1. Bhang HE, Ruddy DA, Krishnamurthy Radhakrishna V, Caushi JX, Zhao R, Hims MM,
et al. Studying clonal dynamics in response to cancer therapy using high-complexity barcoding. Nat Med 2015;21:440–448.
2. Russo M, Siravegna G, Blaszkowsky LS, Corti G, Crisafulli G, Ahronian LG,
et al. Tumor heterogeneity and lesion-specific response to targeted therapy in colorectal cancer. Cancer Discov 2016;6:147–153.
3. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N,
et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 2009;6:377–382.
5. Puram SV, Tirosh I, Parikh AS, Patel AP, Yizhak K, Gillespie S,
et al. Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. Cell 2017;171:1611–1624.e24.
6. Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ,
et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 2016;352:189–196.
7. Venteicher AS, Tirosh I, Hebert C, Yizhak K, Neftel C, Filbin MG,
et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science 2017;355:eaai8478.
9. 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;344:1396–1401.
11. Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X,
et al. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 2012;148:873–885.
12. Azizi E, Carr AJ, Plitas G, Cornish AE, Konopacki C, Prabhakaran S,
et al. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell 2018;174:1293–1308.e36.
13. Miyamoto DT, Zheng Y, Wittner BS, Lee RJ, Zhu H, Broderick KT,
et al. RNA-Seq of single prostate CTCs implicates non-canonical Wnt signaling in antiandrogen resistance. Science 2015;349:1351–1356.
14. Sznol M, Powderly JD, Smith DC, Brahmer JR, Drake CG, McDermott DF,
et al. Safety and antitumor activity of biweekly MDX-1106 (Anti-PD-1, BMS-936558/ONO-4538) in patients with advanced refractory malignancies. J Clin Oncol 2010;28(15 Suppl):2506.
16. Chakraborty S, Hosen MI, Ahmed M, Shekhar HU. Onco-multi-OMICS approach: a new frontier in cancer research. Biomed Res Int 2018;2018:9836256.
19. Kim C, Gao R, Sei E, Brandt R, Hartman J, Hatschek T,
et al. Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell 2018;173:879–893.e13.
20. Bernard V, Semaan A, Huang J, San Lucas FA, Mulu FC, Stephens BM,
et al. Single cell transcriptomics of pancreatic cancer precursors demonstrates epithelial and micro-environmental heterogeneity as an early event in neoplastic progression. Clin Cancer Res 2018 Nov 1 [Epub].
https://doi.org/10.1158/1078-0432.CCR-18-1955.
22. Singer M, Wang C, Cong L, Marjanovic ND, Kowalczyk MS, Zhang H,
et al. A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating
T cells. Cell 2017;171:1221–1223.
23. Zheng C, Zheng L, Yoo JK, Guo H, Zhang Y, Guo X,
et al. Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell 2017;169:1342–1356.e16.
25. Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW,
et al. Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell 2018;175:998–1013.e20.
26. Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC,
et al. A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade. Cell 2018;175:984–997.e24.
27. Krieg C, Nowicka M, Guglietta S, Schindler S, Hartmann FJ, Weber LM,
et al. High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy. Nat Med 2018;24:144–153.
29. 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;12:519–522.
31. 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.
33. Darmanis S, Gallant CJ, Marinescu VD, Niklasson M, Segerman A, Flamourakis G,
et al. Simultaneous multiplexed measurement of RNA and proteins in single cells. Cell Rep 2016;14:380–389.
34. Peterson VM, Zhang KX, Kumar N, Wong J, Li L, Wilson DC,
et al. Multiplexed quantification of proteins and transcripts in single cells. Nat Biotechnol 2017;35:936–939.
35. Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H,
et al. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 2017;14:865–868.
36. Guo F, Li L, Li J, Wu X, Hu B, Zhu P,
et al. Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells. Cell Res 2017;27:967–988.
39. Han KY, Kim KT, Joung JG, Son DS, Kim YJ, Jo A,
et al. SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells. Genome Res 2018;28:75–87.
41. Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP,
et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 2015;523:486–490.
42. Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ,
et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 2018;361:1380–1385.
43. Lavin Y, Kobayashi S, Leader A, Amir ED, Elefant N, Bigenwald C,
et al. Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell 2017;169:750–765.e17.
44. Gubin MM, Esaulova E, Ward JP, Malkova ON, Runci D, Wong P,
et al. High-dimensional analysis delineates myeloid and lymphoid compartment remodeling during successful immune-checkpoint cancer therapy. Cell 2018;175:1443.