TY - JOUR AU - Stubbington, M. J. T. AU - Rozenblatt-Rosen, O. AU - Regev, A. AU - Teichmann, S. A. PY - 2017 DA - 2017// TI - Single-cell transcriptomics to explore the immune system in health and disease JO - Science VL - 358 UR - https://doi.org/10.1126/science.aan6828 DO - 10.1126/science.aan6828 ID - Stubbington2017 ER - TY - JOUR AU - Tanay, A. AU - Regev, A. PY - 2017 DA - 2017// TI - Scaling single-cell genomics from phenomenology to mechanism JO - Nature VL - 541 UR - https://doi.org/10.1038/nature21350 DO - 10.1038/nature21350 ID - Tanay2017 ER - TY - STD TI - Villani A-C, et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science. 2017;356:eaah4573. ID - ref3 ER - TY - JOUR AU - Velten, L. PY - 2017 DA - 2017// TI - Human haematopoietic stem cell lineage commitment is a continuous process JO - Nat Cell Biol VL - 19 UR - https://doi.org/10.1038/ncb3493 DO - 10.1038/ncb3493 ID - Velten2017 ER - TY - JOUR AU - Cao, J. PY - 2017 DA - 2017// TI - Comprehensive single-cell transcriptional profiling of a multicellular organism JO - Science VL - 357 UR - https://doi.org/10.1126/science.aam8940 DO - 10.1126/science.aam8940 ID - Cao2017 ER - TY - JOUR AU - Karaiskos, N. PY - 2017 DA - 2017// TI - The Drosophila embryo at single-cell transcriptome resolution JO - Science VL - 8 ID - Karaiskos2017 ER - TY - JOUR AU - Macosko, E. Z. PY - 2015 DA - 2015// TI - Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets JO - Cell VL - 161 UR - https://doi.org/10.1016/j.cell.2015.05.002 DO - 10.1016/j.cell.2015.05.002 ID - Macosko2015 ER - TY - JOUR AU - Klein, A. M. PY - 2015 DA - 2015// TI - Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells JO - Cell VL - 161 UR - https://doi.org/10.1016/j.cell.2015.04.044 DO - 10.1016/j.cell.2015.04.044 ID - Klein2015 ER - TY - JOUR AU - Zheng, G. X. Y. PY - 2017 DA - 2017// TI - Massively parallel digital transcriptional profiling of single cells JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/s41467-016-0009-6 DO - 10.1038/s41467-016-0009-6 ID - Zheng2017 ER - TY - JOUR AU - Regev, A. PY - 2017 DA - 2017// TI - Science forum: the human cell atlas JO - eLife VL - 6 UR - https://doi.org/10.7554/eLife.27041 DO - 10.7554/eLife.27041 ID - Regev2017 ER - TY - JOUR AU - Stegle, O. AU - Teichmann, S. A. AU - Marioni, J. C. PY - 2015 DA - 2015// TI - Computational and analytical challenges in single-cell transcriptomics JO - Nat Publ Group VL - 16 ID - Stegle2015 ER - TY - STD TI - Hicks SC, Townes FW, Teng M, Irizarry RA. Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics. 2017. https://doi.org/10.1093/biostatistics/kxx053. ID - ref12 ER - TY - STD TI - Kang HM, et al. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Publ Group. 2017. https://doi.org/10.1038/nbt.4042. ID - ref13 ER - TY - JOUR AU - Tung, P. -. Y. PY - 2017 DA - 2017// TI - Batch effects and the effective design of single-cell gene expression studies JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/srep39921 DO - 10.1038/srep39921 ID - Tung2017 ER - TY - JOUR AU - Mei, H. E. AU - Leipold, M. D. AU - Schulz, A. R. AU - Chester, C. AU - Maecker, H. T. PY - 2015 DA - 2015// TI - Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry JO - J Immunol VL - 194 UR - https://doi.org/10.4049/jimmunol.1402661 DO - 10.4049/jimmunol.1402661 ID - Mei2015 ER - TY - JOUR AU - Lai, L. AU - Ong, R. AU - Li, J. AU - Albani, S. PY - 2015 DA - 2015// TI - A CD45-based barcoding approach to multiplex mass-cytometry (CyTOF) JO - Cytometry VL - 87 UR - https://doi.org/10.1002/cyto.a.22640 DO - 10.1002/cyto.a.22640 ID - Lai2015 ER - TY - JOUR AU - Krutzik, P. O. AU - Nolan, G. P. PY - 2006 DA - 2006// TI - Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling JO - Nat Meth VL - 3 UR - https://doi.org/10.1038/nmeth872 DO - 10.1038/nmeth872 ID - Krutzik2006 ER - TY - JOUR AU - Stoeckius, M. PY - 2017 DA - 2017// TI - Simultaneous epitope and transcriptome measurement in single cells JO - Nat Meth VL - 9 ID - Stoeckius2017 ER - TY - STD TI - van Buggenum JAGL, et al. A covalent and cleavable antibody- DNA conjugation strategy for sensitive protein detection via immuno-PCR. Nat Publ Group. 2016:1–12. https://doi.org/10.1038/srep22675. ID - ref19 ER - TY - JOUR AU - Hulspas, R. PY - 2010 DA - 2010// TI - Titration of fluorochrome-conjugated antibodies for labeling cell surface markers on live cells JO - Curr Protoc Cytom VL - Chapter 6 ID - Hulspas2010 ER - TY - STD TI - Uhlen M, Fagerberg L, Hallstrom BM, Lindskog C. Tissue-based map of the human proteome. Science. 2015. https://doi.org/10.1126/science.1260419. ID - ref21 ER - TY - STD TI - Hartmann FJ, Simonds EF, Bendall SC. A universal live cell barcoding-platform for multiplexed human single cell analysis. Sci Rep. 2018;8(10770). ID - ref22 ER - TY - STD TI - Lake BB, et al. A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Sci Rep. 2017:1–8. https://doi.org/10.1038/s41598-017-04426-w. ID - ref23 ER - TY - STD TI - Habib et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods. 2017;14(10):955–8. PMID: 28846088. ID - ref24 ER - TY - STD TI - Delley CL, liu L, Sarhan MF, Abate AR. Combined aptamer and transcriptome sequencing of single cells. bioRxiv. 2017:1–10. https://doi.org/10.1101/228338. ID - ref25 ER - TY - BOOK AU - Shin, D. AU - Lee, W. AU - Lee, J. H. AU - bioRxiv, D. B. PY - 2018 DA - 2018// TI - Multiplexed single-cell RNA-seq via transient barcoding for drug screening UR - https://doi.org/10.1101/359851 DO - 10.1101/359851 ID - Shin2018 ER - TY - STD TI - Gehring J, Park JH, Chen S, Thomson M, Pachter L. Highly multiplexed single-cell RNA-seq for defining cell population and transcriptional spaces. bioRxiv. 2018:1–19. https://doi.org/10.1101/315333. ID - ref27 ER - TY - STD TI - McGinnis, C. S. et al. MULTI-seq: scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices 1–34 (2018). doi:https://doi.org/10.1101/387241. ID - ref28 ER - TY - STD TI - Stuart et al. Comprehensive integration of single cell data. biorxiv. 2018. https://doi.org/10.1101/460147. ID - ref29 ER - TY - STD TI - Guo C, Biddy BA, Kamimoto K, Kong W, Morris SA. CellTag indexing: a genetic barcode-based multiplexing tool for single-cell technologies. 2018:1–20. https://doi.org/10.1101/335547. ID - ref30 ER - TY - JOUR AU - Satija, R. AU - Farrell, J. A. AU - Gennert, D. AU - Schier, A. F. AU - Regev, A. PY - 2015 DA - 2015// TI - Spatial reconstruction of single-cell gene expression data JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3192 DO - 10.1038/nbt.3192 ID - Satija2015 ER - TY - STD TI - Butler A, Satija R. Integrated analysis of single cell transcriptomic data across conditions, technologies, and species. bioRxiv. 2017. https://doi.org/10.1101/164889. ID - ref32 ER - TY - JOUR AU - Blondel, V. D. AU - Guillaume, J. -. L. AU - Lambiotte, R. AU - Lefebvre, E. PY - 2008 DA - 2008// TI - Fast unfolding of communities in large networks JO - J Stat Mech VL - 2008 UR - https://doi.org/10.1088/1742-5468/2008/10/P10008 DO - 10.1088/1742-5468/2008/10/P10008 ID - Blondel2008 ER - TY - JOUR AU - Levine, J. H. PY - 2015 DA - 2015// TI - Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis JO - Cell VL - 162 UR - https://doi.org/10.1016/j.cell.2015.05.047 DO - 10.1016/j.cell.2015.05.047 ID - Levine2015 ER - TY - JOUR AU - Shekhar, K. PY - 2016 DA - 2016// TI - Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics JO - Cell VL - 166 UR - https://doi.org/10.1016/j.cell.2016.07.054 DO - 10.1016/j.cell.2016.07.054 ID - Shekhar2016 ER - TY - STD TI - Wright MN, Ziegler A. Ranger: a fast implementation of random forests for high dimensional data in C and R. J Stat Softw. 2017;77:1–17. ID - ref36 ER - TY - STD TI - Stoeckius M, Zheng S, Houck-Loomis B, Hao S, Yeung B, Smibert P, and Satija R. Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108313 (2018). UR - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108313 ID - ref37 ER - TY - STD TI - Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Github Repository. https://github.com/satijalab/seurat (2018). UR - https://github.com/satijalab/seurat ID - ref38 ER -