Integrated genome and transcriptome sequencing of the same cell

Dey, Siddharth S, Kester, Lennart, Spanjaard, Bastiaan, Bienko, Magda, van Oudenaarden, Alexander·2015·Nature Biotechnology
DOI 10.1038/nbt.3129

Cited by (504)

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  2. Single-Cell Omics in Personalized Medicine
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  5. Studying Epigenomics in Single Cells: What is Feasible and what can we Learn?
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  6. Sequencing-based methods for single-cell multi-omics studies
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  7. Unveiling Long Non-coding RNA Networks from Single-Cell Omics Data Through Artificial Intelligence
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  9. scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase
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  10. A single-cell lens into the co-evolution of genotypes and phenotypes in cancer
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  17. Eukaryotic Single-Cell mRNA Sequencing
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  19. Single Cell Genomics for Tumor Heterogeneity
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  24. An overview of single-cell high-throughput technology in plants
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  25. The landscape of cell lineage tracing
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  48. Gel-Seq: An Approach for Simultaneously Sequencing the Genome and Transcriptome in Small Populations of Cells
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  58. scONE-seq: A one-tube single-cell multi-omics method enables simultaneous dissection of molecular phenotype and genotype heterogeneity from frozen tumors
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  61. Faculty Opinions recommendation of The Systems Biology of Single-Cell Aging.
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  62. Literature Search and Review
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  73. Additional file 3 of Bi-order multimodal integration of single-cell data
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  83. Additional file 1 of Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
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  84. Additional file 4 of Bi-order multimodal integration of single-cell data
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