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

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Items 201–300 of 426

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   Dulken, Ben W., Leeman, Dena S., Boutet, Stéphane C., Hebestreit, Katja, Brunet, Anne · 2017 · Cell Reports
2. Interpretable dimensionality reduction of single cell transcriptome data with deep generative models
   Ding, Jiarui, Condon, Anne, Shah, Sohrab P. · 2018 · Nature Communications
3. Sequencing thousands of single-cell genomes with combinatorial indexing
   Vitak, Sarah A, Torkenczy, Kristof A, Rosenkrantz, Jimi L, Fields, Andrew J, Christiansen, Lena, Wong, Melissa H, Carbone, Lucia, Steemers, Frank J, Adey, Andrew · 2017 · Nature Methods
4. 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
5. Somatic mutations and cell identity linked by Genotyping of Transcriptomes
   Nam, Anna S., Kim, Kyu-Tae, Chaligne, Ronan, Izzo, Franco, Ang, Chelston, Taylor, Justin, Myers, Robert M., Abu-Zeinah, Ghaith, Brand, Ryan, Omans, Nathaniel D. et al. · 2019 · Nature
6. 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
7. 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
8. Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans
   Thrupp, Nicola, Sala Frigerio, Carlo, Wolfs, Leen, Skene, Nathan G., Fattorelli, Nicola, Poovathingal, Suresh, Fourne, Yannick, Matthews, Paul M., Theys, Tom, Mancuso, Renzo et al. · 2020 · Cell Reports
9. Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures
   Ruiz García, Sandra, Deprez, Marie, Lebrigand, Kevin, Cavard, Amélie, Paquet, Agnès, Arguel, Marie-Jeanne, Magnone, Virginie, Truchi, Marin, Caballero, Ignacio, Leroy, Sylvie et al. · 2019 · Development
10. Multivariate genome-wide analyses of the well-being spectrum
    BIOS consortium, Baselmans, Bart M. L., Social Science Genetic Association Consortium, Jansen, Rick, Ip, Hill F., van Dongen, Jenny, Abdellaoui, Abdel, van de Weijer, Margot P., Bao, Yanchun, Smart, Melissa et al. · 2019 · Nature Genetics
11. Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease
    Piwecka, Monika, Rajewsky, Nikolaus, Rybak-Wolf, Agnieszka · 2023 · Nature Reviews Neurology
12. A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA
    Lake, Blue B., Codeluppi, Simone, Yung, Yun C., Gao, Derek, Chun, Jerold, Kharchenko, Peter V., Linnarsson, Sten, Zhang, Kun · 2017 · Scientific Reports
13. Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry
    Oetjen, Karolyn A., Lindblad, Katherine E., Goswami, Meghali, Gui, Gege, Dagur, Pradeep K., Lai, Catherine, Dillon, Laura W., McCoy, J. Philip, Hourigan, Christopher S. · 2018 · JCI Insight
14. High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes
    Singh, Mandeep, Al-Eryani, Ghamdan, Carswell, Shaun, Ferguson, James M., Blackburn, James, Barton, Kirston, Roden, Daniel, Luciani, Fabio, Giang Phan, Tri, Junankar, Simon et al. · 2019 · Nature Communications
15. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity
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16. Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states
    Ma, Peijun, Amemiya, Haley M., He, Lorrie L., Gandhi, Shivam J., Nicol, Robert, Bhattacharyya, Roby P., Smillie, Christopher S., Hung, Deborah T. · 2023 · Cell
17. A systematic performance evaluation of clustering methods for single-cell RNA-seq data
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18. Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei
    Ren, Jing, Isakova, Alina, Friedmann, Drew, Zeng, Jiawei, Grutzner, Sophie M, Pun, Albert, Zhao, Grace Q, Kolluru, Sai Saroja, Wang, Ruiyu, Lin, Rui et al. · 2019 · eLife
19. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
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20. The promises and challenges of human brain organoids as models of neuropsychiatric disease
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21. Joint profiling of histone modifications and transcriptome in single cells from mouse brain
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22. Disentangling neural cell diversity using single-cell transcriptomics
    Poulin, Jean-Francois, Tasic, Bosiljka, Hjerling-Leffler, Jens, Trimarchi, Jeffrey M, Awatramani, Rajeshwar · 2016 · Nature Neuroscience
23. A genetic, genomic, and computational resource for exploring neural circuit function
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24. Highly scalable generation of DNA methylation profiles in single cells
    Mulqueen, Ryan M, Pokholok, Dmitry, Norberg, Steven J, Torkenczy, Kristof A, Fields, Andrew J, Sun, Duanchen, Sinnamon, John R, Shendure, Jay, Trapnell, Cole, O'Roak, Brian J et al. · 2018 · Nature Biotechnology
25. Microglia and the brain: Complementary partners in development and disease
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26. Locus coeruleus cellular and molecular pathology during the progression of Alzheimer’s disease
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27. Predicting cell-to-cell communication networks using NATMI
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28. Neutrophil extracellular traps target senescent vasculature for tissue remodeling in retinopathy
    Binet, François, Cagnone, Gael, Crespo-Garcia, Sergio, Hata, Masayuki, Neault, Mathieu, Dejda, Agnieszka, Wilson, Ariel M., Buscarlet, Manuel, Mawambo, Gaelle Tagne, Howard, Joel P. et al. · 2020 · Science
29. Single-cell sequencing techniques from individual to multiomics analyses
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30. Using single-cell genomics to understand developmental processes and cell fate decisions
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31. Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics
    Harris, Kenneth D., Hochgerner, Hannah, Skene, Nathan G., Magno, Lorenza, Katona, Linda, Bengtsson Gonzales, Carolina, Somogyi, Peter, Kessaris, Nicoletta, Linnarsson, Sten, Hjerling-Leffler, Jens · 2018 · PLoS Biology
32. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
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33. Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq)
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34. Cell type prioritization in single-cell data
    Skinnider, Michael A., Squair, Jordan W., Kathe, Claudia, Anderson, Mark A., Gautier, Matthieu, Matson, Kaya J. E., Milano, Marco, Hutson, Thomas H., Barraud, Quentin, Phillips, Aaron A. et al. · 2021 · Nature Biotechnology
35. Hotspot identifies informative gene modules across modalities of single-cell genomics
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36. Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration
    Pepe-Mooney, Brian J., Dill, Michael T., Alemany, Anna, Ordovas-Montanes, Jose, Matsushita, Yuki, Rao, Anuradha, Sen, Anushna, Miyazaki, Makoto, Anakk, Sayeepriyadarshini, Dawson, Paul A. et al. · 2019 · Cell Stem Cell
37. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes
    Armand, Ethan J., Li, Junhao, Xie, Fangming, Luo, Chongyuan, Mukamel, Eran A. · 2021 · Neuron
38. Building a lineage from single cells: genetic techniques for cell lineage tracking
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39. A systematic evaluation of single cell RNA-seq analysis pipelines
    Vieth, Beate, Parekh, Swati, Ziegenhain, Christoph, Enard, Wolfgang, Hellmann, Ines · 2019 · Nature Communications
40. Mapping gene regulatory networks from single-cell omics data
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41. On the design of CRISPR-based single-cell molecular screens
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42. Multimodal analysis of cell types in a hypothalamic node controlling social behavior
    Kim, Dong-Wook, Yao, Zizhen, Graybuck, Lucas T., Kim, Tae Kyung, Nguyen, Thuc Nghi, Smith, Kimberly A., Fong, Olivia, Yi, Lynn, Koulena, Noushin, Pierson, Nico et al. · 2019 · Cell
43. Single-Cell Analysis of Regional Differences in Adult V-SVZ Neural Stem Cell Lineages
    Mizrak, Dogukan, Levitin, Hanna Mendes, Delgado, Ana C., Crotet, Valerie, Yuan, Jinzhou, Chaker, Zayna, Silva-Vargas, Violeta, Sims, Peter A., Doetsch, Fiona · 2019 · Cell Reports
44. Big data in basic and translational cancer research
    Jiang, Peng, Sinha, Sanju, Aldape, Kenneth, Hannenhalli, Sridhar, Sahinalp, Cenk, Ruppin, Eytan · 2022 · Nature Reviews Cancer
45. Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis
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46. Challenges in measuring and understanding biological noise
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47. Targeted Perturb-seq enables genome-scale genetic screens in single cells
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48. The diversity of GABAergic neurons and neural communication elements
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49. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution
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50. Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells
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51. A curated database reveals trends in single-cell transcriptomics
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52. High throughput error corrected Nanopore single cell transcriptome sequencing
    Lebrigand, Kevin, Magnone, Virginie, Barbry, Pascal, Waldmann, Rainer · 2020 · Nature Communications
53. DNA methylation disruption reshapes the hematopoietic differentiation landscape
    Izzo, Franco, Lee, Stanley C., Poran, Asaf, Chaligne, Ronan, Gaiti, Federico, Gross, Baptiste, Murali, Rekha R., Deochand, Sunil D., Ang, Chelston, Jones, Philippa Wyndham et al. · 2020 · Nature Genetics
54. scSLAM-seq reveals core features of transcription dynamics in single cells
    Erhard, Florian, Baptista, Marisa A. P., Krammer, Tobias, Hennig, Thomas, Lange, Marius, Arampatzi, Panagiota, Jürges, Christopher S., Theis, Fabian J., Saliba, Antoine-Emmanuel, Dölken, Lars · 2019 · Nature
55. Single-cell transcriptome sequencing: recent advances and remaining challenges
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56. Phenotypic convergence: distinct transcription factors regulate common terminal features
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57. Microglia and Astrocytes in Disease: Dynamic Duo or Partners in Crime?
    Liddelow, Shane A., Marsh, Samuel E., Stevens, Beth · 2020 · Trends in Immunology
58. Slide-tags enables single-nucleus barcoding for multimodal spatial genomics
    Russell, Andrew J. C., Weir, Jackson A., Nadaf, Naeem M., Shabet, Matthew, Kumar, Vipin, Kambhampati, Sandeep, Raichur, Ruth, Marrero, Giovanni J., Liu, Sophia, Balderrama, Karol S. et al. · 2024 · Nature
59. The spatiotemporal program of zonal liver regeneration following acute injury
    Ben-Moshe, Shani, Veg, Tamar, Manco, Rita, Dan, Stav, Papinutti, Delfina, Lifshitz, Aviezer, Kolodziejczyk, Aleksandra A., Bahar Halpern, Keren, Elinav, Eran, Itzkovitz, Shalev · 2022 · Cell Stem Cell
60. Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function
    Shah, Prajay T., Stratton, Jo A., Stykel, Morgan Gail, Abbasi, Sepideh, Sharma, Sandeep, Mayr, Kyle A., Koblinger, Kathrin, Whelan, Patrick J., Biernaskie, Jeff · 2018 · Cell
61. CD8+ tissue-resident memory T cells promote liver fibrosis resolution by inducing apoptosis of hepatic stellate cells
    Koda, Yuzo, Teratani, Toshiaki, Chu, Po-Sung, Hagihara, Yuya, Mikami, Yohei, Harada, Yosuke, Tsujikawa, Hanako, Miyamoto, Kentaro, Suzuki, Takahiro, Taniki, Nobuhito et al. · 2021 · Nature Communications
62. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
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63. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data
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64. Cell fixation and preservation for droplet-based single-cell transcriptomics
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65. Single cell transcriptomics of human epidermis identifies basal stem cell transition states
    Wang, Shuxiong, Drummond, Michael L., Guerrero-Juarez, Christian F., Tarapore, Eric, MacLean, Adam L., Stabell, Adam R., Wu, Stephanie C., Gutierrez, Guadalupe, That, Bao T., Benavente, Claudia A. et al. · 2020 · Nature Communications
66. Ultraconserved Enhancers Are Required for Normal Development
    Dickel, Diane E., Ypsilanti, Athena R., Pla, Ramón, Zhu, Yiwen, Barozzi, Iros, Mannion, Brandon J., Khin, Yupar S., Fukuda-Yuzawa, Yoko, Plajzer-Frick, Ingrid, Pickle, Catherine S. et al. · 2018 · Cell
67. Genetic determinants of co-accessible chromatin regions in activated T cells across humans
    Gate, Rachel E., Cheng, Christine S., Aiden, Aviva P., Siba, Atsede, Tabaka, Marcin, Lituiev, Dmytro, Machol, Ido, Gordon, M. Grace, Subramaniam, Meena, Shamim, Muhammad et al. · 2018 · Nature Genetics
68. Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity
    Karmaus, Peer W. F., Chen, Xiang, Lim, Seon Ah, Herrada, Andrés A., Nguyen, Thanh-Long M., Xu, Beisi, Dhungana, Yogesh, Rankin, Sherri, Chen, Wenan, Rosencrance, Celeste et al. · 2019 · Nature
69. A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex
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70. Early Alzheimer’s disease pathology in human cortex involves transient cell states
    Gazestani, Vahid, Kamath, Tushar, Nadaf, Naeem M., Dougalis, Antonios, Burris, S.J., Rooney, Brendan, Junkkari, Antti, Vanderburg, Charles, Pelkonen, Anssi, Gomez-Budia, Mireia et al. · 2023 · Cell
71. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation
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72. Microglia response following acute demyelination is heterogeneous and limits infiltrating macrophage dispersion
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73. Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data
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74. Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
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75. Genetically distinct parallel pathways in the entopeduncular nucleus for limbic and sensorimotor output of the basal ganglia
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76. Single-cell analysis of prenatal and postnatal human cortical development
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77. A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord
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78. Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action
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79. Single cell molecular alterations reveal target cells and pathways of concussive brain injury
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80. Single-Cell Transcriptomics Characterizes Cell Types in the Subventricular Zone and Uncovers Molecular Defects Impairing Adult Neurogenesis
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81. Experimental Considerations for Single-Cell RNA Sequencing Approaches
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82. NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data
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83. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration
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84. Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons
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85. Gene-edited human stem cell–derived β cells from a patient with monogenic diabetes reverse preexisting diabetes in mice
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86. Pathological angiogenesis in retinopathy engages cellular senescence and is amenable to therapeutic elimination via BCL-xL inhibition
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87. Detection of differentially abundant cell subpopulations in scRNA-seq data
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88. scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network
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89. Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq
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90. Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
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91. Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL
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92. Transcriptional and spatial resolution of cell types in the mammalian habenula
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93. Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries
    Giladi, Amir, Amit, Ido · 2018 · Cell
94. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using <tt>CellBender</tt>
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95. Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity
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96. Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells
    Wimmers, Florian, Subedi, Nikita, van Buuringen, Nicole, Heister, Daan, Vivié, Judith, Beeren-Reinieren, Inge, Woestenenk, Rob, Dolstra, Harry, Piruska, Aigars, Jacobs, Joannes F. M. et al. · 2018 · Nature Communications
97. powsimR: power analysis for bulk and single cell RNA-seq experiments
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98. Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing
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99. The evolving concept of cell identity in the single cell era
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100. Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation
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