghong Xu, Mengdi Song, Yifan Tang, Xiaohan Liu, Ye Tao, Tianyu Zhang et al. · 2024 · Nature Microbiology
22. Multiscale topology classifies cells in subcellular spatial transcriptomics
    Katherine Benjamin, Aneesha Bhandari, Jessica D. Kepple, Rui Qi, Zhouchun Shang, Yanan Xing, Yanru An, Nannan Zhang, Yong Hou, Tanya L. Crockford et al. · 2024 · Nature
23. High-throughput identification of repurposable neuroactive drugs with potent anti-glioblastoma activity
    Sohyon Lee, Tobias Weiß, Marcel Bühler, Julien Mena, Zuzanna Lottenbach, Rebekka Wegmann, Miaomiao Sun, Michel Bihl, Bartłomiej Augustynek, Sven P. Baumann et al. · 2024 · Nature Medicine
24. IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer
    Longyong Xu, Fanglue Peng, Qin Luo, Yao Ding, Fei Yuan, Liting Zheng, Wei He, Sophie S. Zhang, Xin Fu, Jin Liu et al. · 2024 · Cell
25. Individualized patient tumor organoids faithfully preserve human brain tumor ecosystems and predict patient response to therapy
    Peng, Tianping, Ma, Xiujian, Hua, Wei, Wang, Changwen, Chu, Youjun, Sun, Meng, Fermi, Valentina, Hamelmann, Stefan, Lindner, Katharina, Shao, Chunxuan et al. · 2025 · Cell Stem Cell
26. High-resolution transcriptional landscape of xeno-free human induced pluripotent stem cell-derived cerebellar organoids
    Sam Nayler, Devika Agarwal, Fabiola Curion, Rory J. Bowden, Esther B. E. Becker · 2021 · Scientific Reports
27. Multiplatform Single-Cell Analysis Identifies Immune Cell Types Enhanced in Pulmonary Fibrosis
    Ana Paula Moreira Serezani, Bruno D. Pascoalino, Júlia Miranda Ribeiro Bazzano, Katherine N. Vowell, Harikrishna Tanjore, Chase J. Taylor, Carla L. Calvi, A. Scott McCall, Matthew D. Bacchetta, Ciara M. Shaver et al. · 2022 · American Journal of Respiratory Cell and Molecular Biology
28. Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination
    Yu Gao, Curtis Cai, David Wullimann, Julia Niessl, Olga Rivera‐Ballesteros, Puran Chen, Joshua Lange, Angélica Cuapio, Ola Blennow, Lotta Hansson et al. · 2022 · Immunity
29. IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma
    Chelsea Alice Taylor, Robert A. Watson, Orion Tong, Weiyu Ye, Isar Nassiri, James J. Gilchrist, Alba Verge de los Aires, Piyush Kumar Sharma, Surya Koturan, Rosalin A. Cooper et al. · 2022 · Nature Medicine
30. Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation
    Michal Mokrý, Arjan Boltjes, Lotte Slenders, Gemma Bel-Bordes, Kai Cui, Eli Brouwer, Joost M. Mekke, Marie A.C. Depuydt, Nathalie Timmerman, Farahnaz Waissi et al. · 2022 · Nature Cardiovascular Research
31. Sortilin enhances fibrosis and calcification in aortic valve disease by inducing interstitial cell heterogeneity
    Farwah Iqbal, Florian Schlotter, DAKOTA R. BECKER-GREENE, Adrien Lupieri, Claudia Goettsch, Joshua D. Hutcheson, Maximillian A. Rogers, Shinsuke Itoh, Arda Halu, Lang Ho Lee et al. · 2023 · European Heart Journal
32. LSD1 Inhibition Disrupts Super-Enhancer–Driven Oncogenic Transcriptional Programs in Castration-Resistant Prostate Cancer
    Muqing Li, Mingyu Liu, Wanting Han, Zifeng Wang, Dong Gwan Han, Susan C. Patalano, Jill A. Macoska, Steven P. Balk, Housheng Hansen He, Eva Corey et al. · 2023 · Cancer Research
33. M2 macrophages drive leukemic transformation by imposing resistance to phagocytosis and improving mitochondrial metabolism
    Isabel Weinhäuser, Diego A. Pereira‐Martins, Luciana Yamamoto Almeida, Jacobien R. Hilberink, Douglas RA Silveira, Lynn Swun Quek, César Alexander Ortiz Rojas, Cleide L. Araujo, Thiago Mantello Bianco, Antonio Roberto Lucena-Araujo et al. · 2023 · Science Advances
34. Immune checkpoint B7-H3 is a therapeutic vulnerability in prostate cancer harboring PTEN and TP53 deficiencies
    Wei Ming Shi, Yin Wang, Yuehui Zhao, Justin J. Kim, Haoyan Li, Chenling Meng, Feiyu Chen, Jie Zhang, Duncan H. F. Mak, Vivien Van et al. · 2023 · Science Translational Medicine
35. Deciphering early human pancreas development at the single-cell level
    Zhuo Ma, Xiaofei Zhang, Wen Zhong, Hongyan Yi, Xiaowei Chen, Yinsuo Zhao, Yanlin Ma, Eli Song, Tao Xu · 2023 · Nature Communications
36. SiGra: single-cell spatial elucidation through an image-augmented graph transformer
    Ziyang Tang, Zuotian Li, Tieying Hou, Tonglin Zhang, Baijian Yang, Jing Su, Qianqian Song · 2023 · Nature Communications
37. A longitudinal single-cell atlas of treatment response in pediatric AML
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38. Scalable generation of functional human iPSC-derived CAR-macrophages that efficiently eradicate CD19-positive leukemia
    Shifaa M. Abdin, Daniela Paasch, Arnold Kloos, Marco Carvalho Oliveira, Mi-Sun Jang, Mania Ackermann, Ανδριάνα Σταμοπούλου, Philipp Joel Mroch, Christine Susanne Falk, Constantin Sylvius von Kaisenberg et al. · 2023 · Journal for ImmunoTherapy of Cancer
39. Hepatic danger signaling triggers TREM2 + macrophage induction and drives steatohepatitis via MS4A7-dependent inflammasome activation
    Linkang Zhou, Xiaoxue Qiu, Ziyi Meng, Tongyu Liu, Zhimin Chen, Peng Zhang, Henry Kuang, Tong Pan, You Lu, Ling Qi et al. · 2024 · Science Translational Medicine
40. Macrophage-fibroblast JAK/STAT dependent crosstalk promotes liver metastatic outgrowth in pancreatic cancer
    Meirion Raymant, Yuliana Astuti, Laura Álvaro‐Espinosa, Daniel M. Green, Valeria Quaranta, Gaia Bellomo, Mark A. Glenn, Vatshala Chandran-Gorner, Daniel H. Palmer, Christopher Michael Halloran et al. · 2024 · Nature Communications
41. Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process
    Sergio Alan Cervantes-Pérez, Prince Zogli, Sahand Amini, Sandra Thibivilliers, Sutton Tennant, Md. Sabbir Hossain, Hengping Xu, Ian Meyer, Akash Nooka, Pengchong Ma et al. · 2024 · Plant Communications
42. A human autoimmune organoid model reveals IL-7 function in coeliac disease
    António J. M. Santos, Vincent van Unen, Zhongqi Lin, Steven M. Chirieleison, Nhi Ha, Arpit Batish, Joshua Elbridge Chan, Jose Cedano, Elisa Zhang, Qinghui Mu et al. · 2024 · Nature
43. Benchmarking algorithms for single-cell multi-omics prediction and integration
    Yinlei Hu, Siyuan Wan, Yuanhanyu Luo, Yuanzhe Li, Tong Wu, Wentao Deng, Chen Jiang, Shan Jiang, Yueping Zhang, Nianping Liu et al. · 2024 · Nature Methods
44. Generating human neural diversity with a multiplexed morphogen screen in organoids
    Neal D. Amin, Kevin W. Kelley, Konstantin Kaganovsky, Massimo M. Onesto, Jin Hao, Yuki Miura, James P. McQueen, Noah Reis, Genta Narazaki, Tommy Li et al. · 2024 · Cell stem cell
45. Senescence-resistant human mesenchymal progenitor cells counter aging in primates
    Jinghui Lei, Zijuan Xin, Ning Liu, Taixin Ning, Ying Jing, Yicheng Qiao, Zan He, Mengmeng Jiang, Yuanhan Yang, Zhiyi Zhang et al. · 2025 · Cell
46. Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells
    Balthasar A. Heesters, Kyah van Megesen, Ilhan Tomris, Robert P. de Vries, Giuliana Magri, Hergen Spits · 2021 · The Journal of Experimental Medicine
47. Analysis and Visualization of Spatial Transcriptomic Data
    Boxiang Liu, Yanjun Li, Liang Zhang · 2022 · Frontiers in Genetics
48. Cooperative learning for multiview analysis
    Daisy Yi Ding, Shuangning Li, Balasubramanian Narasimhan, Robert John Tibshirani · 2022 · Proceedings of the National Academy of Sciences
49. Dentate gyrus astrocytes exhibit layer-specific molecular, morphological and physiological features
    Julian Karpf, P. Unichenko, Nicholas Chalmers, Felix Beyer, M. Wittmann, Julia Schneider, E. Fidan, André Reis, J. Beckervordersandforth, Sebastian Brandner et al. · 2022 · Nature Neuroscience
50. An epithelial-immune circuit amplifies inflammasome and IL-6 responses to SARS-CoV-2
    Katherine Camille Barnett, Yuying Xie, Takanori Asakura, Dingka Song, Kaixin Liang, Sharon Taft-Benz, Haitao Guo, Shuangshuang Yang, Kenichi Okuda, Rodney C. Gilmore et al. · 2022 · Cell Host & Microbe
51. Weight cycling induces innate immune memory in adipose tissue macrophages
    Heather L. Caslin, Matthew A. Cottam, Jacqueline Pinon, Likem Y. Boney, Alyssa H. Hasty · 2023 · Frontiers in Immunology
52. SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics
    Jiaqiang Zhu, Lulu Shang, Xiang Zhou · 2023 · Genome biology
53. Phagocytosis increases an oxidative metabolic and immune suppressive signature in tumor macrophages
    Michael A. Gonzalez, Daniel Lu, Maryam Yousefi, Ashley V. Kroll, Chen Hao Lo, Carlos G. Briseño, J. E. Vivienne Watson, Sergey V. Novitskiy, Vanessa Arias, Hong Zhou et al. · 2023 · The Journal of Experimental Medicine
54. Mapping human adult hippocampal neurogenesis with single-cell transcriptomics: Reconciling controversy or fueling the debate?
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55. Phenotypic diversity of T cells in human primary and metastatic brain tumors revealed by multiomic interrogation
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56. IFNγ-induced stem-like state of cancer cells as a driver of metastatic progression following immunotherapy
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57. KDM6A epigenetically regulates subtype plasticity in small cell lung cancer
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58. Spatial transcriptomics delineates molecular features and cellular plasticity in lung adenocarcinoma progression
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59. Deciphering maternal-fetal cross-talk in the human placenta during parturition using single-cell RNA sequencing
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60. Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell
    Yu Wang, Zhi-Ying Guan, Shao-Wen Shi, Yirong Jiang, Jie Zhang, Yi Yang, Qiong Wu, Jie Wu, Jianbo Chen, Wei-Xin Ying et al. · 2024 · Nature Communications
61. A spatiotemporal atlas of mouse liver homeostasis and regeneration
    Xu, Jiangshan, Guo, Pengcheng, Hao, Shijie, Shangguan, Shuncheng, Shi, Quan, Volpe, Giacomo, Huang, Keke, Zuo, Jing, An, Juan, Yuan, Yue et al. · 2024 · Nature Genetics
62. TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons
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63. Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease
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64. Heterogeneous pericoerulear neurons tune arousal and exploratory behaviours
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65. Computational methods for single-cell multi-omics integration and alignment
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66. Matters of the heart: Cellular sex differences
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67. Integrated analysis of glycan and RNA in single cells
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68. Midbrain organoids mimic early embryonic neurodevelopment and recapitulate LRRK2-p.Gly2019Ser-associated gene expression
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69. DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data
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70. An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure
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71. Distinct immune microenvironment of lung adenocarcinoma in never-smokers from smokers
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72. Single‐cell dissection of cervical cancer reveals key subsets of the tumor immune microenvironment
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73. Human microglia maturation is underpinned by specific gene regulatory networks
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74. B cell lineage reconstitution underlies CAR-T cell therapeutic efficacy in patients with refractory myasthenia gravis
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75. Morphological diversification and functional maturation of human astrocytes in glia-enriched cortical organoid transplanted in mouse brain
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78. Distinct disease-specific Tfh cell populations in 2 different fibrotic diseases: IgG4-related disease and Kimura disease
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79. A slow-cycling/quiescent cells subpopulation is involved in glioma invasiveness
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80. Distinct Mechanisms of Mismatch Repair Deficiency Delineate Two Modes of Response to PD-1 Immunotherapy in Endometrial Carcinoma
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81. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma
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82. Glioblastoma-Infiltrating CD8 + T Cells Are Predominantly a Clonally Expanded GZMK + Effector Population
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83. Spatial transcriptomics reveals segregation of tumor cell states in glioblastoma and marked immunosuppression within the perinecrotic niche
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84. CD276 regulates the immune escape of esophageal squamous cell carcinoma through CXCL1–CXCR2 induced NETs
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85. The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening
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86. Glioblastoma cells increase expression of notch signaling and synaptic genes within infiltrated brain tissue
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87. Machine learning identifies TIME subtypes linking EGFR mutations and immune states in lung adenocarcinoma
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88. Localization of T cell clonotypes using the Visium spatial transcriptomics platform
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89. HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values
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90. Single-cell transcriptome analysis of regenerating RGCs reveals potent glaucoma neural repair genes
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91. A single-cell transcriptome atlas of glial diversity in the human hippocampus across the postnatal lifespan
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92. Human IL-23 is essential for IFN-γ–dependent immunity to mycobacteria
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93. Integrated analysis of single-cell RNA-seq and bulk RNA-seq unravels T cell-related prognostic risk model and tumor immune microenvironment modulation in triple-negative breast cancer
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94. Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin
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95. A village in a dish model system for population-scale hiPSC studies
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