Valkenburg KC, de Groot AE, Pienta KJ. Targeting the tumour stroma to improve cancer therapy. Nat Rev Clin Oncol. 2018;15:366–81.
Article
PubMed
PubMed Central
Google Scholar
Amend SR, Roy S, Brown JS, Pienta KJ. Ecological paradigms to understand the dynamics of metastasis. Cancer Lett. 2016;380:237–42.
Article
CAS
PubMed
Google Scholar
Merlo LMF, Pepper JW, Reid BJ, Maley CC. Cancer as an evolutionary and ecological process. Nat Rev Cancer. 2006;6:924–35.
Article
CAS
PubMed
Google Scholar
Maley CC, Aktipis A, Graham TA, Sottoriva A, Boddy AM, Janiszewska M, et al. Classifying the evolutionary and ecological features of neoplasms. Nat Rev Cancer. 2017;17:605–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Greaves M, Maley CC. Clonal evolution in cancer. Nature. 2012;481:306–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
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;6:377–82.
Article
CAS
PubMed
Google Scholar
Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, et al. Tumour evolution inferred by single-cell sequencing. Nature. 2011;472:90–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, et al. Genome-wide copy number analysis of single cells. Nat Protocols. 2012;7:1024–41.
Article
CAS
PubMed
Google Scholar
Lu S, Zong C, Fan W, Yang M, Li J, Chapman AR, et al. Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science. 2012;338:1627–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
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;148:873–85.
Article
CAS
PubMed
Google Scholar
Hughes AE, Magrini V, Demeter R, Miller CA, Fulton R, Fulton LL, et al. Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. PLoS Genet. 2014;10:e1004462.
Article
CAS
PubMed
PubMed Central
Google Scholar
Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, et al. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell. 2014;26:813–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Demeulemeester J, Kumar P, Moller EK, Nord S, Wedge DC, Peterson A, et al. Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing. Genome Biol. 2016;17:250.
Article
PubMed
PubMed Central
Google Scholar
Jahn K, Kuipers J, Beerenwinkel N. Tree inference for single-cell data. Genome Biol. 2016;17:86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genetics. 2016;48:1193–203.
Article
CAS
PubMed
Google Scholar
Gao Y, Ni X, Guo H, Su Z, Ba Y, Tong Z, et al. Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells. Genome Res. 2017;27:1312–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kuipers J, Jahn K, Raphael BJ, Beerenwinkel N. Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors. Genome Res. 2017;27:1885–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu H, Zhang XY, Hu Z, Hou Q, Zhang H, Li Y, et al. Evolution and heterogeneity of non-hereditary colorectal cancer revealed by single-cell exome sequencing. Oncogene. 2017;36:2857–67.
Article
CAS
PubMed
Google Scholar
Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, et al. Combating subclonal evolution of resistant cancer phenotypes. Nat Commun. 2017;8:1231.
Article
CAS
PubMed
PubMed Central
Google Scholar
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;173:879–93 e13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Casasent AK, Schalck A, Gao R, Sei E, Long A, Pangburn W, et al. Multiclonal invasion in breast tumors identified by topographic single cell sequencing. Cell. 2018;172:205–17 e212.
Article
CAS
PubMed
PubMed Central
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
CAS
PubMed
PubMed Central
Google Scholar
Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol. 2011;29:1120–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Powell AA, Talasaz AH, Zhang H, Coram MA, Reddy A, Deng G, et al. Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines. Plos One. 2012;7:e33788.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee MC, Lopez-Diaz FJ, Khan SY, Tariq MA, Dayn Y, Vaske CJ, et al. Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. Proc Natl Acad Sci U S A. 2014;111:E4726–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cleary AS, Leonard TL, Gestl SA, Gunther EJ. Tumour cell heterogeneity maintained by cooperating subclones in Wnt-driven mammary cancers. Nature. 2014;508:113–7.
Article
CAS
PubMed
PubMed Central
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
Pollen AA, Nowakowski TJ, Shuga J, Wang X, Leyrat AA, Lui JH, et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in develo** cerebral cortex. Nat Biotechnol. 2014;32:1053–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim KT, Lee HW, Lee HO, Kim SC, Seo YJ, Chung W, et al. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biol. 2015;16:127.
Article
CAS
PubMed
PubMed Central
Google Scholar
Janiszewska M, Liu L, Almendro V, Kuang Y, Paweletz C, Sakr RA, et al. In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nat Genet. 2015;47:1212–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miyamoto DT, Zheng Y, Wittner BS, Lee RJ, Zhu H, Broderick KT, et al. RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance. Science. 2015;349:1351–6.
Article
CAS
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
Bakker B, Taudt A, Belderbos ME, Porubsky D, Spierings DC, de Jong TV, et al. Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. Genome Biol. 2016;17:115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mann KM, Newberg JY, Black MA, Jones DJ, Amaya-Manzanares F, Guzman-Rojas L, et al. Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq. Nat Biotechnol. 2016;34:962–72.
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
Liu M, Liu Y, Di J, Su Z, Yang H, Jiang B, et al. Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer. BMC Cancer. 2017;17:787.
Article
PubMed
PubMed Central
Google Scholar
Gao R, Kim C, Sei E, Foukakis T, Crosetto N, Chan LK, et al. Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer. Nat Commun. 2017;8:228.
Article
CAS
PubMed
PubMed Central
Google Scholar
Giustacchini A, Thongjuea S, Barkas N, Woll PS, Povinelli BJ, Booth CAG, et al. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. Nat Med. 2017;23:692–702.
Article
CAS
PubMed
Google Scholar
Zong C, Lu S, Chapman AR, **e XS. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science. 2012;338:1622–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen C, **ng D, Tan L, Li H, Zhou G, Huang L, et al. Single-cell whole-genome analyses by linear amplification via transposon insertion (LIANTI). Science. 2017;356:189–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pastushenko I, Brisebarre A, Sifrim A, Fioramonti M, Revenco T, Boumahdi S, et al. Identification of the tumour transition states occurring during EMT. Nature. 2018;556:463–8.
Article
CAS
PubMed
Google Scholar
Roerink SF, Sasaki N, Lee-Six H, Young MD, Alexandrov LB, Behjati S, et al. Intra-tumour diversification in colorectal cancer at the single-cell level. Nature. 2018;556:457–62.
Article
CAS
PubMed
Google Scholar
Carter L, Rothwell DG, Mesquita B, Smowton C, Leong HS, Fernandez-Gutierrez F, et al. Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer. Nat Med. 2017;23:114–9.
Article
CAS
PubMed
Google Scholar
Lawson DA, Bhakta NR, Kessenbrock K, Prummel KD, Yu Y, Takai K, et al. Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells. Nature. 2015;526:131–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martelotto LG, Baslan T, Kendall J, Geyer FC, Burke KA, Spraggon L, et al. Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Nat Med. 2017;23:376–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Suzuki A, Matsushima K, Makinoshima H, Sugano S, Kohno T, Tsuchihara K, et al. Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment. Genome Biol. 2015;16:66.
Article
CAS
PubMed
PubMed Central
Google Scholar
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;352:189–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
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;171:1611–24 e1624.
Article
CAS
PubMed
PubMed Central
Google Scholar
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;169:1342–56 e1316.
Article
CAS
PubMed
Google Scholar
Li H, Courtois ET, Sengupta D, Tan Y, Chen KH, Goh JJL, et al. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat Genet. 2017;49:708–18.
Article
CAS
PubMed
Google Scholar
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. https://doi.org/10.1126/science.aai8478.
Chung W, Eum HH, Lee H-O, Lee K-M, Lee H-B, Kim K-T, et al. Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer. Nat Commun. 2017;8:15081.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lavin Y, Kobayashi S, Leader A, Amir El-Ad D, Elefant N, Bigenwald C, et al. Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell. 2017;169:750–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chevrier S, Levine JH, Zanotelli VRT, Silina K, Schulz D, Bacac M, et al. An immune atlas of clear cell renal cell carcinoma. Cell. 2017;169:736–49 e718.
Article
CAS
PubMed
PubMed Central
Google Scholar
Savas P, Virassamy B, Ye C, Salim A, Mintoff CP, Caramia F, et al. Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis. Nat Med. 2018;24:986–93.
Article
CAS
PubMed
Google Scholar
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;173:1293–308.
Article
CAS
Google Scholar
Guo X, Zhang Y, Zheng L, Zheng C, Song J, Zhang Q, Kang B, Liu Z, ** L, **ng R, et al. Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. Nat Med. 2018;174:1293–308.
Google Scholar
Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, et al. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science. 2018;361:594–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lambrechts D, Wauters E, Boeckx B, Aibar S, Nittner D, Burton O, et al. Phenotype molding of stromal cells in the lung tumor microenvironment. Nat Med. 2018;24:1277–89.
Article
CAS
PubMed
Google Scholar
Navin NE. The first five years of single-cell cancer genomics and beyond. Genome Res. 2015;25:1499–507.
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
PubMed Central
Google Scholar
Müller S, Diaz A. Single-cell mRNA sequencing in cancer research: integrating the genomic fingerprint. Front Genet. 2017;8:73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shapiro E, Biezuner T, Linnarsson S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet. 2013;14:618–30.
Article
CAS
PubMed
Google Scholar
Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet. 2016;17:175–88.
Article
CAS
PubMed
Google Scholar
Wu AR, Wang J, Streets AM, Huang Y. Single-cell transcriptional analysis. Annu Rev Anal Chem (Palo Alto Calif). 2017;10:439–62.
Article
CAS
Google Scholar
Stubbington MJT, Rozenblatt-Rosen O, Regev A, Teichmann SA. Single-cell transcriptomics to explore the immune system in health and disease. Science. 2017;358:58–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wen L, Tang F. Single cell epigenome sequencing technologies. Mol Aspects Med. 2018;59:62–9.
Article
CAS
PubMed
Google Scholar
Potter SS. Single-cell RNA sequencing for the study of development, physiology and disease. Nat Rev Nephrol. 2018;14:479–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwartzman O, Tanay A. Single-cell epigenomics: techniques and emerging applications. Nat Rev Genet. 2015;16:716–26.
Article
CAS
PubMed
Google Scholar
Svensson V, Natarajan KN, Ly L-H, Miragaia RJ, Labalette C, Macaulay IC, et al. Power analysis of single-cell RNA-sequencing experiments. Nat Methods. 2017;14:381–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kelsey G, Stegle O, Reik W. Single-cell epigenomics: recording the past and predicting the future. Science. 2017;358:69–75.
Article
CAS
PubMed
Google Scholar
Livesey FJ. Strategies for microarray analysis of limiting amounts of RNA. Brief Funct Genomic Proteomic. 2003;2:31–6.
Article
CAS
PubMed
Google Scholar
Navin NE. Cancer genomics: one cell at a time. Genome Biol. 2014;15:452.
Article
PubMed
PubMed Central
Google Scholar
Clark SJ, Lee HJ, Smallwood SA, Kelsey G, Reik W. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol. 2016;17:72.
Article
CAS
PubMed
PubMed Central
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
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;27:967–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Clark SJ, Argelaguet R, Kapourani C-A, Stubbs TM, Lee HJ, Alda-Catalinas C, et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat Commun. 2018;9:781.
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
CAS
PubMed
PubMed Central
Google Scholar
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;14:865–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zheng GXY, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017;8:14049.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science. 2014;343:776–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gole J, Gore A, Richards A, Chiu Y-J, Fung H-L, Bushman D, et al. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotechnol. 2013;31:1126–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161:1202–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rotem A, Ram O, Shoresh N, Sperling RA, Schnall-Levin M, Zhang H, et al. High-throughput single-cell labeling (Hi-SCL) for RNA-seq using drop-based microfluidics. PLoS One. 2015;10:e0116328.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rosenberg AB, Roco CM, Muscat RA, Kuchina A, Sample P, Yao Z, et al. Single-cell profiling of the develo** mouse brain and spinal cord with split-pool barcoding. Science. 2018;360:176–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, et al. High-throughput spatial map** of single-cell RNA-seq data to tissue of origin. Nat Biotechnol. 2015;33:503–9.
Article
CAS
PubMed
Google Scholar
Halpern KB, Shenhav R, Matcovitch-Natan O, Tóth B, Lemze D, Golan M, et al. Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. Nature. 2017;542:352–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Medaglia C, Giladi A, Stoler-Barak L, De Giovanni M, Salame TM, Biram A, et al. Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq. Science. 2017;358:1622–6.
Article
CAS
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 J, Suo S, Tam PP, Han JJ, Peng G, **g N. Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. Nat Protoc. 2017;12:566–80.
Article
CAS
PubMed
Google Scholar
Lin P, Troup M, Ho JWK. CIDR: ultrafast and accurate clustering through imputation for single-cell RNA-seq data. Genome Biol. 2017;18:59.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pierson E, Yau C. ZIFA: dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome Biol. 2015;16:241.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li WV, Li JJ. An accurate and robust imputation method scImpute for single-cell RNA-seq data. Nat Commun. 2018;9:997.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gong W, Kwak IY, Pota P, Koyano-Nakagawa N, Garry DJ. DrImpute: imputing dropout events in single cell RNA sequencing data. BMC Bioinformatics. 2018;19:220.
Article
PubMed
PubMed Central
Google Scholar
Bacher R, Chu L-F, Leng N, Gasch AP, Thomson JA, Stewart RM, et al. SCnorm: robust normalization of single-cell RNA-seq data. Nat Methods. 2017;14:584–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
McCarthy DJ, Campbell KR, Lun ATL, Wills QF. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics. 2017;33:1179–86.
CAS
PubMed
PubMed Central
Google Scholar
Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36:411–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nat Biotechnol. 2018;36:421–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC. Normalizing single-cell RNA sequencing data: challenges and opportunities. Nat Methods. 2017;14:565–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, et al. SC3: consensus clustering of single-cell RNA-seq data. Nat Methods. 2017;14:483–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang B, Zhu J, Pierson E, Ramazzotti D, Batzoglou S. Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. Nat Methods. 2017;14:414–6.
Article
CAS
PubMed
Google Scholar
Žurauskienė J, Yau C. pcaReduce: hierarchical clustering of single cell transcriptional profiles. BMC Bioinformatics. 2016;17:140.
Article
CAS
PubMed
PubMed Central
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
CAS
PubMed
Google Scholar
Tsoucas D, Yuan G-C. GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection. Genome Biol. 2018;19:58.
Article
PubMed
PubMed Central
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
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
PubMed Central
Google Scholar
Jiang H, Sohn LL, Huang H, Chen L. Single cell clustering based on cell-pair differentiability correlation and variance analysis. Bioinformatics. 2018;34:3684–94.
PubMed
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
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
Teschendorff AE, Enver T. Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome. Nat Commun. 2017;8:15599.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ji Z, Ji H. TSCAN: pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis. Nucleic Acids Res. 2016;44:e117.
Article
CAS
PubMed
PubMed Central
Google Scholar
El-ad DA, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, et al. viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat Biotechnol. 2013;31:545–52.
Article
CAS
Google Scholar
Weinreb C, Wolock S, Klein AM. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. Bioinformatics. 2018;34:1246–8.
Article
CAS
PubMed
Google Scholar
Ding J, Condon A, Shah SP. Interpretable dimensionality reduction of single cell transcriptome data with deep generative models. Nat Commun. 2018;9:2002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rostom R, Svensson V, Teichmann SA, Kar G. Computational approaches for interpreting scRNA-seq data. FEBS Lett. 2017;591:2213–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wen L, Tang F. Single-cell sequencing in stem cell biology. Genome Biol. 2016;17:71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Poirion OB, Zhu X, Ching T, Garmire L. Single-cell transcriptomics bioinformatics and computational challenges. Front Genet. 2016;7:163.
Article
PubMed
PubMed Central
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
PubMed Central
Google Scholar
Huang L, Ma F, Chapman A, Lu S, **e XS. Single-cell whole-genome amplification and sequencing: methodology and applications. Annu Rev Genomics Hum Genet. 2015;16:79–102.
Article
CAS
PubMed
Google Scholar
Stegle O, Teichmann SA, Marioni JC. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet. 2015;16:133–45.
Article
CAS
PubMed
Google Scholar
de Vargas RL, Claassen M. Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics. Curr Opin Biotechnol. 2015;34:9–15.
Google Scholar
Grun D, van Oudenaarden A. Design and analysis of single-cell sequencing experiments. Cell. 2015;163:799–810.
Article
CAS
PubMed
Google Scholar
Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang F, et al. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 2015;16:148.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, et al. Scalable microfluidics for single-cell RNA printing and sequencing. Genome Biol. 2015;16:120.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu M, Ting DT, Stott SL, Wittner BS, Ozsolak F, Paul S, et al. RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis. Nature. 2012;487:510–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salehi S, Steif A, Roth A, Aparicio S, Bouchard-Cote A, Shah SP. ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data. Genome Biol. 2017;18:44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12:453–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li B, Severson E, Pignon J-C, Zhao H, Li T, Novak J, et al. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biol. 2016;17:174.
Article
CAS
PubMed
PubMed Central
Google Scholar
Racle J, de Jonge K, Baumgaertner P, Speiser DE, Gfeller D. Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. eLife. 2017;6:e26476.
Article
PubMed
PubMed Central
Google Scholar
Schelker M, Feau S, Du J, Ranu N, Klipp E, MacBeath G, et al. Estimation of immune cell content in tumour tissue using single-cell RNA-seq data. Nat Commun. 2017;8:2032.
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
PubMed Central
Google Scholar
Stahl PL, Salmen F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016;353:78–82.
Article
CAS
PubMed
Google Scholar
Wahlby C. The quest for multiplexed spatially resolved transcriptional profiling. Nat Methods. 2016;13:623–4.
Article
CAS
PubMed
Google Scholar
Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science. 2015;348:aaa6090.
Article
CAS
PubMed
PubMed Central
Google Scholar
Crosetto N, Bienko M, van Oudenaarden A. Spatially resolved transcriptomics and beyond. Nat Rev Genet. 2015;16:57–66.
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
Lovatt D, Ruble BK, Lee J, Dueck H, Kim TK, Fisher S, et al. Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nat Methods. 2014;11:190–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, et al. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc. 2015;10:442–58.
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
Larsson C, Grundberg I, Soderberg O, Nilsson M. In situ detection and genoty** of individual mRNA molecules. Nat Methods. 2010;7:395–7.
Article
CAS
PubMed
Google Scholar
Wen L, Tang F. Reconstructing complex tissues from single-cell analyses. Cell. 2014;157:771–3.
Article
CAS
PubMed
Google Scholar
Liu Z, Lou H, **e K, Wang H, Chen N, Aparicio OM, et al. Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. Nat Commun. 2017;8:22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, et al. Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods. 2015;85:54–61.
Article
CAS
PubMed
Google Scholar
Leng N, Chu L-F, Barry C, Li Y, Choi J, Li X, et al. Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nat Methods. 2015;12:947–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sima C, Hua J, Bittner ML, Kim S, Dougherty ER. Phenotype classification using moment features of single-cell data. Cancer Inform. 2018;17:1176935118771701.
Article
PubMed
PubMed Central
Google Scholar
Rozenblatt-Rosen O, Stubbington MJT, Regev A, Teichmann SA. The human cell atlas: from vision to reality. Nature. 2017;550:451–3.
Article
CAS
PubMed
Google Scholar
Iacono G, Mereu E, Guillaumet-Adkins A, Corominas R, Cusco I, Rodriguez-Esteban G, et al. bigSCale: an analytical framework for big-scale single-cell data. Genome Res. 2018;28:878–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolf FA, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 2018;19:15.
Article
PubMed
PubMed Central
Google Scholar
Sinha D, Kumar A, Kumar H. Bandyopadhyay S. Sengupta D. dropClust: efficient clustering of ultra-large scRNA-seq data. Nucleic Acids Res. 2018;46:e36.
PubMed
Google Scholar
Andor N, Graham TA, Jansen M, **a LC, Aktipis CA, Petritsch C, et al. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat Med. 2016;22:105–13.
Article
CAS
PubMed
Google Scholar
Maman S, Witz IP. A history of exploring cancer in context. Nat Rev Cancer. 2018;18:359–76.
Article
CAS
PubMed
Google Scholar
Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012;366:883–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang J, Fujimoto J, Zhang J, Wedge DC, Song X, Zhang J, et al. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science. 2014;346:256–9.
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
Eirew P, Steif A, Khattra J, Ha G, Yap D, Farahani H, et al. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature. 2015;518:422–6.
Article
CAS
PubMed
Google Scholar
Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, et al. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell. 2012;148:886–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li Y, Xu X, Song L, Hou Y, Li Z, Tsang S, et al. Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. Gigascience. 2012;1:12.
Article
PubMed
PubMed Central
Google Scholar
Yu C, Yu J, Yao X, Wu WKK, Lu Y, Tang S, et al. Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. Cell Res. 2014;24:701–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heitzer E, Auer M, Gasch C, Pichler M, Ulz P, Hoffmann EM, et al. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res. 2013;73:2965–75.
Article
CAS
PubMed
Google Scholar
Francis JM, Zhang C-Z, Maire CL, Jung J, Manzo VE, Adalsteinsson VA, et al. EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. Cancer Discov. 2014;4:956–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jan M, Snyder TM, Corces-Zimmerman MR, Vyas P, Weissman IL, Quake SR, et al. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci Transl Med. 2012;4:149ra118.
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
Ebinger S, Ozdemir EZ, Ziegenhain C, Tiedt S, Castro Alves C, Grunert M, et al. Characterization of rare, dormant, and therapy-resistant cells in acute lymphoblastic leukemia. Cancer Cell. 2016;30:849–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, et al. Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol. 2016;12:889.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aceto N, Bardia A, Miyamoto DT, Donaldson MC, Wittner BS, Spencer JA, et al. Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell. 2014;158:1110–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li Y, Wu S, Bai F. Molecular characterization of circulating tumor cells-from bench to bedside. Semin Cell Dev Biol. 2018;75:88–97.
Article
CAS
PubMed
Google Scholar
Ruiz C, Li J, Luttgen MS, Kolatkar A, Kendall JT, Flores E, et al. Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Phys Biol. 2015;12:016008.
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
Dago AE, Stepansky A, Carlsson A, Luttgen M, Kendall J, Baslan T, et al. Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells. PLoS One. 2014;9:e101777.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, et al. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol. 2014;32:479–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ramskold D, Luo SJ, Wang YC, Li R, Deng QL, Faridani OR, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol. 2012;30:777–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ting DT, Wittner BS, Ligorio M, Jordan NV, Shah AM, Miyamoto DT, et al. Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells. Cell Rep. 2014;8:1905–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luria SE, Delbruck M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics. 1943;28:491–511.
CAS
PubMed
PubMed Central
Google Scholar
Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, et al. Single-cell RNA-seq analysis of infiltrating neoplastic cells at the migrating front of human glioblastoma. Cell Rep. 2017;21:1399–410.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sharma P, Hu-Lieskovan S, Wargo JA, Ribas A. Primary, adaptive, and acquired resistance to cancer immunotherapy. Cell. 2017;168:707–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei SC, Levine JH, Cogdill AP, Zhao Y, Anang N-AAS, Andrews MC, et al. Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade. Cell. 2017;170:1120–33 e1117.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zappasodi R, Budhu S, Hellmann MD, Postow MA, Senbabaoglu Y, Manne S, et al. Non-conventional inhibitory CD4+Foxp3–PD-1hi T Cells as a biomarker of immune checkpoint blockade activity. Cancer Cell. 2018;33:1017–32 e7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stelzer Y, Shivalila CS, Soldner F, Markoulaki S, Jaenisch R. Tracing dynamic changes of DNA methylation at single-cell resolution. Cell. 2015;163:218–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu C, Gao Y, Guo H, **a B, Song J, Wu X, et al. Single-cell 5-formylcytosine landscapes of mammalian early embryos and ESCs at single-base resolution. Cell Stem Cell. 2017;20:720–31 e5.
Article
CAS
PubMed
Google Scholar
Guo H, Zhu P, Guo F, Li X, Wu X, Fan X, et al. Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nat Protoc. 2015;10:645–59.
Article
CAS
PubMed
Google Scholar
Stevens TJ, Lando D, Basu S, Atkinson LP, Cao Y, Lee SF, et al. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature. 2017;544:59–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Flyamer IM, Gassler J, Imakaev M, Brandao HB, Ulianov SV, Abdennur N, et al. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature. 2017;544:110–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, et al. Massively multiplex single-cell Hi-C. Nat Methods. 2017;14:263–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature. 2013;502:59–64.
Article
CAS
PubMed
Google Scholar
Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, et al. Transcript-indexed ATAC-seq for precision immune profiling. Nat Med. 2018;24:580–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015;348:910–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
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;523:486–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015;33:1165–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Leite de Oliveira R, Huijberts S, Bosdriesz E, Pencheva N, Brunen D, et al. An acquired vulnerability of drug-resistant melanoma with therapeutic potential. Cell. 2018;173:1413–25.
Article
CAS
PubMed
Google Scholar
Friedman N, Rando OJ. Epigenomics and the structure of the living genome. Genome Res. 2015;25:1482–90.
Article
CAS
PubMed
PubMed Central
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
Boisset J-C, Vivié J, Grün D, Muraro MJ, Lyubimova A, van Oudenaarden A. Map** the physical network of cellular interactions. Nat Methods. 2018;15:547–53.
Article
CAS
PubMed
Google Scholar
Halpern KB, Shenhav R, Massalha H, Toth B, Egozi A, Massasa EE, et al. Paired-cell sequencing enables spatial gene expression map** of liver endothelial cells. Nat Biotechnol. 2018;36:962–70.
CAS
PubMed
PubMed Central
Google Scholar
Edsgärd D, Johnsson P, Sandberg R. Identification of spatial expression trends in single-cell gene expression data. Nat Methods. 2018;15:339–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Svensson V, Teichmann SA, Stegle O. SpatialDE: identification of spatially variable genes. Nat Methods. 2018;15:343–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Russell MR, D'Amato A, Graham C, Crosbie EJ, Gentry-Maharaj A, Ryan A, et al. Novel risk models for early detection and screening of ovarian cancer. Oncotarget. 2017;8:785–97.
Article
PubMed
Google Scholar
Bowtell DD, Boehm S, Ahmed AA, Aspuria P-J, Bast RC Jr, Beral V, et al. Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer. Nat Rev Cancer. 2015;15:668–79.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baudino TA. Targeted cancer therapy: the next generation of cancer treatment. Curr Drug Discov Technol. 2015;12:3–20.
Article
CAS
PubMed
Google Scholar
Scher HI, Lu D, Schreiber NA, Louw J, Graf RP, Vargas HA, et al. Association of AR-V7 on circulating tumor cells as a treatment-specific biomarker with outcomes and survival in castration-resistant prostate cancer. JAMA Oncol. 2016;2:1441–9.
Article
PubMed
PubMed Central
Google Scholar
Burrell RA, McGranahan N, Bartek J, Swanton C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature. 2013;501:338–45.
Article
CAS
PubMed
Google Scholar
Murugaesu N, Chew SK, Swanton C. Adapting clinical paradigms to the challenges of cancer clonal evolution. Am J Pathol. 2013;182:1962–71.
Article
PubMed
Google Scholar
Almendro V, Cheng Y-K, Randles A, Itzkovitz S, Marusyk A, Ametller E, et al. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Rep. 2014;6:514–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sadanandam A, Lyssiotis CA, Homicsko K, Collisson EA, Gibb WJ, Wullschleger S, et al. A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med. 2013;19:619–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baslan T, Kendall J, Ward B, Cox H, Leotta A, Rodgers L, et al. Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Res. 2015;25:714–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dean FB, Hosono S, Fang LH, Wu XH, Faruqi AF, Bray-Ward P, et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A. 2002;99:5261–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leung K, Klaus A, Lin BK, Laks E, Biele J, Lai D, et al. Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates. Proc Natl Acad Sci U S A. 2016;113:8484–9.
Article
CAS
PubMed
PubMed Central
Google Scholar