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Volumn 45, Issue 11, 2017, Pages

Differential expression analysis for RNAseq using Poisson mixed models

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ALGORITHM; ARTICLE; EFFECT SIZE; ERROR; FEMALE; GENE EXPRESSION; HUMAN; INTERMETHOD COMPARISON; MALE; NONHUMAN; POISSON DISTRIBUTION; POISSON MIXED MODEL; PRIORITY JOURNAL; RNA SEQUENCE; STATISTICAL ANALYSIS; STATISTICAL MODEL; STRUCTURAL EQUATION MODELING; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; MARKOV CHAIN; MONTE CARLO METHOD; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE;

EID: 85026667037     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx204     Document Type: Article
Times cited : (55)

References (134)
  • 1
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi,U.,Wang,Z., Waern,K., Shou,C., Raha,D., Gerstein,M. and Snyder,M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 4
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang,Z., Gerstein,M. and Snyder,M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 5
    • 78650539308 scopus 로고    scopus 로고
    • From RNA-seq reads to differential expression results
    • Oshlack,A., Robinson,M.D. and Young,M.D. (2010) From RNA-seq reads to differential expression results. Genome Biol., 11, 220.
    • (2010) Genome Biol , vol.11 , pp. 220
    • Oshlack, A.1    Robinson, M.D.2    Young, M.D.3
  • 6
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: Advances, challenges and opportunities
    • Ozsolak,F. and Milos,P.M. (2011) RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet., 12, 87-98.
    • (2011) Nat. Rev. Genet , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 7
    • 84964699021 scopus 로고    scopus 로고
    • The genetic architecture of gene expression levels in wild baboons
    • Tung,J., Zhou,X., Alberts,S.C., Stephens,M. and Gilad,Y. (2015) The genetic architecture of gene expression levels in wild baboons. Elife, 4, e04729.
    • (2015) Elife , vol.4 , pp. e04729
    • Tung, J.1    Zhou, X.2    Alberts, S.C.3    Stephens, M.4    Gilad, Y.5
  • 9
    • 84863003734 scopus 로고    scopus 로고
    • Genome-wide efficient mixed-model analysis for association studies
    • Zhou,X. and Stephens,M. (2012) Genome-wide efficient mixed-model analysis for association studies. Nat. Genet., 44, 821-824.
    • (2012) Nat. Genet , vol.44 , pp. 821-824
    • Zhou, X.1    Stephens, M.2
  • 12
    • 77949507153 scopus 로고    scopus 로고
    • RNA-Seq gene expression estimation with read mapping uncertainty
    • Li,B., Ruotti,V., Stewart,R.M., Thomson,J.A. and Dewey,C.N. (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics, 26, 493-500.
    • (2010) Bioinformatics , vol.26 , pp. 493-500
    • Li, B.1    Ruotti, V.2    Stewart, R.M.3    Thomson, J.A.4    Dewey, C.N.5
  • 13
    • 84855162597 scopus 로고    scopus 로고
    • Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq
    • Hu,M., Zhu,Y., Taylor,J.M.G., Liu,J.S. and Qin,Z.H.S. (2012) Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. Bioinformatics, 28, 63-68.
    • (2012) Bioinformatics , vol.28 , pp. 63-68
    • Hu, M.1    Zhu, Y.2    Taylor, J.M.G.3    Liu, J.S.4    Qin, Z.H.S.5
  • 14
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li,B. and Dewey,C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics, 12, 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 15
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders,S. and Huber,W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
    • (2010) Genome Biol , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 17
    • 77951940273 scopus 로고    scopus 로고
    • Modeling non-uniformity in short-read rates in RNA-Seq data
    • Li,J., Jiang,H. and Wong,W.H. (2010) Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol., 11, R50.
    • (2010) Genome Biol , vol.11 , pp. R50
    • Li, J.1    Jiang, H.2    Wong, W.H.3
  • 18
    • 80053451880 scopus 로고    scopus 로고
    • A powerful and flexible approach to the analysis of RNA sequence count data
    • Zhou,Y.H., Xia,K. and Wright,F.A. (2011) A powerful and flexible approach to the analysis of RNA sequence count data. Bioinformatics, 27, 2672-2678.
    • (2011) Bioinformatics , vol.27 , pp. 2672-2678
    • Zhou, Y.H.1    Xia, K.2    Wright, F.A.3
  • 19
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni,J.C., Mason,C.E., Mane,S.M., Stephens,M. and Gilad,Y. (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res., 18, 1509-1517.
    • (2008) Genome Res , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 20
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: An R package for identifying differentially expressed genes from RNA-seq data
    • Wang,L.K., Feng,Z.X., Wang,X., Wang,X.W. and Zhang,X.G. (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 26, 136-138.
    • (2010) Bioinformatics , vol.26 , pp. 136-138
    • Wang, L.K.1    Feng, Z.X.2    Wang, X.3    Wang, X.W.4    Zhang, X.G.5
  • 21
    • 77955343193 scopus 로고    scopus 로고
    • Cloud-scale RNA-sequencing differential expression analysis with Myrna
    • Langmead,B., Hansen,K.D. and Leek,J.T. (2010) Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol., 11, R83.
    • (2010) Genome Biol , vol.11 , pp. R83
    • Langmead, B.1    Hansen, K.D.2    Leek, J.T.3
  • 22
    • 84863562292 scopus 로고    scopus 로고
    • Normalization, testing, and false discovery rate estimation for RNA-sequencing data
    • Li,J., Witten,D.M., Johnstone,I.M. and Tibshirani,R. (2012) Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics, 13, 523-538.
    • (2012) Biostatistics , vol.13 , pp. 523-538
    • Li, J.1    Witten, D.M.2    Johnstone, I.M.3    Tibshirani, R.4
  • 23
    • 79958115654 scopus 로고    scopus 로고
    • A two-stage poisson model for testing RNA-Seq data
    • Auer,P.L. and Doerge,R.W. (2011) A two-stage poisson model for testing RNA-Seq data. Stat. Appl. Genet. Mol., 10, 1-26.
    • (2011) Stat. Appl. Genet. Mol , vol.10 , pp. 1-26
    • Auer, P.L.1    Doerge, R.W.2
  • 24
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love,M.I., Huber,W. and Anders,S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 550.
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 25
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A bioconductor package for differential expression analysis of digital gene expression data
    • Robinson,M.D.,McCarthy,D.J. and Smyth,G.K. (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 26
    • 84858041341 scopus 로고    scopus 로고
    • Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
    • McCarthy,D.J., Chen,Y.S. and Smyth,G.K. (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res., 40, 4288-4297.
    • (2012) Nucleic Acids Res , vol.40 , pp. 4288-4297
    • McCarthy, D.J.1    Chen, Y.S.2    Smyth, G.K.3
  • 27
    • 79958117254 scopus 로고    scopus 로고
    • The NBP negative binomial model for assessing differential gene expression from RNA-Seq
    • Di,Y.M., Schafer,D.W., Cumbie,J.S. and Chang,J.H. (2011) The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Stat. Appl. Genet. Mol., 10, 1-28.
    • (2011) Stat. Appl. Genet. Mol , vol.10 , pp. 1-28
    • Di, Y.M.1    Schafer, D.W.2    Cumbie, J.S.3    Chang, J.H.4
  • 28
    • 84874912212 scopus 로고    scopus 로고
    • A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
    • Wu,H., Wang,C. and Wu,Z. (2013) A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics, 14, 232-243.
    • (2013) Biostatistics , vol.14 , pp. 232-243
    • Wu, H.1    Wang, C.2    Wu, Z.3
  • 30
    • 77955298482 scopus 로고    scopus 로고
    • BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
    • Hardcastle,T.J. and Kelly,K.A. (2010) baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics, 11, 422.
    • (2010) BMC Bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 31
    • 84886557480 scopus 로고    scopus 로고
    • Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
    • Li,J. and Tibshirani,R. (2013) Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat. Methods Med. Res., 22, 519-536.
    • (2013) Stat. Methods Med. Res , vol.22 , pp. 519-536
    • Li, J.1    Tibshirani, R.2
  • 33
    • 84896735766 scopus 로고    scopus 로고
    • Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law,C.W., Chen,Y.S., Shi,W. and Smyth,G.K. (2014) voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol., 15, R29.
    • (2014) Genome Biol , vol.15 , pp. R29
    • Law, C.W.1    Chen, Y.S.2    Shi, W.3    Smyth, G.K.4
  • 34
    • 84896973299 scopus 로고    scopus 로고
    • Transforming RNA-Seq data to improve the performance of prognostic gene signatures
    • Zwiener,I., Frisch,B. and Binder,H. (2014) Transforming RNA-Seq data to improve the performance of prognostic gene signatures. PLoS One, 9, e85150.
    • (2014) PLoS One , vol.9 , pp. e85150
    • Zwiener, I.1    Frisch, B.2    Binder, H.3
  • 35
    • 84874677498 scopus 로고    scopus 로고
    • A comparison of methods for differential expression analysis of RNA-seq data
    • Soneson,C. and Delorenzi,M. (2013) A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics, 14, 91.
    • (2013) BMC Bioinformatics , vol.14 , pp. 91
    • Soneson, C.1    Delorenzi, M.2
  • 36
    • 84858606519 scopus 로고    scopus 로고
    • A comparison of statistical methods for detecting differentially expressed genes from RNA-Seq data
    • Kvam,V.M., Lu,P. and Si,Y.Q. (2012) A comparison of statistical methods for detecting differentially expressed genes from Rna-Seq data. Am. J. Bot., 99, 248-256.
    • (2012) Am. J. Bot , vol.99 , pp. 248-256
    • Kvam, V.M.1    Lu, P.2    Si, Y.Q.3
  • 39
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson,M.D. and Oshlack,A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol., 11, R25.
    • (2010) Genome Biol , vol.11 , pp. R25
    • Robinson, M.D.1    Oshlack, A.2
  • 40
    • 79952263851 scopus 로고    scopus 로고
    • Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals
    • Price,A.L., Helgason,A., Thorleifsson,G., McCarroll,S.A., Kong,A. and Stefansson,K. (2011) Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet., 7, e1001317.
    • (2011) PLoS Genet , vol.7 , pp. e1001317
    • Price, A.L.1    Helgason, A.2    Thorleifsson, G.3    McCarroll, S.A.4    Kong, A.5    Stefansson, K.6
  • 44
    • 84892148636 scopus 로고    scopus 로고
    • Genome-wide eQTLs and heritability for gene expression traits in unrelated individuals
    • Yang,S.J., Liu,Y.Y., Jiang,N., Chen,J., Leach,L., Luo,Z.W. and Wang,M.H. (2014) Genome-wide eQTLs and heritability for gene expression traits in unrelated individuals. BMC Genomics, 15, 13.
    • (2014) BMC Genomics , vol.15 , pp. 13
    • Yang, S.J.1    Liu, Y.Y.2    Jiang, N.3    Chen, J.4    Leach, L.5    Luo, Z.W.6    Wang, M.H.7
  • 48
    • 84861734626 scopus 로고    scopus 로고
    • Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
    • Stegle,O., Parts,L., Piipari,M., Winn,J. and Durbin,R. (2012) Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat. Protoc., 7, 500-507.
    • (2012) Nat. Protoc , vol.7 , pp. 500-507
    • Stegle, O.1    Parts, L.2    Piipari, M.3    Winn, J.4    Durbin, R.5
  • 49
    • 84925226706 scopus 로고    scopus 로고
    • Svaseq: Removing batch effects and other unwanted noise from sequencing data
    • Leek,J.T. (2014) Svaseq: removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res., 42, e161.
    • (2014) Nucleic Acids Res , vol.42 , pp. e161
    • Leek, J.T.1
  • 50
    • 34848914038 scopus 로고    scopus 로고
    • Capturing heterogeneity in gene expression studies by surrogate variable analysis
    • Leek,J.T. and Storey,J.D. (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet., 3, 1724-1735.
    • (2007) PLoS Genet , vol.3 , pp. 1724-1735
    • Leek, J.T.1    Storey, J.D.2
  • 51
    • 84909644283 scopus 로고    scopus 로고
    • Normalization of RNA-seq data using factor analysis of control genes or samples
    • Risso,D., Ngai,J., Speed,T.P. and Dudoit,S. (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol., 32, 896-902.
    • (2014) Nat. Biotechnol , vol.32 , pp. 896-902
    • Risso, D.1    Ngai, J.2    Speed, T.P.3    Dudoit, S.4
  • 52
    • 61849171085 scopus 로고    scopus 로고
    • Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots
    • Kang,H.M., Ye,C. and Eskin,E. (2008) Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics, 180, 1909-1925.
    • (2008) Genetics , vol.180 , pp. 1909-1925
    • Kang, H.M.1    Ye, C.2    Eskin, E.3
  • 53
    • 78049312702 scopus 로고    scopus 로고
    • Correction for hidden confounders in the genetic analysis of gene expression
    • Listgarten,J., Kadie,C., Schadt,E.E. and Heckerman,D. (2010) Correction for hidden confounders in the genetic analysis of gene expression. Proc. Natl. Acad. Sci. U.S.A., 107, 16465-16470.
    • (2010) Proc. Natl. Acad. Sci. U. S. A , vol.107 , pp. 16465-16470
    • Listgarten, J.1    Kadie, C.2    Schadt, E.E.3    Heckerman, D.4
  • 54
    • 84895540377 scopus 로고    scopus 로고
    • Epigenome-wide association studies without the need for cell-type composition
    • Zou,J., Lippert,C., Heckerman,D., Aryee,M. and Listgarten,J. (2014) Epigenome-wide association studies without the need for cell-type composition. Nat. Methods, 11, 309-311.
    • (2014) Nat. Methods , vol.11 , pp. 309-311
    • Zou, J.1    Lippert, C.2    Heckerman, D.3    Aryee, M.4    Listgarten, J.5
  • 57
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • Price,A.L., Patterson,N.J., Plenge,R.M., Weinblatt,M.E., Shadick,N.A. and Reich,D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
    • (2006) Nat. Genet , vol.38 , pp. 904-909
    • Price, A.L.1    Patterson, N.J.2    Plenge, R.M.3    Weinblatt, M.E.4    Shadick, N.A.5    Reich, D.6
  • 58
    • 84897954264 scopus 로고    scopus 로고
    • Efficient multivariate linear mixed model algorithms for genome-wide association studies
    • Zhou,X. and Stephens,M. (2014) Efficient multivariate linear mixed model algorithms for genome-wide association studies. Nat. Methods, 11, 407-409.
    • (2014) Nat. Methods , vol.11 , pp. 407-409
    • Zhou, X.1    Stephens, M.2
  • 59
    • 84949294819 scopus 로고    scopus 로고
    • A flexible, efficient binomial mixed model for identifying differential DNA methylation in bisulfite sequencing data
    • Lea,A.J., Alberts,S.C., Tung,J. and Zhou,X. (2015) A flexible, efficient binomial mixed model for identifying differential DNA methylation in bisulfite sequencing data. PLoS Genet., 11, e1005650.
    • (2015) PLoS Genet , vol.11 , pp. e1005650
    • Lea, A.J.1    Alberts, S.C.2    Tung, J.3    Zhou, X.4
  • 61
    • 33845796064 scopus 로고    scopus 로고
    • Auxiliary mixture sampling for parameter-driven models of time series of counts with applications to state space modelling
    • Fruhwirth-Schnatter,S. and Wagner,H. (2006) Auxiliary mixture sampling for parameter-driven models of time series of counts with applications to state space modelling. Biometrika, 93, 827-841.
    • (2006) Biometrika , vol.93 , pp. 827-841
    • Fruhwirth-Schnatter, S.1    Wagner, H.2
  • 62
    • 79951767740 scopus 로고    scopus 로고
    • Data augmentation, frequentist estimation, and the Bayesian analysis of multinomial logit models
    • Scott,S.L. (2011) Data augmentation, frequentist estimation, and the Bayesian analysis of multinomial logit models. Stat. Pap., 52, 87-109.
    • (2011) Stat. Pap , vol.52 , pp. 87-109
    • Scott, S.L.1
  • 65
    • 84874783818 scopus 로고    scopus 로고
    • Polygenic modeling with Bayesian sparse linear mixed models
    • Zhou,X., Carbonetto,P. and Stephens,M. (2013) Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet., 9, e1003264.
    • (2013) PLoS Genet , vol.9 , pp. e1003264
    • Zhou, X.1    Carbonetto, P.2    Stephens, M.3
  • 69
    • 84926507971 scopus 로고    scopus 로고
    • Limma powers differential expression analyses for RNA-sequencing and microarray studies
    • Ritchie,M.E., Phipson,B., Wu,D., Hu,Y.F., Law,C.W., Shi,W. and Smyth,G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47.
    • (2015) Nucleic Acids Res , vol.43 , pp. e47
    • Ritchie, M.E.1    Phipson, B.2    Wu, D.3    Hu, Y.F.4    Law, C.W.5    Shi, W.6    Smyth, G.K.7
  • 70
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • Bullard,J.H., Purdom,E., Hansen,K.D. and Dudoit,S. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 11, 94.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3    Dudoit, S.4
  • 71
    • 84949178527 scopus 로고    scopus 로고
    • In: Kappeler, PM and Watts, DP (eds)Springer, Berlin Heidelberg
    • Alberts,S. and Altmann,J. (2012) In: Kappeler,PM and Watts,DP (eds). Long-Term Field Studies of Primates. Springer, Berlin Heidelberg, pp. 261-287.
    • (2012) Long-Term Field Studies of Primates , pp. 261-287
    • Alberts, S.1    Altmann, J.2
  • 72
    • 33750359350 scopus 로고    scopus 로고
    • Sexual selection in wild baboons: From mating opportunities to paternity success
    • Alberts,S.C., Buchan,J.C. and Altmann,J. (2006) Sexual selection in wild baboons: from mating opportunities to paternity success. Anim. Behav., 72, 1177-1196.
    • (2006) Anim. Behav , vol.72 , pp. 1177-1196
    • Alberts, S.C.1    Buchan, J.C.2    Altmann, J.3
  • 73
    • 0141607967 scopus 로고    scopus 로고
    • True paternal care in a multi-Male primate society
    • Buchan,J.C., Alberts,S.C., Silk,J.B. and Altmann,J. (2003) True paternal care in a multi-male primate society. Nature, 425, 179-181.
    • (2003) Nature , vol.425 , pp. 179-181
    • Buchan, J.C.1    Alberts, S.C.2    Silk, J.B.3    Altmann, J.4
  • 74
    • 84996084638 scopus 로고
    • Physical maturation and age estimates of yellow baboons, papio-cynocephalus, in amboseli national-park, Kenya
    • Altmann,J., Altmann,S. and Hausfater,G. (1981) Physical maturation and age estimates of yellow baboons, Papio-Cynocephalus, in Amboseli National-Park, Kenya. Am. J. Primatol., 1, 389-399.
    • (1981) Am. J. Primatol , vol.1 , pp. 389-399
    • Altmann, J.1    Altmann, S.2    Hausfater, G.3
  • 75
    • 84921510500 scopus 로고    scopus 로고
    • Social affiliation matters: Both same-sex and opposite-sex relationships predict survival in wild female baboons
    • Archie,E.A., Tung,J., Clark,M., Altmann,J. and Alberts,S.C. (2014) Social affiliation matters: both same-sex and opposite-sex relationships predict survival in wild female baboons. Proc. R. Soc. B., 281, 20141261.
    • (2014) Proc. R. Soc. B , vol.281 , pp. 20141261
    • Archie, E.A.1    Tung, J.2    Clark, M.3    Altmann, J.4    Alberts, S.C.5
  • 77
    • 85027926229 scopus 로고    scopus 로고
    • Quality of life along the diabetes continuum: A cross-sectional view of health-related quality of life and general health status in middle-aged and older Finns
    • Vaatainen,S., Keinanen-Kiukaanniemi,S., Saramies,J., Uusitalo,H., Tuomilehto,J. and Martikainen,J. (2014) Quality of life along the diabetes continuum: a cross-sectional view of health-related quality of life and general health status in middle-aged and older Finns. Qual. Life Res., 23, 1935-1944.
    • (2014) Qual. Life Res , vol.23 , pp. 1935-1944
    • Vaatainen, S.1    Keinanen-Kiukaanniemi, S.2    Saramies, J.3    Uusitalo, H.4    Tuomilehto, J.5    Martikainen, J.6
  • 78
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 79
    • 40849100588 scopus 로고    scopus 로고
    • Naive application of permutation testing leads to inflated type i error rates
    • Churchill,G.A. and Doerge,R.W. (2008) Naive application of permutation testing leads to inflated type I error rates. Genetics, 178, 609-610.
    • (2008) Genetics , vol.178 , pp. 609-610
    • Churchill, G.A.1    Doerge, R.W.2
  • 80
    • 84928091332 scopus 로고    scopus 로고
    • Permutation testing in the presence of polygenic variation
    • Abney,M. (2015) Permutation testing in the presence of polygenic variation. Genet. Epidemiol., 39, 249-258.
    • (2015) Genet. Epidemiol , vol.39 , pp. 249-258
    • Abney, M.1
  • 81
    • 84903146127 scopus 로고    scopus 로고
    • Robustly detecting differential expression in RNA sequencing data using observation weights
    • Zhou,X., Lindsay,H. and Robinson,M.D. (2014) Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Res., 42, e91.
    • (2014) Nucleic Acids Res , vol.42 , pp. e91
    • Zhou, X.1    Lindsay, H.2    Robinson, M.D.3
  • 82
    • 84931265950 scopus 로고    scopus 로고
    • An iterative leave-one-out approach to outlier detection in RNA-seq data
    • George,N.I., Bowyer,J.F., Crabtree,N.M. and Chang,C.W. (2015) An iterative leave-one-out approach to outlier detection in RNA-seq data. PLoS One, 10, e0125224.
    • (2015) PLoS One , vol.10 , pp. e0125224
    • George, N.I.1    Bowyer, J.F.2    Crabtree, N.M.3    Chang, C.W.4
  • 84
    • 45149105926 scopus 로고    scopus 로고
    • Efficient control of population structure in model organism association mapping
    • Kang,H.M., Zaitlen,N.A., Wade,C.M., Kirby,A., Heckerman,D., Daly,M.J. and Eskin,E. (2008) Efficient control of population structure in model organism association mapping. Genetics, 178, 1709-1723.
    • (2008) Genetics , vol.178 , pp. 1709-1723
    • Kang, H.M.1    Zaitlen, N.A.2    Wade, C.M.3    Kirby, A.4    Heckerman, D.5    Daly, M.J.6    Eskin, E.7
  • 85
    • 0030003478 scopus 로고    scopus 로고
    • A mixed effects model for overdispersed count data in animal breeding
    • Tempelman,R.J. and Gianola,D. (1996) A mixed effects model for overdispersed count data in animal breeding. Biometrics, 52, 265-279.
    • (1996) Biometrics , vol.52 , pp. 265-279
    • Tempelman, R.J.1    Gianola, D.2
  • 86
    • 0032064691 scopus 로고    scopus 로고
    • Generalized linear mixed models in dairy cattle breeding
    • Tempelman,R.J. (1998) Generalized linear mixed models in dairy cattle breeding. J. Dairy Sci., 81, 1428-1444.
    • (1998) J. Dairy Sci , vol.81 , pp. 1428-1444
    • Tempelman, R.J.1
  • 87
    • 33645565987 scopus 로고    scopus 로고
    • Efficient Laplacian and adaptive Gaussian quadrature algorithms for multilevel generalized linear mixed models
    • Pinheiro,J.C. and Chao,E.C. (2006) Efficient Laplacian and adaptive Gaussian quadrature algorithms for multilevel generalized linear mixed models. J. Comput. Graph. Stat., 15, 58-81.
    • (2006) J. Comput. Graph. Stat , vol.15 , pp. 58-81
    • Pinheiro, J.C.1    Chao, E.C.2
  • 88
    • 77956891017 scopus 로고
    • Nonlinear multilevel models, with an application to discrete response data
    • Goldstein,H. (1991) Nonlinear multilevel models, with an application to discrete response data. Biometrika, 78, 45-51.
    • (1991) Biometrika , vol.78 , pp. 45-51
    • Goldstein, H.1
  • 89
    • 0011241944 scopus 로고
    • Approximate inference in generalized linear mixed models
    • Breslow,N.E. and Clayton,D.G. (1993) Approximate Inference in Generalized Linear Mixed Models. J. Am. Stat. Assoc., 88, 9-25.
    • (1993) J. Am. Stat. Assoc , vol.88 , pp. 9-25
    • Breslow, N.E.1    Clayton, D.G.2
  • 90
    • 0003020981 scopus 로고
    • Bias correction in generalized linear mixed models with a single-component of dispersion
    • Breslow,N.E. and Lin,X.H. (1995) Bias correction in generalized linear mixed models with a single-component of dispersion. Biometrika, 82, 81-91.
    • (1995) Biometrika , vol.82 , pp. 81-91
    • Breslow, N.E.1    Lin, X.H.2
  • 91
    • 33847083094 scopus 로고    scopus 로고
    • A comparison of Bayesian and likelihood-based methods for fitting multilevel models
    • Browne,W.J. and Draper,D. (2006) A comparison of Bayesian and likelihood-based methods for fitting multilevel models. Bayesian Anal., 1, 473-513.
    • (2006) Bayesian Anal , vol.1 , pp. 473-513
    • Browne, W.J.1    Draper, D.2
  • 92
    • 0030336576 scopus 로고    scopus 로고
    • Bias correction in generalized linear mixed models with multiple components of dispersion
    • Lin,X.H. and Breslow,N.E. (1996) Bias correction in generalized linear mixed models with multiple components of dispersion. J. Am. Stat. Assoc., 91, 1007-1016.
    • (1996) J. Am. Stat. Assoc , vol.91 , pp. 1007-1016
    • Lin, X.H.1    Breslow, N.E.2
  • 93
    • 0039862130 scopus 로고    scopus 로고
    • Improved approximations for multilevel models with binary responses
    • Goldstein,H. and Rasbash,J. (1996) Improved approximations for multilevel models with binary responses. J. R. Stat. Soc. A, 159, 505-513.
    • (1996) J. R. Stat. Soc. A , vol.159 , pp. 505-513
    • Goldstein, H.1    Rasbash, J.2
  • 94
    • 0035648129 scopus 로고    scopus 로고
    • Improved estimation procedures for multilevel models with binary response: A case-study
    • Rodriguez,G. and Goldman,N. (2001) Improved estimation procedures for multilevel models with binary response: a case-study. J. R. Stat. Soc. A, 164, 339-355.
    • (2001) J. R. Stat. Soc. A , vol.164 , pp. 339-355
    • Rodriguez, G.1    Goldman, N.2
  • 95
    • 60849085468 scopus 로고    scopus 로고
    • A numerical study of PQL estimation biases in generalized linear mixed models under heterogeneity of random effects
    • Jang,W. and Lim,J. (2009) A numerical study of PQL estimation biases in generalized linear mixed models under heterogeneity of random effects. Commun. Stat., 38, 692-702.
    • (2009) Commun. Stat , vol.38 , pp. 692-702
    • Jang, W.1    Lim, J.2
  • 96
    • 77956640383 scopus 로고    scopus 로고
    • Bayesian inference for generalized linear mixed models
    • Fong,Y.Y., Rue,H. and Wakefield,J. (2010) Bayesian inference for generalized linear mixed models. Biostatistics, 11, 397-412.
    • (2010) Biostatistics , vol.11 , pp. 397-412
    • Fong, Y.Y.1    Rue, H.2    Wakefield, J.3
  • 97
    • 0003053548 scopus 로고
    • Bayesian computation via the gibbs sampler and related markov-chain monte-carlo methods
    • Smith,A.F.M. and Roberts,G.O. (1993) Bayesian computation via the gibbs sampler and related markov-chain monte-carlo methods. J. R. Stat. Soc. B, 55, 3-23.
    • (1993) J. R. Stat. Soc. B , vol.55 , pp. 3-23
    • Smith, A.F.M.1    Roberts, G.O.2
  • 100
    • 77749249761 scopus 로고    scopus 로고
    • MCMC methods for multi-response generalized linear mixed models: The MCMCglmm R package
    • Hadfield,J.D. (2010) MCMC methods for multi-response generalized linear mixed models: The MCMCglmm R package. J. Stat. Softw., 33, 1-22.
    • (2010) J. Stat. Softw , vol.33 , pp. 1-22
    • Hadfield, J.D.1
  • 101
    • 84928199480 scopus 로고    scopus 로고
    • Comparison of software packages for detecting differential expression in RNA-seq studies
    • Seyednasrollah,F., Laiho,A. and Elo,L.L. (2015) Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform., 16, 59-70.
    • (2015) Brief Bioinform , vol.16 , pp. 59-70
    • Seyednasrollah, F.1    Laiho, A.2    Elo, L.L.3
  • 102
    • 33846006923 scopus 로고    scopus 로고
    • Population structure and eigenanalysis
    • Patterson,N., Price,A.L. and Reich,D. (2006) Population structure and eigenanalysis. PLoS Genet., 2, 2074-2093.
    • (2006) PLoS Genet , vol.2 , pp. 2074-2093
    • Patterson, N.1    Price, A.L.2    Reich, D.3
  • 103
    • 84895801913 scopus 로고    scopus 로고
    • Advantages and pitfalls in the application of mixed-model association methods
    • Yang,J., Zaitlen,N.A., Goddard,M.E., Visscher,P.M. and Price,A.L. (2014) Advantages and pitfalls in the application of mixed-model association methods. Nat. Genet., 46, 100-106.
    • (2014) Nat. Genet , vol.46 , pp. 100-106
    • Yang, J.1    Zaitlen, N.A.2    Goddard, M.E.3    Visscher, P.M.4    Price, A.L.5
  • 108
    • 84892742200 scopus 로고    scopus 로고
    • Genome-wide gene expression effects of sex chromosome imprinting in Drosophila
    • Lemos,B., Branco,A.T., Jiang,P.P., Hartl,D.L. and Meiklejohn,C.D. (2014) Genome-wide gene expression effects of sex chromosome imprinting in Drosophila. G3, 4, 1-10.
    • (2014) G3 , vol.4 , pp. 1-10
    • Lemos, B.1    Branco, A.T.2    Jiang, P.P.3    Hartl, D.L.4    Meiklejohn, C.D.5
  • 111
    • 53549129190 scopus 로고    scopus 로고
    • The role of mTOR in the adaptation and failure of beta-cells in type 2 diabetes
    • Leibowitz,G., Cerasi,E. and Ketzinel-Gilad,A. (2008) The role of mTOR in the adaptation and failure of beta-cells in type 2 diabetes. Diabetes Obes. Metab., 10, 157-169.
    • (2008) Diabetes Obes. Metab , vol.10 , pp. 157-169
    • Leibowitz, G.1    Cerasi, E.2    Ketzinel-Gilad, A.3
  • 113
    • 84859778293 scopus 로고    scopus 로고
    • MTOR signaling in growth control and disease
    • Laplante,M. and Sabatini,D.M. (2012) mTOR signaling in growth control and disease. Cell, 149, 274-293.
    • (2012) Cell , vol.149 , pp. 274-293
    • Laplante, M.1    Sabatini, D.M.2
  • 114
    • 78650510609 scopus 로고    scopus 로고
    • MTOR: From growth signal integration to cancer, diabetes and ageing
    • Zoncu,R., Efeyan,A. and Sabatini,D.M. (2011) mTOR: from growth signal integration to cancer, diabetes and ageing. Nat. Rev. Mol. Cell Biol., 12, 21-35.
    • (2011) Nat. Rev. Mol. Cell Biol , vol.12 , pp. 21-35
    • Zoncu, R.1    Efeyan, A.2    Sabatini, D.M.3
  • 115
    • 0021813187 scopus 로고
    • Homeostasis model assessment-insulin resistance and beta-cell function from fasting plasma-glucose and insulin concentrations in man
    • Matthews,D.R., Hosker,J.P., Rudenski,A.S., Naylor,B.A., Treacher,D.F. and Turner,R.C. (1985) Homeostasis model assessment-insulin resistance and beta-cell function from fasting plasma-glucose and insulin concentrations in man. Diabetologia, 28, 412-419.
    • (1985) Diabetologia , vol.28 , pp. 412-419
    • Matthews, D.R.1    Hosker, J.P.2    Rudenski, A.S.3    Naylor, B.A.4    Treacher, D.F.5    Turner, R.C.6
  • 119
    • 84862250978 scopus 로고    scopus 로고
    • Using control genes to correct for unwanted variation in microarray data
    • Gagnon-Bartsch,J.A. and Speed,T.P. (2012) Using control genes to correct for unwanted variation in microarray data. Biostatistics, 13, 539-552.
    • (2012) Biostatistics , vol.13 , pp. 539-552
    • Gagnon-Bartsch, J.A.1    Speed, T.P.2
  • 122
    • 85027250934 scopus 로고    scopus 로고
    • Imputation from the 1000 Genomes Project identifies rare large effect variants of BRCA2-K3326X and CHEK2-I157T as risk factors for lung cancer; A study from the TRICL consortium
    • Landi,M.T., Wang,Y.F., Mckay,J.D., Rafnar,T., Wang,Z.M., Timofeeva,M., Broderick,P., Stefansson,K., Risch,A., Chanock,S.J. et al. (2014) Imputation from the 1000 Genomes Project identifies rare large effect variants of BRCA2-K3326X and CHEK2-I157T as risk factors for lung cancer; a study from the TRICL consortium. Cancer Res., 74, 942-942.
    • (2014) Cancer Res , vol.74 , pp. 942
    • Landi, M.T.1    Wang, Y.F.2    Mckay, J.D.3    Rafnar, T.4    Wang, Z.M.5    Timofeeva, M.6    Broderick, P.7    Stefansson, K.8    Risch, A.9    Chanock, S.J.10
  • 123
    • 68249140383 scopus 로고    scopus 로고
    • The 1001 genomes project for arabidopsis thaliana
    • Weigel,D. and Mott,R. (2009) The 1001 genomes project for arabidopsis thaliana. Genome Biol., 10, 107.
    • (2009) Genome Biol , vol.10 , pp. 107
    • Weigel, D.1    Mott, R.2
  • 125
    • 84937691256 scopus 로고    scopus 로고
    • Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
    • Kanitz,A., Gypas,F., Gruber,A.J., Gruber,A.R., Martin,G. and Zavolan,M. (2015) Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol., 16, 150.
    • (2015) Genome Biol , vol.16 , pp. 150
    • Kanitz, A.1    Gypas, F.2    Gruber, A.J.3    Gruber, A.R.4    Martin, G.5    Zavolan, M.6
  • 126
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead,B. and Salzberg,S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 129
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim,D., Pertea,G., Trapnell,C., Pimentel,H., Kelley,R. and Salzberg,S.L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 130
  • 133
    • 65649126066 scopus 로고    scopus 로고
    • Transcript length bias in RNA-seq data confounds systems biology
    • Oshlack,A. and Wakefield,M.J. (2009) Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct, 4, 14.
    • (2009) Biol. Direct , vol.4 , pp. 14
    • Oshlack, A.1    Wakefield, M.J.2
  • 134
    • 84858068675 scopus 로고    scopus 로고
    • Removing technical variability in RNA-seq data using conditional quantile normalization
    • Hansen,K.D., Irizarry,R.A. and Wu,Z.J. (2012) Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics, 13, 204-216.
    • (2012) Biostatistics , vol.13 , pp. 204-216
    • Hansen, K.D.1    Irizarry, R.A.2    Wu, Z.J.3


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