Quantitative single-cell RNA-seq with unique molecular identifiers

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Items 101–200 of 1,000

1. M3Drop: dropout-based feature selection for scRNASeq
   Tallulah S. Andrews, Martin Hemberg · 2018 · Bioinformatics
2. Challenges in measuring and understanding biological noise
   Eling, Nils, Morgan, Michael D., Marioni, John C. · 2019 · Nature Reviews Genetics
3. Single-cell epigenomics: techniques and emerging applications
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4. scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3′ mRNA profiling
   Burak Dura, Jin-Young Choi, Kerou Zhang, William Damsky, Durga Thakral, Marcus Bosenberg, Joseph E. Craft, Rong Fan · 2018 · Nucleic Acids Research
5. Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses
   The CRUK IMAXT Grand Challenge Team, Ciara H. O’Flanagan, Kieran R. Campbell, Allen W. Zhang, Farhia Kabeer, Jamie L. Lim, Justina Biele, Peter D. Eirew, Daniel Lai, Andrew McPherson et al. · 2019 · Genome biology
6. Microfluidic single-cell whole-transcriptome sequencing
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7. Single‐Cell Analysis Using Droplet Microfluidics
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8. DEsingle for detecting three types of differential expression in single-cell RNA-seq data
   Zhun Miao, Ke Deng, Xiaowo Wang, Xuegong Zhang · 2018 · Bioinformatics
9. Single‐cell RNA sequencing in breast cancer: Understanding tumor heterogeneity and paving roads to individualized therapy
   Shuning Ding, Xiaosong Chen, Kunwei Shen · 2020 · 癌症：英文版
10. Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq
    Johannes Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas Esteban Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann, Wolfgang Enard · 2018 · Nature Communications
11. Effective detection of variation in single-cell transcriptomes using MATQ-seq
    Kuanwei Sheng, Wenjian Cao, Yichi Niu, Qing Deng, Chenghang Chuck Zong · 2017 · Nature Methods
12. Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview
    Shaked Slovin, Annamaria Carissimo, Francesco Panariello, Antonio Grimaldi, Valentina Bouchè, Gennaro Gambardella, Davide Cacchiarelli · 2021 · Methods in molecular biology
13. Identifying cell populations with scRNASeq
    Tallulah S. Andrews, Martin Hemberg · 2017 · Molecular Aspects of Medicine
14. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing
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15. Classification of midbrain dopamine neurons using single-cell gene expression profiling approaches
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16. Single-cell RNA-sequencing: The future of genome biology is now
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17. Revolutionizing immunology with single-cell RNA sequencing
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18. Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis
    Sarkar, Abhishek, Stephens, Matthew · 2021 · Nature Genetics
19. Macrophage subsets in atherosclerosis as defined by single‐cell technologies
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20. Single-cell transcriptome sequencing: recent advances and remaining challenges
    Liu, Serena, Trapnell, Cole · 2016 · F1000Research
21. High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery
    Xiaonan Yang, Ling Kui, Min Tang, Dawei Li, Kunhua Wei, Wei Chen, Jianhua Miao, Yang Dong · 2020 · Frontiers in Genetics
22. Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
    Van den Berge, Koen, Perraudeau, Fanny, Soneson, Charlotte, Love, Michael I., Risso, Davide, Vert, Jean-Philippe, Robinson, Mark D., Dudoit, Sandrine, Clement, Lieven · 2018 · Genome Biology
23. Single-nucleus and in situ RNA-sequencing reveal cell topographies in the human pancreas
    Tosti, Luca, Hang, Yan, Debnath, Olivia, Tiesmeyer, Sebastian, Trefzer, Timo, Steiger, Katja, Ten, Foo Wei, Lukassen, Sören, Ballke, Simone, Kühl, Anja A. et al. · 2021 · Gastroenterology
24. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
    Lafzi, Atefeh, Moutinho, Catia, Picelli, Simone, Heyn, Holger · 2018 · Nature Protocols
25. Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology
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26. Spatially resolved transcriptome profiling in model plant species
    Stefania Giacomello, Fredrik Salmén, Barbara K. Terebieniec, Sanja Vicković, José Fernández Navarro, Andrey Alexeyenko, Johan Reimegård, Lauren Sara McKee, Chanaka Mannapperuma, Vincent Bulone et al. · 2017 · Nature Plants
27. Advances and Opportunities in Single-Cell Transcriptomics for Plant Research
    Carolin Seyfferth, Jim Renema, Jos R. Wendrich, Thomas Eekhout, Ruth Seurinck, Niels Vandamme, Bernhard Blob, Yvan Saeys, Ykä Helariutta, Kenneth D. Birnbaum et al. · 2021 · Annual Review of Plant Biology
28. Clustering and classification methods for single-cell RNA-sequencing data
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29. Mex3a Marks a Slowly Dividing Subpopulation of Lgr5+ Intestinal Stem Cells
    Francisco M. Barriga, Elisa Montagni, Miyeko Mana, María Méndez-Lago, Xavier Hernando‐Momblona, Marta Sevillano, Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Simon J. A. Buczacki, Marta Gut et al. · 2017 · Cell stem cell
30. Aire controls gene expression in the thymic epithelium with ordered stochasticity
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31. Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing
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32. Tumor Functional Heterogeneity Unraveled by scRNA-seq Technologies
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33. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers
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34. Microglia-dependent synapse loss in type I interferon-mediated lupus
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35. dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
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36. How Do Sensory Neurons Sense Danger Signals?
    Christopher R. Donnelly, Chen Ouyang, Ru‐Rong Ji · 2020 · Trends in Neurosciences
37. Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation
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38. Single-cell sequencing in stem cell biology
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39. Introduction to Single‐Cell RNA Sequencing
    Thale Kristin Olsen, Ninib Baryawno · 2018 · Current Protocols in Molecular Biology
40. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development
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41. A Single-Cell Sequencing Guide for Immunologists
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42. Experimental Considerations for Single-Cell RNA Sequencing Approaches
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43. Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation
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44. Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
    Yu Fu, Pei‐Hsuan Wu, Timothy Jason Beane, Phillip D. Zamore, Zhiping Weng · 2018 · BMC Genomics
45. Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels
    Tobias Roider, Julian Seufert, Alexey Uvarovskii, Felix Frauhammer, Marie Bordas, Nima Abedpour, Marta Stolarczyk, Jan‐Philipp Mallm, Sophie A. Herbst, Peter‐Martin Bruch et al. · 2020 · Nature Cell Biology
46. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments
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47. Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing
    Mei-Chong Wendy Lee, Fernando J. López-Díaz, Shahid Y. Khan, Muhammad Tariq, Yelena Dayn, Charles Joseph Vaske, Amie Radenbaugh, Hyunsung John Kim, Beverly M. Emerson, Nader Pourmand · 2014 · Proceedings of the National Academy of Sciences
48. Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery
    William H. Robinson · 2014 · Nature Reviews Rheumatology
49. A reference tissue atlas for the human kidney
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50. Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries
    Giladi, Amir, Amit, Ido · 2018 · Cell
51. Platforms for Single-Cell Collection and Analysis
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52. Targeting vascular and leukocyte communication in angiogenesis, inflammation and fibrosis
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53. Single-Cell RNA Sequencing Resolves Spatiotemporal Development of Pre-thymic Lymphoid Progenitors and Thymus Organogenesis in Human Embryos
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54. Single-Cell RNA Sequencing: Unraveling the Brain One Cell at a Time
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55. DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
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56. Upcoming progress of transcriptomics studies on plants: An overview
    Parul Tyagi, Deeksha Singh, Shivangi Mathur, Ayushi Singh, Rajiv Ranjan · 2022 · Frontiers in Plant Science
57. Single-cell RNA-seq uncovers a robust transcriptional response to morphine by glia
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58. Light-Sheet Microscopy and Its Potential for Understanding Developmental Processes
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59. Single-cell RNAseq for the study of isoforms—how is that possible?
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60. Profiling chromatin states using single-cell itChIP-seq
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61. Single Cell RNA Sequencing in Atherosclerosis Research
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62. Cancer Diagnosis Using a Liquid Biopsy: Challenges and Expectations
    Francesc Castro-Giner, Sofia Gkountela, Cinzia Donato, Ilaria Alborelli, Luca Quagliata, Charlotte K.Y. Ng, Salvatore Piscuoglio, Nicola Aceto · 2018 · Diagnostics
63. Clonal CD4+ T cells in the HIV-1 latent reservoir display a distinct gene profile upon reactivation
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64. Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR)
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65. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
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66. Kupffer-cell-derived IL-6 is repurposed for hepatocyte dedifferentiation via activating progenitor genes from injury-specific enhancers
    Li, Lu, Cui, Lei, Lin, Ping, Liu, Zhaoyuan, Bao, Shujie, Ma, Xiaolong, Nan, Haitao, Zhu, Wencheng, Cen, Jin, Mao, Yunuo et al. · 2023 · Cell Stem Cell
67. Recent developments in application of single-cell RNA sequencing in the tumour immune microenvironment and cancer therapy
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68. K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data
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69. Experimental design for single-cell RNA sequencing
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70. Scalable microfluidics for single-cell RNA printing and sequencing
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71. An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
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72. Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis
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73. Transcriptional landscape of highly lignified poplar stems at single-cell resolution
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74. Simulating multiple faceted variability in single cell RNA sequencing
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75. Demystifying “drop-outs” in single-cell UMI data
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76. Computational approaches for interpreting sc<scp>RNA</scp>‐seq data
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77. Embryonic endothelial evolution towards first hematopoietic stem cells revealed by single-cell transcriptomic and functional analyses
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78. The Sox2 transcription factor binds RNA
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79. Single-Cell Transcriptomics Bioinformatics and Computational Challenges
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80. Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform
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81. Massively parallel nanowell-based single-cell gene expression profiling
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82. A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation
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83. Understanding development and stem cells using single cell-based analyses of gene expression
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84. Single Cell RNA Sequencing of Rare Immune Cell Populations
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85. Tools for the analysis of high-dimensional single-cell RNA sequencing data
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86. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects
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87. Dissecting Cellular Heterogeneity Using Single-Cell RNA Sequencing.
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88. A new era for plant science: spatial single-cell transcriptomics
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89. SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression
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90. Analysis and correction of compositional bias in sparse sequencing count data
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91. Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes
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92. Appyters: Turning Jupyter Notebooks into data-driven web apps
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93. From bench to bedside: Single-cell analysis for cancer immunotherapy
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94. An Introduction to the Analysis of Single-Cell RNA-Sequencing Data
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95. Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer
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96. bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
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97. Plant Systems Biology at the Single-Cell Level
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98. The Comparison of Two Single-cell Sequencing Platforms: BD Rhapsody and 10x Genomics Chromium
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99. Passive Noise Filtering by Cellular Compartmentalization
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100. Methodologies for Transcript Profiling Using Long-Read Technologies
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