Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Cited by (413)

Items 101–200 of 413

1. Scaling single-cell genomics from phenomenology to mechanism
   Tanay, Amos, Regev, Aviv · 2017 · Nature
2. Signaling pathways in cancer-associated fibroblasts and targeted therapy for cancer
   Wu, Fanglong, Yang, Jin, Liu, Junjiang, Wang, Ye, Mu, Jingtian, Zeng, Qingxiang, Deng, Shuzhi, Zhou, Hongmei · 2021 · Signal Transduction and Targeted Therapy
3. A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex
   Zhong, Suijuan, Zhang, Shu, Fan, Xiaoying, Wu, Qian, Yan, Liying, Dong, Ji, Zhang, Haofeng, Li, Long, Sun, Le, Pan, Na et al. · 2018 · Nature
4. Decoding myofibroblast origins in human kidney fibrosis
   Kuppe, Christoph, Ibrahim, Mahmoud M., Kranz, Jennifer, Zhang, Xiaoting, Ziegler, Susanne, Perales-Patón, Javier, Jansen, Jitske, Reimer, Katharina C., Smith, James R., Dobie, Ross et al. · 2021 · Nature
5. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
   McGinnis, Christopher S., Patterson, David M., Winkler, Juliane, Conrad, Daniel N., Hein, Marco Y., Srivastava, Vasudha, Hu, Jennifer L., Murrow, Lyndsay M., Weissman, Jonathan S., Werb, Zena et al. · 2019 · Nature Methods
6. Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis
   Wu, Haojia, Kirita, Yuhei, Donnelly, Erinn L., Humphreys, Benjamin D. · 2019 · Journal of the American Society of Nephrology
7. Single-cell transcriptomic profiling of the aging mouse brain
   Ximerakis, Methodios, Lipnick, Scott L., Innes, Brendan T., Simmons, Sean K., Adiconis, Xian, Dionne, Danielle, Mayweather, Brittany A., Nguyen, Lan, Niziolek, Zachary, Ozek, Ceren et al. · 2019 · Nature Neuroscience
8. Revealing the vectors of cellular identity with single-cell genomics
   Wagner, Allon, Regev, Aviv, Yosef, Nir · 2016 · Nature Biotechnology
9. Human immune system variation
   Brodin, Petter, Davis, Mark M. · 2017 · Nature reviews. Immunology
10. A general and flexible method for signal extraction from single-cell RNA-seq data
    Risso, Davide, Perraudeau, Fanny, Gribkova, Svetlana, Dudoit, Sandrine, Vert, Jean-Philippe · 2018 · Nature Communications
11. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
    Angelidis, Ilias, Simon, Lukas M., Fernandez, Isis E., Strunz, Maximilian, Mayr, Christoph H., Greiffo, Flavia R., Tsitsiridis, George, Ansari, Meshal, Graf, Elisabeth, Strom, Tim-Matthias et al. · 2019 · Nature Communications
12. GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks
    Moerman, Thomas, Aibar Santos, Sara, Bravo González-Blas, Carmen, Simm, Jaak, Moreau, Yves, Aerts, Jan, Aerts, Stein · 2019 · Bioinformatics
13. Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
    Xu, Chenling, Lopez, Romain, Mehlman, Edouard, Regier, Jeffrey, Jordan, Michael I, Yosef, Nir · 2021 · Molecular Systems Biology
14. Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution
    Cowan, Cameron S., Renner, Magdalena, De Gennaro, Martina, Gross-Scherf, Brigitte, Goldblum, David, Hou, Yanyan, Munz, Martin, Rodrigues, Tiago M., Krol, Jacek, Szikra, Tamas et al. · 2020 · Cell
15. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
    Denisenko, Elena, Guo, Belinda B., Jones, Matthew, Hou, Rui, de Kock, Leanne, Lassmann, Timo, Poppe, Daniel, Clément, Olivier, Simmons, Rebecca K., Lister, Ryan et al. · 2020 · Genome Biology
16. Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes
    Tran, Nicholas M., Shekhar, Karthik, Whitney, Irene E., Jacobi, Anne, Benhar, Inbal, Hong, Guosong, Yan, Wenjun, Adiconis, Xian, Arnold, McKinzie E., Lee, Jung Min et al. · 2019 · Neuron
17. De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data
    Grün, Dominic, Muraro, Mauro J., Boisset, Jean-Charles, Wiebrands, Kay, Lyubimova, Anna, Dharmadhikari, Gitanjali, van den Born, Maaike, van Es, Johan, Jansen, Erik, Clevers, Hans et al. · 2016 · Cell Stem Cell
18. Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures
    Chan, Thalia E., Stumpf, Michael P.H., Babtie, Ann C. · 2017 · Cell Systems
19. Spatially resolved transcriptomes—next generation tools for tissue exploration
    Asp, Michaela, Bergenstråhle, Joseph, Lundeberg, Joakim · 2020 · BioEssays
20. Missing data and technical variability in single-cell RNA-sequencing experiments
    Hicks, Stephanie C, Townes, F William, Teng, Mingxiang, Irizarry, Rafael A · 2018 · Biostatistics
21. Wishbone identifies bifurcating developmental trajectories from single-cell data
    Setty, Manu, Tadmor, Michelle D, Reich-Zeliger, Shlomit, Angel, Omer, Salame, Tomer Meir, Kathail, Pooja, Choi, Kristy, Bendall, Sean, Friedman, Nir, Pe'er, Dana · 2016 · Nature Biotechnology
22. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
    Raghavan, Srivatsan, Winter, Peter S., Navia, Andrew W., Williams, Hannah L., DenAdel, Alan, Lowder, Kristen E., Galvez-Reyes, Jennyfer, Kalekar, Radha L., Mulugeta, Nolawit, Kapner, Kevin S. et al. · 2021 · Cell
23. Decontamination of ambient RNA in single-cell RNA-seq with DecontX
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24. Tumour heterogeneity and metastasis at single-cell resolution
    Lawson, Devon A., Kessenbrock, Kai, Davis, Ryan T., Pervolarakis, Nicholas, Werb, Zena · 2018 · Nature Cell Biology
25. Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
    Bakken, Trygve E., Hodge, Rebecca D., Miller, Jeremy A., Yao, Zizhen, Nguyen, Thuc Nghi, Aevermann, Brian, Barkan, Eliza, Bertagnolli, Darren, Casper, Tamara, Dee, Nick et al. · 2018 · PLoS ONE
26. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons
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27. Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis
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28. Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity
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29. The expanding vistas of spatial transcriptomics
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30. Design and Analysis of Single-Cell Sequencing Experiments
    Grün, Dominic, van Oudenaarden, Alexander · 2015 · Cell
31. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation
    Polioudakis, Damon, de la Torre-Ubieta, Luis, Langerman, Justin, Elkins, Andrew G., Shi, Xu, Stein, Jason L., Vuong, Celine K., Nichterwitz, Susanne, Gevorgian, Melinda, Opland, Carli K. et al. · 2019 · Neuron
32. Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming
    Solé-Boldo, Llorenç, Raddatz, Günter, Schütz, Sabrina, Mallm, Jan-Philipp, Rippe, Karsten, Lonsdorf, Anke S., Rodríguez-Paredes, Manuel, Lyko, Frank · 2020 · Communications Biology
33. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells
    Mimitou, Eleni P., Lareau, Caleb A., Chen, Kelvin Y., Zorzetto-Fernandes, Andre L., Hao, Yuhan, Takeshima, Yusuke, Luo, Wendy, Huang, Tse-Shun, Yeung, Bertrand Z., Papalexi, Efthymia et al. · 2021 · Nature Biotechnology
34. Rapid non-uniform adaptation to conformation-specific KRAS(G12C) inhibition
    Xue, Jenny Y., Zhao, Yulei, Aronowitz, Jordan, Mai, Trang T., Vides, Alberto, Qeriqi, Besnik, Kim, Dongsung, Li, Chuanchuan, de Stanchina, Elisa, Mazutis, Linas et al. · 2020 · Nature
35. Power analysis of single-cell RNA-sequencing experiments
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36. Transcriptional and Cellular Diversity of the Human Heart
    Tucker, Nathan R., Chaffin, Mark, Fleming, Stephen J., Hall, Amelia W., Parsons, Victoria A., Bedi, Kenneth C., Akkad, Amer-Denis, Herndon, Caroline N., Arduini, Alessandro, Papangeli, Irinna et al. · 2020 · Circulation
37. Developmental diversification of cortical inhibitory interneurons
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38. Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
    Brunner, Andreas‐David, Thielert, Marvin, Vasilopoulou, Catherine, Ammar, Constantin, Coscia, Fabian, Mund, Andreas, Hoerning, Ole B, Bache, Nicolai, Apalategui, Amalia, Lubeck, Markus et al. · 2022 · Molecular Systems Biology
39. Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars
    Spanjaard, Bastiaan, Hu, Bo, Mitic, Nina, Olivares-Chauvet, Pedro, Janjuha, Sharan, Ninov, Nikolay, Junker, Jan Philipp · 2018 · Nature Biotechnology
40. Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients
    Bost, Pierre, Giladi, Amir, Liu, Yang, Bendjelal, Yanis, Xu, Gang, David, Eyal, Blecher-Gonen, Ronnie, Cohen, Merav, Medaglia, Chiara, Li, Hanjie et al. · 2020 · Cell
41. Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons
    Nagy, Corina, Maitra, Malosree, Tanti, Arnaud, Suderman, Matthew, Théroux, Jean-Francois, Davoli, Maria Antonietta, Perlman, Kelly, Yerko, Volodymyr, Wang, Yu Chang, Tripathy, Shreejoy J. et al. · 2020 · Nature Neuroscience
42. Normalizing single-cell RNA sequencing data: challenges and opportunities
    Vallejos, Catalina A, Risso, Davide, Scialdone, Antonio, Dudoit, Sandrine, Marioni, John C · 2017 · Nature Methods
43. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing
    Replogle, Joseph M., Norman, Thomas M., Xu, Albert, Hussmann, Jeffrey A., Chen, Jin, Cogan, J. Zachery, Meer, Elliott J., Terry, Jessica M., Riordan, Daniel P., Srinivas, Niranjan et al. · 2020 · Nature Biotechnology
44. Auto-aggressive CXCR6+ CD8 T cells cause liver immune pathology in NASH
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45. A test metric for assessing single-cell RNA-seq batch correction
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46. Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes
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47. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes
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48. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex
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49. Brain Cell Type Specific Gene Expression and Co-expression Network Architectures
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50. hESC-Derived Thalamic Organoids Form Reciprocal Projections When Fused with Cortical Organoids
    Xiang, Yangfei, Tanaka, Yoshiaki, Cakir, Bilal, Patterson, Benjamin, Kim, Kun-Yong, Sun, Pingnan, Kang, Young-Jin, Zhong, Mei, Liu, Xinran, Patra, Prabir et al. · 2019 · Cell Stem Cell
51. Single-cell analysis tools for drug discovery and development
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52. What is a cell type and how to define it?
    Zeng, Hongkui · 2022 · Cell
53. Single-cell multiomics: multiple measurements from single cells
    Macaulay, Iain C., Ponting, Chris P., Voet, Thierry · 2017 · Trends in Genetics
54. Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model
    Townes, F. William, Hicks, Stephanie C., Aryee, Martin J., Irizarry, Rafael A. · 2019 · Genome Biology
55. Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
    Plass, Mireya, Solana, Jordi, Wolf, F. Alexander, Ayoub, Salah, Misios, Aristotelis, Glažar, Petar, Obermayer, Benedikt, Theis, Fabian J., Kocks, Christine, Rajewsky, Nikolaus · 2018 · Science
56. Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs
    LifeLines Cohort Study, van der Wijst, Monique G. P., BIOS Consortium, Brugge, Harm, de Vries, Dylan H., Deelen, Patrick, Swertz, Morris A., Franke, Lude · 2018 · Nature Genetics
57. Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
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58. Brain circuit dysfunction in post-traumatic stress disorder: from mouse to man
    Fenster, Robert J., Lebois, Lauren A. M., Ressler, Kerry J., Suh, Junghyup · 2018 · Nature Reviews Neuroscience
59. Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Casasent, Anna K., Schalck, Aislyn, Gao, Ruli, Sei, Emi, Long, Annalyssa, Pangburn, William, Casasent, Tod, Meric-Bernstam, Funda, Edgerton, Mary E., Navin, Nicholas E. · 2018 · Cell
60. Mapping microglia states in the human brain through the integration of high-dimensional techniques
    Sankowski, Roman, Böttcher, Chotima, Masuda, Takahiro, Geirsdottir, Laufey, Sagar, Sindram, Elena, Seredenina, Tamara, Muhs, Andreas, Scheiwe, Christian, Shah, Mukesch Johannes et al. · 2019 · Nature Neuroscience
61. Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor
    Crow, Megan, Paul, Anirban, Ballouz, Sara, Huang, Z. Josh, Gillis, Jesse · 2018 · Nature Communications
62. Detecting Activated Cell Populations Using Single-Cell RNA-Seq
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63. Cell type transcriptome atlas for the planarian <i>Schmidtea mediterranea</i>
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64. The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing
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65. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
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66. Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity
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67. Human Lung Stem Cell-Based Alveolospheres Provide Insights into SARS-CoV-2-Mediated Interferon Responses and Pneumocyte Dysfunction
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68. Population snapshots predict early haematopoietic and erythroid hierarchies
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69. Synovial cell cross-talk with cartilage plays a major role in the pathogenesis of osteoarthritis
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70. Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Neurons and Their Activity during Behavior
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71. Cell-cell communication: New insights and clinical implications
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72. Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR
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73. Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells
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74. Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways
    the Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium, Der, Evan, Suryawanshi, Hemant, Morozov, Pavel, Kustagi, Manjunath, Goilav, Beatrice, Ranabothu, Saritha, Izmirly, Peter, Clancy, Robert, Belmont, H. Michael et al. · 2019 · Nature Immunology
75. Platelet GPIbα is a mediator and potential interventional target for NASH and subsequent liver cancer
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76. Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome
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77. How to build the virtual cell with artificial intelligence: Priorities and opportunities
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78. Spatial-CUT&amp;Tag: Spatially resolved chromatin modification profiling at the cellular level
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79. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
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80. Single-Cell Transcriptomics Meets Lineage Tracing
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81. Batch effects and the effective design of single-cell gene expression studies
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82. Innovations present in the primate interneuron repertoire
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83. Innovations in Primate Interneuron Repertoire
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84. Fundamental limits on dynamic inference from single-cell snapshots
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85. Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells
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86. FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data
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87. Droplet scRNA-seq is not zero-inflated
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88. Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus
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89. Microbial single-cell RNA sequencing by split-pool barcoding
    Kuchina, Anna, Brettner, Leandra M., Paleologu, Luana, Roco, Charles M., Rosenberg, Alexander B., Carignano, Alberto, Kibler, Ryan, Hirano, Matthew, DePaolo, R. William, Seelig, Georg · 2021 · Science
90. Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging
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91. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
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92. Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics
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93. Gut-licensed IFNγ+ NK cells drive LAMP1+TRAIL+ anti-inflammatory astrocytes
    Sanmarco, Liliana M., Wheeler, Michael A., Gutiérrez-Vázquez, Cristina, Polonio, Carolina Manganeli, Linnerbauer, Mathias, Pinho-Ribeiro, Felipe A., Li, Zhaorong, Giovannoni, Federico, Batterman, Katelyn V., Scalisi, Giulia et al. · 2021 · Nature
94. Single-cell transcriptomic analysis defines heterogeneity and transcriptional dynamics in the adult neural stem cell lineage
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95. Interpretable dimensionality reduction of single cell transcriptome data with deep generative models
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96. Sequencing thousands of single-cell genomes with combinatorial indexing
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97. Immune-evasive human islet-like organoids ameliorate diabetes
    Yoshihara, Eiji, O’Connor, Carolyn, Gasser, Emanuel, Wei, Zong, Oh, Tae Gyu, Tseng, Tiffany W., Wang, Dan, Cayabyab, Fritz, Dai, Yang, Yu, Ruth T. et al. · 2020 · Nature
98. Somatic mutations and cell identity linked by Genotyping of Transcriptomes
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99. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
    Menon, Madhvi, Mohammadi, Shahin, Davila-Velderrain, Jose, Goods, Brittany A., Cadwell, Tanina D., Xing, Yu, Stemmer-Rachamimov, Anat, Shalek, Alex K., Love, John Christopher, Kellis, Manolis et al. · 2019 · Nature Communications
100. Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type
     Boldog, Eszter, Bakken, Trygve E., Hodge, Rebecca D., Novotny, Mark, Aevermann, Brian D., Baka, Judith, Bordé, Sándor, Close, Jennie L., Diez-Fuertes, Francisco, Ding, Song-Lin et al. · 2018 · Nature Neuroscience