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Volumn 17, Issue 1, 2016, Pages

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

Author keywords

Cellular heterogeneity; Differential expression; Mixture modeling; Single cell RNA seq

Indexed keywords

GENE EXPRESSION; STATISTICAL MODEL; ALGORITHM; BIOLOGY; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; SEQUENCE ANALYSIS; SINGLE CELL ANALYSIS; SOFTWARE; STATISTICS AND NUMERICAL DATA;

EID: 84992327075     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-1077-y     Document Type: Article
Times cited : (178)

References (69)
  • 1
    • 84923292191 scopus 로고    scopus 로고
    • Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
    • 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; 32(2):155-60.
    • (2015) Nat Biotechnol , vol.32 , Issue.2 , pp. 155-160
    • Buettner, F.1    Natarajan, K.N.2    Casale, F.P.3    Proserpio, V.4    Scialdone, A.5    Theis, F.J.6
  • 3
    • 77956412152 scopus 로고    scopus 로고
    • Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-seq analysis
    • Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X, et al. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-seq analysis. Cell Stem Cell. 2010; 6(5):468-78.
    • (2010) Cell Stem Cell , vol.6 , Issue.5 , pp. 468-478
    • Tang, F.1    Barbacioru, C.2    Bao, S.3    Lee, C.4    Nordman, E.5    Wang, X.6
  • 4
    • 84883743509 scopus 로고    scopus 로고
    • Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells
    • Yan L, Yang M, Guo H, Yang L, Wu J, Li R, et al. Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol. 2013; 20(9):1131-9.
    • (2013) Nat Struct Mol Biol , vol.20 , Issue.9 , pp. 1131-1139
    • Yan, L.1    Yang, M.2    Guo, H.3    Yang, L.4    Wu, J.5    Li, R.6
  • 5
    • 84883134780 scopus 로고    scopus 로고
    • Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
    • Xue Z, Huang K, Cai C, Cai L, Jiang C-y, Feng Y, et al. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature. 2013; 500(7464):593-7.
    • (2013) Nature , vol.500 , Issue.7464 , pp. 593-597
    • Xue, Z.1    Huang, K.2    Cai, C.3    Cai, L.4    Jiang, C.-Y.5    Feng, Y.6
  • 6
    • 84902668801 scopus 로고    scopus 로고
    • Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
    • 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(6190):1396-401.
    • (2014) Science , vol.344 , Issue.6190 , pp. 1396-1401
    • Patel, A.P.1    Tirosh, I.2    Trombetta, J.J.3    Shalek, A.K.4    Gillespie, S.M.5    Wakimoto, H.6
  • 7
    • 84878997106 scopus 로고    scopus 로고
    • Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
    • Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature. 2013; 498(7453):236-40.
    • (2013) Nature , vol.498 , Issue.7453 , pp. 236-240
    • Shalek, A.K.1    Satija, R.2    Adiconis, X.3    Gertner, R.S.4    Gaublomme, J.T.5    Raychowdhury, R.6
  • 8
    • 84900529199 scopus 로고    scopus 로고
    • Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
    • 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(7500):371-5.
    • (2014) Nature , vol.509 , Issue.7500 , pp. 371-375
    • Treutlein, B.1    Brownfield, D.G.2    Wu, A.R.3    Neff, N.F.4    Mantalas, G.L.5    Espinoza, F.H.6
  • 9
    • 84877249559 scopus 로고    scopus 로고
    • Canonical correlation analysis for RNA-seq co-expression networks
    • Hong S, Chen X, Jin L, Xiong M. Canonical correlation analysis for RNA-seq co-expression networks. Nucleic Acids Res. 2013; 41(8):95-5.
    • (2013) Nucleic Acids Res , vol.41 , Issue.8 , pp. 95-95
    • Hong, S.1    Chen, X.2    Jin, L.3    Xiong, M.4
  • 10
    • 84864880991 scopus 로고    scopus 로고
    • Full-length mRNA-seq from single-cell levels of RNA and individual circulating tumor cells
    • Ramsköld D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, et al. Full-length mRNA-seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol. 2012; 30(8):777-82.
    • (2012) Nat Biotechnol , vol.30 , Issue.8 , pp. 777-782
    • Ramsköld, D.1    Luo, S.2    Wang, Y.C.3    Li, R.4    Deng, Q.5    Faridani, O.R.6
  • 11
    • 84937573360 scopus 로고    scopus 로고
    • Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
    • 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(1):127.
    • (2015) Genome Biol , vol.16 , Issue.1 , pp. 127
    • Kim, K.T.1    Lee, H.W.2    Lee, H.O.3    Kim, S.C.4    Seo, Y.J.5    Chung, W.6
  • 12
    • 84914706587 scopus 로고    scopus 로고
    • Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing
    • Lee M-CW, 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. 2014; 111(44):4726-35.
    • (2014) Proc Natl Acad Sci , vol.111 , Issue.44 , pp. 4726-4735
    • Lee, M.-C.1    Lopez-Diaz, F.J.2    Khan, S.Y.3    Tariq, M.A.4    Dayn, Y.5    Vaske, C.J.6
  • 13
    • 84860601923 scopus 로고    scopus 로고
    • Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines
    • 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(5):33788.
    • (2012) PloS ONE , vol.7 , Issue.5 , pp. 33788
    • Powell, A.A.1    Talasaz, A.H.2    Zhang, H.3    Coram, M.A.4    Reddy, A.5    Deng, G.6
  • 14
    • 84866953427 scopus 로고    scopus 로고
    • CEL-seq: single-cell RNA-seq by multiplexed linear amplification
    • Hashimshony T, Wagner F, Sher N, Yanai I. CEL-seq: single-cell RNA-seq by multiplexed linear amplification. Cell Rep. 2012; 2(3):666-73.
    • (2012) Cell Rep , vol.2 , Issue.3 , pp. 666-673
    • Hashimshony, T.1    Wagner, F.2    Sher, N.3    Yanai, I.4
  • 15
    • 84904624915 scopus 로고    scopus 로고
    • Single cell dissection of early kidney development: multilineage priming
    • Brunskill EW, Park JS, Chung E, Chen F, Magella B, Potter SS. Single cell dissection of early kidney development: multilineage priming. Development. 2014; 141(15):3093-101.
    • (2014) Development , vol.141 , Issue.15 , pp. 3093-3101
    • Brunskill, E.W.1    Park, J.S.2    Chung, E.3    Chen, F.4    Magella, B.5    Potter, S.S.6
  • 16
    • 84895562012 scopus 로고    scopus 로고
    • From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing
    • 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(3):496-510.
    • (2014) Genome Res , vol.24 , Issue.3 , pp. 496-510
    • Marinov, G.K.1    Williams, B.A.2    McCue, K.3    Schroth, G.P.4    Gertz, J.5    Myers, R.M.6
  • 17
    • 84903574951 scopus 로고    scopus 로고
    • Bayesian approach to single-cell differential expression analysis
    • Kharchenko PV, Silberstein L, Scadden DT. Bayesian approach to single-cell differential expression analysis. Nat Methods. 2014; 11(7):740-2.
    • (2014) Nat Methods , vol.11 , Issue.7 , pp. 740-742
    • Kharchenko, P.V.1    Silberstein, L.2    Scadden, D.T.3
  • 18
    • 84951574149 scopus 로고    scopus 로고
    • Mast: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
    • 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(1):1-13.
    • (2015) Genome Biol , vol.16 , Issue.1 , pp. 1-13
    • Finak, G.1    McDavid, A.2    Yajima, M.3    Deng, J.4    Gersuk, V.5    Shalek, A.K.6
  • 19
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: from theories to phenotypes
    • Kærn M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet. 2005; 6(6):451-64.
    • (2005) Nat Rev Genet , vol.6 , Issue.6 , pp. 451-464
    • Kærn, M.1    Elston, T.C.2    Blake, W.J.3    Collins, J.J.4
  • 20
    • 84865298239 scopus 로고    scopus 로고
    • Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise
    • Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzyński M, Hoek JB, et al. Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. BMC Syst Biol. 2012; 6(1):109.
    • (2012) BMC Syst Biol , vol.6 , Issue.1 , pp. 109
    • Birtwistle, M.R.1    Rauch, J.2    Kiyatkin, A.3    Aksamitiene, E.4    Dobrzyński, M.5    Hoek, J.B.6
  • 23
    • 84905055041 scopus 로고    scopus 로고
    • Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses
    • Dobrzyński M, Nguyen LK, Birtwistle MR, von Kriegsheim A, Fernández AB, Cheong A, et al. Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses. J R Soc Interface. 2014; 11(98):20140383.
    • (2014) J R Soc Interface , vol.11 , Issue.98 , pp. 20140383
    • Dobrzyński, M.1    Nguyen, L.K.2    Birtwistle, M.R.3    von Kriegsheim, A.4    Fernández, A.B.5    Cheong, A.6
  • 26
    • 0035902599 scopus 로고    scopus 로고
    • Intrinsic noise in gene regulatory networks
    • Thattai M, Van Oudenaarden A. Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci. 2001; 98(15):8614-19.
    • (2001) Proc Natl Acad Sci , vol.98 , Issue.15 , pp. 8614-8619
    • Thattai, M.1    Van Oudenaarden, A.2
  • 27
    • 84992435422 scopus 로고    scopus 로고
    • Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data
    • bioRxiv
    • Delmans M, Hemberg M. Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data. bioRxiv. 2015. doi: 10.1101/020735.
    • (2015)
    • Delmans, M.1    Hemberg, M.2
  • 28
    • 84890060756 scopus 로고    scopus 로고
    • SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization
    • Katayama S, Töhönen V, Linnarsson S, Kere J. SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization. Bioinformatics. 2013; 29(22):2943-5.
    • (2013) Bioinformatics , vol.29 , Issue.22 , pp. 2943-2945
    • Katayama, S.1    Töhönen, V.2    Linnarsson, S.3    Kere, J.4
  • 29
    • 77954541844 scopus 로고    scopus 로고
    • Single-cell NF- Κ B dynamics reveal digital activation and analogue information processing
    • Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Single-cell NF- Κ B dynamics reveal digital activation and analogue information processing. Nature. 2010; 466(7303):267-71.
    • (2010) Nature , vol.466 , Issue.7303 , pp. 267-271
    • Tay, S.1    Hughey, J.J.2    Lee, T.K.3    Lipniacki, T.4    Quake, S.R.5    Covert, M.W.6
  • 30
    • 84982085158 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm
    • Chu Li-Fang, et al.Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Genome Biol. 2016; 17(1):173.
    • (2016) Genome Biol. , vol.17 , Issue.1 , pp. 173
    • Chu, L.-F.1
  • 31
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • 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(4):381-6.
    • (2014) Nat Biotechnol , vol.32 , Issue.4 , pp. 381-386
    • Trapnell, C.1    Cacchiarelli, D.2    Grimsby, J.3    Pokharel, P.4    Li, S.5    Morse, M.6
  • 32
    • 84923188586 scopus 로고    scopus 로고
    • Deconstructing transcriptional heterogeneity in pluripotent stem cells
    • Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, et al. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 2014; 516(7529):56-61.
    • (2014) Nature , vol.516 , Issue.7529 , pp. 56-61
    • Kumar, R.M.1    Cahan, P.2    Shalek, A.K.3    Satija, R.4    DaleyKeyser, A.J.5    Li, H.6
  • 33
    • 84883644707 scopus 로고    scopus 로고
    • Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
    • Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, et al. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol. 2013; 14(9):95.
    • (2013) Genome Biol , vol.14 , Issue.9 , pp. 95
    • Rapaport, F.1    Khanin, R.2    Liang, Y.3    Pirun, M.4    Krek, A.5    Zumbo, P.6
  • 34
    • 84896735766 scopus 로고    scopus 로고
    • Voom: precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014; 15(2):29.
    • (2014) Genome Biol , vol.15 , Issue.2 , pp. 29
    • Law, C.W.1    Chen, Y.2    Shi, W.3    Smyth, G.K.4
  • 35
    • 84992397587 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 1995; 57(1):289-300.
    • (1995) J R Stat Soc Ser B Methodol , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 36
    • 38149042002 scopus 로고    scopus 로고
    • Permutation-based adjustments for the significance of partial regression coefficients in microarray data analysis
    • Wagner BD, Zerbe GO, Mexal S, Leonard SS. Permutation-based adjustments for the significance of partial regression coefficients in microarray data analysis. Genet Epidemiol. 2008; 32(1):1-8.
    • (2008) Genet Epidemiol , vol.32 , Issue.1 , pp. 1-8
    • Wagner, B.D.1    Zerbe, G.O.2    Mexal, S.3    Leonard, S.S.4
  • 37
    • 19944429407 scopus 로고    scopus 로고
    • Monitoring early differentiation events in human embryonic stem cells by massively parallel signature sequencing and expressed sequence tag scan
    • Miura T, Luo Y, Khrebtukova I, Brandenberger R, Zhou D, Scott Thies R, et al. Monitoring early differentiation events in human embryonic stem cells by massively parallel signature sequencing and expressed sequence tag scan. Stem Cells Dev. 2004; 13(6):694-715.
    • (2004) Stem Cells Dev , vol.13 , Issue.6 , pp. 694-715
    • Miura, T.1    Luo, Y.2    Khrebtukova, I.3    Brandenberger, R.4    Zhou, D.5    Scott Thies, R.6
  • 38
    • 33744758028 scopus 로고    scopus 로고
    • The role of pi3k/akt, mapk/erk and nf Κβ signalling in the maintenance of human embryonic stem cell pluripotency and viability highlighted by transcriptional profiling and functional analysis
    • Armstrong L, Hughes O, Yung S, Hyslop L, Stewart R, Wappler I, et al. The role of pi3k/akt, mapk/erk and nf Κ β signalling in the maintenance of human embryonic stem cell pluripotency and viability highlighted by transcriptional profiling and functional analysis. Hum Mol Genet. 2006; 15(11):1894-913.
    • (2006) Hum Mol Genet , vol.15 , Issue.11 , pp. 1894-1913
    • Armstrong, L.1    Hughes, O.2    Yung, S.3    Hyslop, L.4    Stewart, R.5    Wappler, I.6
  • 39
    • 84905662103 scopus 로고    scopus 로고
    • Developmental transcriptome analysis of humwan erythropoiesis
    • Shi L, Lin YH, Sierant M, Zhu F, Cui S, Guan Y, et al. Developmental transcriptome analysis of humwan erythropoiesis. Hum Mol Genet. 2014; 23(17):4528-42.
    • (2014) Hum Mol Genet , vol.23 , Issue.17 , pp. 4528-4542
    • Shi, L.1    Lin, Y.H.2    Sierant, M.3    Zhu, F.4    Cui, S.5    Guan, Y.6
  • 41
    • 0033710224 scopus 로고    scopus 로고
    • Cell-cycle checkpoint kinases: checking in on the cell cycle
    • Walworth NC. Cell-cycle checkpoint kinases: checking in on the cell cycle. Curr Opin Cell Biol. 2000; 12(6):697-704.
    • (2000) Curr Opin Cell Biol , vol.12 , Issue.6 , pp. 697-704
    • Walworth, N.C.1
  • 42
    • 27544470656 scopus 로고    scopus 로고
    • Mammalian cyclin-dependent kinases
    • Malumbres M, Barbacid M. Mammalian cyclin-dependent kinases. Trends Biochem Sci. 2005; 30(11):630-41.
    • (2005) Trends Biochem Sci , vol.30 , Issue.11 , pp. 630-641
    • Malumbres, M.1    Barbacid, M.2
  • 43
    • 30444461346 scopus 로고    scopus 로고
    • Cell cycle control of embryonic stem cells
    • White J, Dalton S. Cell cycle control of embryonic stem cells. Stem Cell Rev. 2005; 1(2):131-8.
    • (2005) Stem Cell Rev , vol.1 , Issue.2 , pp. 131-138
    • White, J.1    Dalton, S.2
  • 44
    • 80052223272 scopus 로고    scopus 로고
    • An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming
    • Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O'Hanlon D, Sung HK, et al. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell. 2011; 147(1):132-46.
    • (2011) Cell , vol.147 , Issue.1 , pp. 132-146
    • Gabut, M.1    Samavarchi-Tehrani, P.2    Wang, X.3    Slobodeniuc, V.4    O'Hanlon, D.5    Sung, H.K.6
  • 45
    • 84862840388 scopus 로고    scopus 로고
    • A putative role for the immunoproteasome in the maintenance of pluripotency in human embryonic stem cells
    • Atkinson SP, Collin J, Irina N, Anyfantis G, Kyung BK, Lako M, et al. A putative role for the immunoproteasome in the maintenance of pluripotency in human embryonic stem cells. Stem Cells. 2012; 30(7):1373-84.
    • (2012) Stem Cells , vol.30 , Issue.7 , pp. 1373-1384
    • Atkinson, S.P.1    Collin, J.2    Irina, N.3    Anyfantis, G.4    Kyung, B.K.5    Lako, M.6
  • 46
    • 84954396263 scopus 로고    scopus 로고
    • Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data
    • Kim JK, Marioni JC. Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data. Genome Biol. 2013; 14(1):7.
    • (2013) Genome Biol , vol.14 , Issue.1 , pp. 7
    • Kim, J.K.1    Marioni, J.C.2
  • 47
    • 84963641621 scopus 로고    scopus 로고
    • R: a language and environment for statistical computing
    • Vienna: R Foundation for Statistical Computing R Foundation for Statistical Computing
    • R Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2014. http://www.R-project.org. R Foundation for Statistical Computing.
    • (2014)
  • 48
    • 84959122613 scopus 로고    scopus 로고
    • Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments
    • Leng N, Chu LF, 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(10):947-50.
    • (2015) Nat Methods , vol.12 , Issue.10 , pp. 947-950
    • Leng, N.1    Chu, L.F.2    Barry, C.3    Li, Y.4    Choi, J.5    Li, X.6
  • 50
    • 84878282421 scopus 로고    scopus 로고
    • Epigenomic analysis of multilineage differentiation of human embryonic stem cells
    • Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 2013; 153(5):1134-48.
    • (2013) Cell , vol.153 , Issue.5 , pp. 1134-1148
    • Xie, W.1    Schultz, M.D.2    Lister, R.3    Hou, Z.4    Rajagopal, N.5    Ray, P.6
  • 51
    • 84943372486 scopus 로고    scopus 로고
    • Human pluripotent stem cell-derived neural constructs for predicting neural toxicity
    • Schwartz MP, Hou Z, Propson NE, Zhang J, Engstrom CJ, Costa VS, et al. Human pluripotent stem cell-derived neural constructs for predicting neural toxicity. Proc Natl Acad Sci. 2015; 112(40):12516-21.
    • (2015) Proc Natl Acad Sci , vol.112 , Issue.40 , pp. 12516-12521
    • Schwartz, M.P.1    Hou, Z.2    Propson, N.E.3    Zhang, J.4    Engstrom, C.J.5    Costa, V.S.6
  • 52
    • 79961123152 scopus 로고    scopus 로고
    • Rsem: accurate transcript quantification from RNA-seq data with or without a reference genome
    • Li B, Dewey CN. Rsem: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinform. 2011; 12(1):323.
    • (2011) BMC Bioinform , vol.12 , Issue.1 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 53
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010; 11(10):106.
    • (2010) Genome Biol , vol.11 , Issue.10 , pp. 106
    • Anders, S.1    Huber, W.2
  • 54
    • 84876263777 scopus 로고    scopus 로고
    • Ebseq: an empirical Bayes hierarchical model for inference in RNA-seq experiments
    • Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, et al. Ebseq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 2013; 29(8):1035-43.
    • (2013) Bioinformatics , vol.29 , Issue.8 , pp. 1035-1043
    • Leng, N.1    Dawson, J.A.2    Thomson, J.A.3    Ruotti, V.4    Rissman, A.I.5    Smits, B.M.6
  • 55
    • 0036081355 scopus 로고    scopus 로고
    • Gene expression omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002; 30(1):207-10.
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 56
  • 57
    • 84868309107 scopus 로고    scopus 로고
    • The transcriptional landscape and mutational profile of lung adenocarcinoma
    • Seo JS, Ju YS, Lee WC, Shin JY, Lee JK, Bleazard T, et al. The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res. 2012; 22:2109-19.
    • (2012) Genome Res , vol.22 , pp. 2109-2119
    • Seo, J.S.1    Ju, Y.S.2    Lee, W.C.3    Shin, J.Y.4    Lee, J.K.5    Bleazard, T.6
  • 59
    • 84860856946 scopus 로고    scopus 로고
    • Bayesian outlier detection with dirichlet process mixtures
    • Shotwell MS, Slate EH. Bayesian outlier detection with dirichlet process mixtures. Bayesian Anal. 2011; 6(4):665-90.
    • (2011) Bayesian Anal , vol.6 , Issue.4 , pp. 665-690
    • Shotwell, M.S.1    Slate, E.H.2
  • 60
    • 84972808999 scopus 로고
    • Estimating normal means with a conjugate style Dirichlet process prior
    • MacEachern SN. Estimating normal means with a conjugate style Dirichlet process prior. Commun Stat Simul Comput. 1994; 23(3):727-41.
    • (1994) Commun Stat Simul Comput , vol.23 , Issue.3 , pp. 727-741
    • MacEachern, S.N.1
  • 61
    • 0000904732 scopus 로고    scopus 로고
    • A semiparametric Bayesian model for randomised block designs
    • Bush CA, MacEachern SN. A semiparametric Bayesian model for randomised block designs. Biometrika. 1996; 83(2):275-85.
    • (1996) Biometrika , vol.83 , Issue.2 , pp. 275-285
    • Bush, C.A.1    MacEachern, S.N.2
  • 62
    • 0032221058 scopus 로고    scopus 로고
    • Estimating mixture of Dirichlet process models
    • MacEachern SN, Müller P. Estimating mixture of Dirichlet process models. J Comput Graph Stat. 1998; 7(2):223-38.
    • (1998) J Comput Graph Stat , vol.7 , Issue.2 , pp. 223-238
    • MacEachern, S.N.1    Müller, P.2
  • 63
    • 84944178665 scopus 로고
    • Hierarchical grouping to optimize an objective function
    • Ward Jr JH. Hierarchical grouping to optimize an objective function. J Am Stat Assoc. 1963; 58(301):236-44.
    • (1963) J Am Stat Assoc , vol.58 , Issue.301 , pp. 236-244
    • Ward, J.H.1
  • 64
    • 79952782467 scopus 로고    scopus 로고
    • Fast Bayesian inference in Dirichlet process mixture models
    • Wang L, Dunson DB. Fast Bayesian inference in Dirichlet process mixture models. J Comput Graph Stat. 2011; 20(1):196-216.
    • (2011) J Comput Graph Stat , vol.20 , Issue.1 , pp. 196-216
    • Wang, L.1    Dunson, D.B.2
  • 65
    • 84878534275 scopus 로고    scopus 로고
    • profdpm: An R package for MAP estimation in a class of conjugate product partition models
    • Shotwell MS. profdpm: An R package for MAP estimation in a class of conjugate product partition models. J Stat Softw. 2013; 53(8):1-18.
    • (2013) J Stat Softw , vol.53 , Issue.8 , pp. 1-18
    • Shotwell, M.S.1
  • 66
    • 84869235386 scopus 로고    scopus 로고
    • MCLUST version 4 for r: Normal mixture modeling for model-based clustering, classification, and density estimation
    • University of Washington, Department of Statistics. Technical report 597
    • Fraley C, Raftery AE, Murphy TB, Scrucca L. MCLUST version 4 for r: Normal mixture modeling for model-based clustering, classification, and density estimation. University of Washington, Department of Statistics. 2012. Technical report 597.
    • (2012)
    • Fraley, C.1    Raftery, A.E.2    Murphy, T.B.3    Scrucca, L.4
  • 67
    • 55249111031 scopus 로고    scopus 로고
    • Model misspecification finite mixture or homogeneous?
    • Tarpey T, Yun D, Petkova E. Model misspecification finite mixture or homogeneous?Stat Model. 2008; 8(2):199-218.
    • (2008) Stat Model , vol.8 , Issue.2 , pp. 199-218
    • Tarpey, T.1    Yun, D.2    Petkova, E.3
  • 68
    • 77649269338 scopus 로고    scopus 로고
    • The bimodality index: a criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data
    • Wang J, Wen S, Symmans WF, Pusztai L, Coombes KR. The bimodality index: a criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data. Cancer Informat. 2009; 7:199.
    • (2009) Cancer Informat , vol.7 , pp. 199
    • Wang, J.1    Wen, S.2    Symmans, W.F.3    Pusztai, L.4    Coombes, K.R.5
  • 69
    • 84962861088 scopus 로고    scopus 로고
    • Beyond comparisons of means: understanding changes in gene expression at the single-cell level
    • Vallejos CA, Richardson S, Marioni JC. Beyond comparisons of means: understanding changes in gene expression at the single-cell level. Genome Biol. 2016; 17(1):1.
    • (2016) Genome Biol , vol.17 , Issue.1 , pp. 1
    • Vallejos, C.A.1    Richardson, S.2    Marioni, J.C.3


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