Eberwine J, Sul JY, Bartfai T, Kim J. The promise of single-cell sequencing. Nat Methods. 2014;11:25–7.
Article
CAS
PubMed
Google Scholar
Blainey PC, Quake SR. Dissecting genomic diversity, one cell at a time. Nat Methods. 2014;11:19–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sandberg R. Entering the era of single-cell transcriptomics in biology and medicine. Nat Methods. 2014;11:22–4.
Article
CAS
PubMed
Google Scholar
Spitzer MH, Nolan GP. Mass cytometry: single cells, many features. Cell. 2016;165:780–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zenobi R. Single-cell metabolomics: analytical and biological perspectives. Science. 2013;342:1243259.
Article
CAS
PubMed
Google Scholar
Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL, Espinoza FH, et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature. 2014;509:371–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zeisel A, Munoz-Manchado AB, Codeluppi S, Lonnerberg P, La Manno G, Jureus A, et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science. 2015;347:1138–42.
Article
CAS
PubMed
Google Scholar
Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, et al. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell. 2016;166:1308–23. e1330.
Article
CAS
PubMed
Google Scholar
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32:381–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bendall SC, Davis KL, Amir e-AD, Tadmor MD, Simonds EF, Chen TJ, et al. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell. 2014;157:714–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, et al. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc Natl Acad Sci U S A. 2014;111:E5643–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TM, Kathail P, et al. Wishbone identifies bifurcating developmental trajectories from single-cell data. Nat Biotechnol. 2016;34:637–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haghverdi L, Buttner M, Wolf FA, Buettner F, Theis FJ. Diffusion pseudotime robustly reconstructs lineage branching. Nat Methods. 2016;13:845–8.
Article
CAS
PubMed
Google Scholar
Guo G, Luc S, Marco E, Lin TW, Peng C, Kerenyi MA, et al. Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire. Cell Stem Cell. 2013;13:492–505.
Article
CAS
PubMed
Google Scholar
Paul F, Arkin Y, Giladi A, Jaitin DA, Kenigsberg E, Keren-Shaul H, et al. Transcriptional heterogeneity and lineage commitment in myeloid progenitors. Cell. 2015;163:1663–77.
Article
CAS
PubMed
Google Scholar
Olsson A, Venkatasubramanian M, Chaudhri VK, Aronow BJ, Salomonis N, Singh H, et al. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016;537:698–702.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hoppe PS, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Moritz N, et al. Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios. Nature. 2016;535:299–302.
Article
CAS
PubMed
Google Scholar
Kim TK, Sul JY, Peternko NB, Lee JH, Lee M, Patel VV, et al. Transcriptome transfer provides a model for understanding the phenotype of cardiomyocytes. Proc Natl Acad Sci U S A. 2011;108:11918–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim J, Eberwine J. RNA: state memory and mediator of cellular phenotype. Trends Cell Biol. 2010;20:311–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ni X, Zhuo M, Su Z, Duan J, Gao Y, Wang Z, et al. Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proc Natl Acad Sci U S A. 2013;110:21083–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 2014;512:155–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gawad C, Koh W, Quake SR. Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics. Proc Natl Acad Sci U S A. 2014;111:17947–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tirosh I, Izar B, Prakadan SM, Wadsworth 2nd MH, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352:189–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bacher R, Kendziorski C. Design and computational analysis of single-cell RNA-sequencing experiments. Genome Biol. 2016;17:63.
Article
PubMed
PubMed Central
Google Scholar
Skylaki S, Hilsenbeck O, Schroeder T. Challenges in long-term imaging and quantification of single-cell dynamics. Nat Biotechnol. 2016;34:1137–44.
Article
CAS
PubMed
Google Scholar
Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol. 2016;34:1145–60.
Article
CAS
PubMed
Google Scholar
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol. 2015;33:155–60.
Article
CAS
PubMed
Google Scholar
Kharchenko PV, Silberstein L, Scadden DT. Bayesian approach to single-cell differential expression analysis. Nat Methods. 2014;11:740–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lun AT, Bach K, Marioni JC. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 2016;17:75.
Article
PubMed
Google Scholar
Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 2015;16:278.
Article
PubMed
PubMed Central
Google Scholar
Hicks SC, Teng M, Irizarry RA. On the widespread and critical impact of systematic bias and batch effects in single-cell RNA-Seq data. bioRxiv. 2015. doi:10.1101/025528.
Google Scholar
Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, et al. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res. 2014;24:496–510.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, et al. Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. Genome Biol. 2015;16:122.
Article
PubMed
PubMed Central
Google Scholar
Baker SC, Bauer SR, Beyer RP, Brenton JD, Bromley B, Burrill J, et al. The external RNA controls consortium: a progress report. Nat Methods. 2005;2:731–4.
Article
CAS
PubMed
Google Scholar
Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, et al. Power analysis of single-cell RNA-sequencing experiments. Nat Methods. 2017;14:381–7.
Article
PubMed
Google Scholar
Femino AM, Fay FS, Fogarty K, Singer RH. Visualization of single RNA transcripts in situ. Science. 1998;280:585–90.
Article
CAS
PubMed
Google Scholar
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 2006;4:e309.
Article
PubMed
PubMed Central
Google Scholar
Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science. 2006;313:1642–5.
Article
CAS
PubMed
Google Scholar
Rust MJ, Bates M, Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods. 2006;3:793–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lubeck E, Cai L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods. 2012;9:743–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lubeck E, Coskun AF, Zhiyentayev T, Ahmad M, Cai L. Single-cell in situ RNA profiling by sequential hybridization. Nat Methods. 2014;11:360–1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ke R, Mignardi M, Pacureanu A, Svedlund J, Botling J, Wahlby C, et al. In situ sequencing for RNA analysis in preserved tissue and cells. Nat Methods. 2013;10:857–60.
Article
CAS
PubMed
Google Scholar
Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, et al. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014;343:1360–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science. 2015;348:aaa6090.
Article
PubMed
PubMed Central
Google Scholar
Moffitt JR, Hao J, Wang G, Chen KH, Babcock HP, Zhuang X. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc Natl Acad Sci U S A. 2016;113:11046–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shah S, Lubeck E, Schwarzkopf M, He TF, Greenbaum A, Sohn CH, et al. Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing. Development. 2016;143:2862–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Choi HM, Chang JY, le Trinh A, Padilla JE, Fraser SE, Pierce NA. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat Biotechnol. 2010;28:1208–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shah S, Lubeck E, Zhou W, Cai L. In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus. Neuron. 2016;92:342–57.
Article
CAS
PubMed
Google Scholar
Legant WR, Shao L, Grimm JB, Brown TA, Milkie DE, Avants BB, et al. High-density three-dimensional localization microscopy across large volumes. Nat Methods. 2016;13:359–65.
Article
PubMed
PubMed Central
Google Scholar
Satija R, Farrell JA, Gennert D, Schier AF, Regev A. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol. 2015;33:495–502.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen F, Tillberg PW, Boyden ES. Optical imaging. Expansion microscopy. Science. 2015;347:543–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coskun AF, Cai L. Dense transcript profiling in single cells by image correlation decoding. Nat Methods. 2016;13:657–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Etzrodt M, Endele M, Schroeder T. Quantitative single-cell approaches to stem cell research. Cell Stem Cell. 2014;15:546–58.
Article
CAS
PubMed
Google Scholar
McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science. 2016;353:aaf7907.
Article
PubMed
PubMed Central
Google Scholar
Junker JP, Spanjaard B, Peterson-Maduro J, Alemany A, Hu B, Florescu M, et al. Massively parallel whole-organism lineage tracing using CRISPR/Cas9 induced genetic scars. bioRxiv. 2016. doi:10.1101/056499.
Google Scholar
Perli SD, Cui CH, Lu TK. Continuous genetic recording with self-1 targeting CRISPR-Cas in human cells. Science. 2016;353:aag0511.
Article
PubMed
Google Scholar
Schmidt ST, Zimmerman SM, Wang J, Kim SK, Quake SR. Quantitative analysis of synthetic cell lineage tracing using nuclease barcoding. ACS Synth Biol. 2017. doi:10.1021/acssynbio.6b00309.
Google Scholar
Kalhor R, Mali P, Church GM. Rapidly evolving homing CRISPR barcodes. Nat Methods. 2017;14:195–200.
Article
CAS
PubMed
Google Scholar
Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods. 2015;12:519–22.
Article
CAS
PubMed
Google Scholar
Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A. Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol. 2015;33:285–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, et al. Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat Methods. 2016;13:229–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu Y, Huang K, An Q, Du G, Hu G, Xue J, et al. Simultaneous profiling of transcriptome and DNA methylome from a single cell. Genome Biol. 2016;17:88.
Article
PubMed
PubMed Central
Google Scholar
Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, et al. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res. 2016;26:304–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheow LF, Courtois ET, Tan Y, Viswanathan R, Xing Q, Tan RZ, et al. Single-cell multimodal profiling reveals cellular epigenetic heterogeneity. Nat Methods. 2016;13:833–6.
Article
CAS
PubMed
Google Scholar
Genshaft AS, Li S, Gallant CJ, Darmanis S, Prakadan SM, Ziegler CG, et al. Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction. Genome Biol. 2016;17:188.
Article
PubMed
PubMed Central
Google Scholar
Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, et al. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol. 2015;16:20.
Article
PubMed
PubMed Central
Google Scholar
Wang S, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, et al. Spatial organization of chromatin domains and compartments in single chromosomes. Science. 2016;353:598–602.
Article
CAS
PubMed
PubMed Central
Google Scholar
Levine JH, Simonds EF, Bendall SC, Davis KL, el Amir AD, Tadmor MD, et al. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell. 2015;162:184–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu C, Su Z. Identification of cell types from single-cell transcriptomes using a novel clustering method. Bioinformatics. 2015;31:1974–80.
Article
CAS
PubMed
Google Scholar
Grun D, Lyubimova A, Kester L, Wiebrands K, Basak O, Sasaki N, et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature. 2015;525:251–5.
Article
PubMed
Google Scholar
Jiang L, Chen H, Pinello L, Yuan GC. GiniClust: detecting rare cell types from single-cell gene expression data with Gini index. Genome Biol. 2016;17:144.
Article
PubMed
PubMed Central
Google Scholar
Prabhakaran S, Azizi E, Carr A, Pe’er D. Dirichlet process mixture model for correcting technical variation in single-cell gene expression data. J Mach Learn Res. 2016;48:1070–9.
Google Scholar
Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, et al. Inflammation-induced emergency megakaryopoiesis driven by hematopoietic stem cell-like megakaryocyte progenitors. Cell Stem Cell. 2015;17:422–34.
Article
CAS
PubMed
Google Scholar
Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey F, Voet T, et al. Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells. Cell Rep. 2016;14:966–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kauffman SA. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol. 1969;22:437–67.
Article
CAS
PubMed
Google Scholar
Grun D, Muraro MJ, Boisset JC, Wiebrands K, Lyubimova A, Dharmadhikari G, et al. De Novo prediction of stem cell identity using single-cell transcriptome data. Cell Stem Cell. 2016;19:266–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Teschendorff AE. Single-cell entropy for quantification of differentiation potency from a cell’s transcriptome. bioRxiv. 2016. doi:10.1101/084202.
Google Scholar
Wilson NK, Kent DG, Buettner F, Shehata M, Macaulay IC, Calero-Nieto FJ, et al. Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations. Cell Stem Cell. 2015;16:712–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grover A, Sanjuan-Pla A, Thongjuea S, Carrelha J, Giustacchini A, Gambardella A, et al. Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells. Nat Commun. 2016;7:11075.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343:84–7.
Article
CAS
PubMed
Google Scholar
Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014;343:80–4.
Article
CAS
PubMed
Google Scholar
Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, et al. Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell. 2016;167:1853–66. e1817.
Article
CAS
PubMed
Google Scholar
Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, et al. Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq. Cell. 2016;167:1883–96. e1815.
Article
CAS
PubMed
Google Scholar
Adamson B, Norman TM, Jost M, Cho MY, Nunez JK, Chen Y, et al. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell. 2016;167:1867–82. e1821.
Article
CAS
PubMed
Google Scholar
Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, et al. Pooled CRISPR screening with single-cell transcriptome readout. Nat Methods. 2017;14:297–301.
Article
CAS
PubMed
Google Scholar
Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014;344:1396–401.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saadatpour A, Lai S, Guo G, Yuan GC. Single-cell analysis in cancer genomics. Trends Genet. 2015;31:576–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tsoucas D, Yuan GC. Recent progress in single-cell cancer genomics. Curr Opin Genet Dev. 2017;42:22–32.
Article
CAS
PubMed
Google Scholar
Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016;539:309–13.
Article
PubMed
Google Scholar
van den Bos H, Spierings DC, Taudt AS, Bakker B, Porubsky D, Falconer E, et al. Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer’s disease neurons. Genome Biol. 2016;17:116.
Article
PubMed
PubMed Central
Google Scholar
Gaudilliere B, Fragiadakis GK, Bruggner RV, Nicolau M, Finck R, Tingle M, et al. Clinical recovery from surgery correlates with single-cell immune signatures. Sci Transl Med. 2014;6:255ra131.
Article
PubMed
PubMed Central
Google Scholar
Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol. 2014;15:525.
Article
PubMed
PubMed Central
Google Scholar
Van Noorden R. Interdisciplinary research by the numbers. Nature. 2015;525:306–7.
Article
PubMed
Google Scholar