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Volumn 4, Issue , 2017, Pages 85-91

Single cells make big data: New challenges and opportunities in transcriptomics

Author keywords

Big data; Machine learning; Single cell RNA seq; Single cell transcriptomics

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

EID: 85041430720     PISSN: None     EISSN: 24523100     Source Type: Journal    
DOI: 10.1016/j.coisb.2017.07.004     Document Type: Review
Times cited : (165)

References (62)
  • 3
    • 84883788980 scopus 로고    scopus 로고
    • "Big data", Hadoop and cloud computing in genomics
    • O'Driscoll A., Daugelaite J., Sleator R.D. "Big data", Hadoop and cloud computing in genomics. J Biomed Inf 2013, 46:774-781.
    • (2013) J Biomed Inf , vol.46 , pp. 774-781
    • O'Driscoll, A.1    Daugelaite, J.2    Sleator, R.D.3
  • 4
    • 84971238065 scopus 로고    scopus 로고
    • Single-cell genomics: coming of age
    • Linnarsson S., Teichmann S.A. Single-cell genomics: coming of age. Genome Biol 2016, 17:97.
    • (2016) Genome Biol , vol.17 , pp. 97
    • Linnarsson, S.1    Teichmann, S.A.2
  • 10
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • Shapiro E., Biezuner T., Linnarsson S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 2013, 14:618-630.
    • (2013) Nat Rev Genet , vol.14 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3
  • 11
    • 40649084023 scopus 로고    scopus 로고
    • Method for single-cell microarray analysis and application to gene-expression profiling of GABAergic neuron progenitors
    • Esumi S., Wu S.-X., Yanagawa Y., Obata K., Sugimoto Y., Tamamaki N. Method for single-cell microarray analysis and application to gene-expression profiling of GABAergic neuron progenitors. Neurosci Res 2008, 60:439-451.
    • (2008) Neurosci Res , vol.60 , pp. 439-451
    • Esumi, S.1    Wu, S.-X.2    Yanagawa, Y.3    Obata, K.4    Sugimoto, Y.5    Tamamaki, N.6
  • 17
    • 84861115379 scopus 로고    scopus 로고
    • Comprehensive qPCR profiling of gene expression in single neuronal cells
    • Citri A., Pang Z.P., Südhof T.C., Wernig M., Malenka R.C. Comprehensive qPCR profiling of gene expression in single neuronal cells. Nat Protoc 2011, 7:118-127.
    • (2011) Nat Protoc , vol.7 , pp. 118-127
    • Citri, A.1    Pang, Z.P.2    Südhof, T.C.3    Wernig, M.4    Malenka, R.C.5
  • 18
    • 0034671678 scopus 로고    scopus 로고
    • Quantitative analysis of globin gene induction in single human erythroleukemic cells
    • Smith R.D., Malley J.D., Schechter A.N. Quantitative analysis of globin gene induction in single human erythroleukemic cells. Nucleic Acids Res 2000, 28:4998-5004.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4998-5004
    • Smith, R.D.1    Malley, J.D.2    Schechter, A.N.3
  • 23
    • 33644850222 scopus 로고    scopus 로고
    • Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling
    • Nygaard V., Hovig E. Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling. Nucleic Acids Res 2006, 34:996-1014.
    • (2006) Nucleic Acids Res , vol.34 , pp. 996-1014
    • Nygaard, V.1    Hovig, E.2
  • 24
    • 78549251736 scopus 로고    scopus 로고
    • Analysing biological pathways in genome-wide association studies
    • Wang K., Li M., Hakonarson H. Analysing biological pathways in genome-wide association studies. Nat Rev Genet 2010, 11:843-854.
    • (2010) Nat Rev Genet , vol.11 , pp. 843-854
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 26
    • 84923647450 scopus 로고    scopus 로고
    • Computational and analytical challenges in single-cell transcriptomics
    • Stegle O., Teichmann S.A., Marioni J.C. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet 2015, 16:133-145.
    • (2015) Nat Rev Genet , vol.16 , pp. 133-145
    • Stegle, O.1    Teichmann, S.A.2    Marioni, J.C.3
  • 29
    • 84963632004 scopus 로고    scopus 로고
    • Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity
    • Clark S.J., Lee H.J., Smallwood S.A., Kelsey G., Reik W. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol 2016, 17:72.
    • (2016) Genome Biol , vol.17 , pp. 72
    • Clark, S.J.1    Lee, H.J.2    Smallwood, S.A.3    Kelsey, G.4    Reik, W.5
  • 30
    • 84947617259 scopus 로고    scopus 로고
    • Single-cell epigenomics: techniques and emerging applications
    • Schwartzman O., Tanay A. Single-cell epigenomics: techniques and emerging applications. Nat Rev Genet 2015, 16:716-726.
    • (2015) Nat Rev Genet , vol.16 , pp. 716-726
    • Schwartzman, O.1    Tanay, A.2
  • 31
    • 84929661801 scopus 로고    scopus 로고
    • Advances and applications of single-cell sequencing technologies
    • Wang Y., Navin N.E. Advances and applications of single-cell sequencing technologies. Mol Cell 2015, 58:598-609.
    • (2015) Mol Cell , vol.58 , pp. 598-609
    • Wang, Y.1    Navin, N.E.2
  • 32
    • 84958606331 scopus 로고    scopus 로고
    • Single-cell genome sequencing: current state of the science
    • Gawad C., Koh W., Quake S.R. Single-cell genome sequencing: current state of the science. Nat Rev Genet 2016, 17:175-188.
    • (2016) Nat Rev Genet , vol.17 , pp. 175-188
    • Gawad, C.1    Koh, W.2    Quake, S.R.3
  • 34
    • 3543069879 scopus 로고    scopus 로고
    • Seventeen-colour flow cytometry: unravelling the immune system
    • Perfetto S.P., Chattopadhyay P.K., Roederer M. Seventeen-colour flow cytometry: unravelling the immune system. Nat Rev Immunol 2004, 4:648-655.
    • (2004) Nat Rev Immunol , vol.4 , pp. 648-655
    • Perfetto, S.P.1    Chattopadhyay, P.K.2    Roederer, M.3
  • 35
    • 68849103521 scopus 로고    scopus 로고
    • Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry
    • Bandura D.R., Baranov V.I., Ornatsky O.I., Antonov A., Kinach R., Lou X., Pavlov S., Vorobiev S., Dick J.E., Tanner S.D. Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem 2009, 81:6813-6822.
    • (2009) Anal Chem , vol.81 , pp. 6813-6822
    • Bandura, D.R.1    Baranov, V.I.2    Ornatsky, O.I.3    Antonov, A.4    Kinach, R.5    Lou, X.6    Pavlov, S.7    Vorobiev, S.8    Dick, J.E.9    Tanner, S.D.10
  • 36
    • 33745072443 scopus 로고    scopus 로고
    • A microengraving method for rapid selection of single cells producing antigen-specific antibodies
    • Love J.C., Ronan J.L., Grotenbreg G.M., van der Veen A.G., Ploegh H.L. A microengraving method for rapid selection of single cells producing antigen-specific antibodies. Nat Biotechnol 2006, 24:703-707.
    • (2006) Nat Biotechnol , vol.24 , pp. 703-707
    • Love, J.C.1    Ronan, J.L.2    Grotenbreg, G.M.3    van der Veen, A.G.4    Ploegh, H.L.5
  • 38
    • 84877585171 scopus 로고    scopus 로고
    • Whole-brain functional imaging at cellular resolution using light-sheet microscopy
    • Ahrens M.B., Orger M.B., Robson D.N., Li J.M., Keller P.J. Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat Methods 2013, 10:413-420.
    • (2013) Nat Methods , vol.10 , pp. 413-420
    • Ahrens, M.B.1    Orger, M.B.2    Robson, D.N.3    Li, J.M.4    Keller, P.J.5
  • 41
    • 47349112642 scopus 로고    scopus 로고
    • Quantitative image based apoptotic index measurement using multispectral imaging flow cytometry: a comparison with standard photometric methods
    • Henery S., George T., Hall B., Basiji D., Ortyn W., Morrissey P. Quantitative image based apoptotic index measurement using multispectral imaging flow cytometry: a comparison with standard photometric methods. Apoptosis 2008, 13:1054-1063.
    • (2008) Apoptosis , vol.13 , pp. 1054-1063
    • Henery, S.1    George, T.2    Hall, B.3    Basiji, D.4    Ortyn, W.5    Morrissey, P.6
  • 42
    • 79953280811 scopus 로고    scopus 로고
    • Long-term single-cell imaging of mammalian stem cells
    • Schroeder T. Long-term single-cell imaging of mammalian stem cells. Nat Methods 2011, 8:S30-S35.
    • (2011) Nat Methods , vol.8 , pp. S30-S35
    • Schroeder, T.1
  • 43
    • 84960091878 scopus 로고    scopus 로고
    • Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas
    • Hou Y., Guo H., Cao C., Li X., Hu B., Zhu P., Wu X., Wen L., Tang F., Huang Y., Peng J. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res 2016, 26:304-319.
    • (2016) Cell Res , vol.26 , pp. 304-319
    • Hou, Y.1    Guo, H.2    Cao, C.3    Li, X.4    Hu, B.5    Zhu, P.6    Wu, X.7    Wen, L.8    Tang, F.9    Huang, Y.10    Peng, J.11
  • 44
    • 85009781625 scopus 로고    scopus 로고
    • Single-cell multiomics: multiple measurements from single cells
    • Macaulay I.C., Ponting C.P., Voet T. Single-cell multiomics: multiple measurements from single cells. Trends Genet 2017, 33:155-168.
    • (2017) Trends Genet , vol.33 , pp. 155-168
    • Macaulay, I.C.1    Ponting, C.P.2    Voet, T.3
  • 48
    • 84959921188 scopus 로고    scopus 로고
    • Single-cell transcriptome study as big data
    • Yu P., Lin W. Single-cell transcriptome study as big data. Genomics Proteomics Bioinforma 2016, 14:21-30.
    • (2016) Genomics Proteomics Bioinforma , vol.14 , pp. 21-30
    • Yu, P.1    Lin, W.2
  • 50
    • 84966711505 scopus 로고    scopus 로고
    • Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots
    • Marr C., Zhou J.X., Huang S. Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots. Curr Opin Biotechnol 2016, 39:207-214.
    • (2016) Curr Opin Biotechnol , vol.39 , pp. 207-214
    • Marr, C.1    Zhou, J.X.2    Huang, S.3
  • 51
    • 84866463531 scopus 로고    scopus 로고
    • A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
    • Buettner F., Theis F.J. A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Bioinformatics 2012, 28:i626-i632.
    • (2012) Bioinformatics , vol.28 , pp. 626
    • Buettner, F.1    Theis, F.J.2
  • 55
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014, 15:550.
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 56
    • 84937114276 scopus 로고    scopus 로고
    • Implications of big data for cell biology
    • Dolinski K., Troyanskaya O.G. Implications of big data for cell biology. Mol Biol Cell 2015, 26:2575-2578.
    • (2015) Mol Biol Cell , vol.26 , pp. 2575-2578
    • Dolinski, K.1    Troyanskaya, O.G.2
  • 57
    • 84878979335 scopus 로고    scopus 로고
    • Biology: the big challenges of big data
    • Marx V. Biology: the big challenges of big data. Nature 2013, 498:255-260.
    • (2013) Nature , vol.498 , pp. 255-260
    • Marx, V.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.