-
1
-
-
57749195712
-
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
-
2
-
-
84883364264
-
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
-
Anders, S., McCarthy, D.J., Chen, Y., Okoniewski, M., Smyth, G.K., Huber, W. and Robinson, M.D. (2013) Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protocols, 8, 1765-1786.
-
(2013)
Nat. Protocols
, vol.8
, pp. 1765-1786
-
-
Anders, S.1
McCarthy, D.J.2
Chen, Y.3
Okoniewski, M.4
Smyth, G.K.5
Huber, W.6
Robinson, M.D.7
-
3
-
-
79961123152
-
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
-
4
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29, 644-652.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
-
5
-
-
81055124271
-
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets
-
Frazee, A.C., Langmead, B. and Leek, J.T. (2011) ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics, 12, 449.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 449
-
-
Frazee, A.C.1
Langmead, B.2
Leek, J.T.3
-
6
-
-
84874677498
-
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
-
7
-
-
84883644707
-
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
-
Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C.E., Socci, N.D. and Betel, D. (2013) Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol., 14, R95.
-
(2013)
Genome Biol.
, vol.14
-
-
Rapaport, F.1
Khanin, R.2
Liang, Y.3
Pirun, M.4
Krek, A.5
Zumbo, P.6
Mason, C.E.7
Socci, N.D.8
Betel, D.9
-
8
-
-
84858041341
-
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
-
McCarthy, D.J., Chen, Y. and Smyth, G.K. (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res., 40, 1-10.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 1-10
-
-
McCarthy, D.J.1
Chen, Y.2
Smyth, G.K.3
-
9
-
-
77958471357
-
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
-
-
Anders, S.1
Huber, W.2
-
10
-
-
77950458649
-
Transcriptome genetics using second generation sequencing in a Caucasian population
-
Montgomery, S.B., Sammeth, M., Gutierrez-Arcelus, M., Lach, R.P., Ingle, C., Nisbett, J., Guigo, R. and Dermitzakis, E.T. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature, 464, 773-777.
-
(2010)
Nature
, vol.464
, pp. 773-777
-
-
Montgomery, S.B.1
Sammeth, M.2
Gutierrez-Arcelus, M.3
Lach, R.P.4
Ingle, C.5
Nisbett, J.6
Guigo, R.7
Dermitzakis, E.T.8
-
11
-
-
84896735766
-
Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
-
Law, C.W., Chen, Y., 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
-
-
Law, C.W.1
Chen, Y.2
Shi, W.3
Smyth, G.K.4
-
12
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
-
(2004)
Genome Biol.
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
-
13
-
-
75249087100
-
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
-
14
-
-
84871184589
-
Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors
-
Van De Wiel, M.A., Leday, G. G.R., Pardo, L., Rue, H.v., Van Der Vaart, A.W. and Van Wieringen, W.N. (2013) Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors. Biostatistics, 14, 113-128.
-
(2013)
Biostatistics
, vol.14
, pp. 113-128
-
-
Van De Wiel, M.A.1
Leday, G.G.R.2
Pardo, L.3
Rue, H.V.4
Van Der Vaart, A.W.5
Van Wieringen, W.N.6
-
15
-
-
77955298482
-
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
-
16
-
-
84874912212
-
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
-
17
-
-
0001645443
-
On robustness in the logistic regression model
-
Carroll, R.J. and Pederson, S. (1993) On robustness in the logistic regression model. J. R. Stat. Soc. Ser. B, 84, 693-706.
-
(1993)
J. R. Stat. Soc. Ser. B
, vol.84
, pp. 693-706
-
-
Carroll, R.J.1
Pederson, S.2
-
18
-
-
0442312206
-
Robust inference for generalized linear models
-
Cantoni, E. and Ronchetti, E. (2001) Robust inference for generalized linear models. J. Am. Stat. Assoc., 96, 1022-1030.
-
(2001)
J. Am. Stat. Assoc.
, vol.96
, pp. 1022-1030
-
-
Cantoni, E.1
Ronchetti, E.2
-
20
-
-
0036473684
-
Robust model selection in regression via weighted likelihood methodology
-
Agostinelli, C. (2002) Robust model selection in regression via weighted likelihood methodology. Stat. Probab. Lett., 56, 289-300.
-
(2002)
Stat. Probab. Lett.
, vol.56
, pp. 289-300
-
-
Agostinelli, C.1
-
21
-
-
0002738159
-
Parameter orthogonality and approximate conditional inference
-
Cox, D.R. and Reid, N. (1987) Parameter orthogonality and approximate conditional inference. J. R. Stat. Soc. Ser. B Methodol., 49, 1-39.
-
(1987)
J. R. Stat. Soc. Ser. B Methodol.
, vol.49
, pp. 1-39
-
-
Cox, D.R.1
Reid, N.2
-
22
-
-
41149085992
-
Small-sample estimation of negative binomial dispersion with applications to SAGE data
-
Robinson, M.D. and Smyth, G.K. (2008) Small-sample estimation of negative binomial dispersion with applications to SAGE data. Biostatistics, 9, 321-332.
-
(2008)
Biostatistics
, vol.9
, pp. 321-332
-
-
Robinson, M.D.1
Smyth, G.K.2
-
23
-
-
36448981743
-
Moderated statistical tests for assessing differences in tag abundance
-
Robinson, M.D. and Smyth, G.K. (2007) Moderated statistical tests for assessing differences in tag abundance. Bioinformatics, 23, 2881-2887.
-
(2007)
Bioinformatics
, vol.23
, pp. 2881-2887
-
-
Robinson, M.D.1
Smyth, G.K.2
-
24
-
-
33745697199
-
Robust regression
-
Fox, J. (2002) Robust Regression. Behav. Res. Methods, 1, 1-8.
-
(2002)
Behav. Res. Methods
, vol.1
, pp. 1-8
-
-
Fox, J.1
-
25
-
-
77951953494
-
Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls
-
Witten, D., Tibshirani, R., Gu, S.G., Fire, A. and Lui, W.-O. (2010) Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls. BMC Biol., 8, 58.
-
(2010)
BMC Biol.
, vol.8
, pp. 58
-
-
Witten, D.1
Tibshirani, R.2
Gu, S.G.3
Fire, A.4
Lui, W.-O.5
-
26
-
-
77957920003
-
Polymorphic cis-and trans-regulation of human gene expression
-
Cheung, V.G., Nayak, R.R., Wang, I.X., Elwyn, S., Cousins, S.M., Morley, M. and Spielman, R.S. (2010) Polymorphic Cis-and Trans-Regulation of Human Gene Expression. PLoS Biol., 8, 14.
-
(2010)
PLoS Biol.
, vol.8
, pp. 14
-
-
Cheung, V.G.1
Nayak, R.R.2
Wang, I.X.3
Elwyn, S.4
Cousins, S.M.5
Morley, M.6
Spielman, R.S.7
-
27
-
-
84886557480
-
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, 519-39.
-
(2013)
Stat. Methods Med. Res.
, vol.22
, pp. 519-539
-
-
Li, J.1
Tibshirani, R.2
-
28
-
-
84876263777
-
EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments
-
Leng, N., Dawson, J.A., Thomson, J.A., Ruotti, V., Rissman, A.I., Smits, B. M.G., Haag, J.D., Gould, M.N., Stewart, R.M. and Kendziorski, C. (2013) EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics, 29, 1035-1043.
-
(2013)
Bioinformatics
, vol.29
, pp. 1035-1043
-
-
Leng, N.1
Dawson, J.A.2
Thomson, J.A.3
Ruotti, V.4
Rissman, A.I.5
Smits, B.M.G.6
Haag, J.D.7
Gould, M.N.8
Stewart, R.M.9
Kendziorski, C.10
-
29
-
-
77953176036
-
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
-
-
Robinson, M.D.1
Oshlack, A.2
-
30
-
-
62849120031
-
Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations
-
Rue, H.v., Martino, S. and Chopin, N. (2009) Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations. J. R. Stat. Soc. Ser. B: Stat. Methodol., 71, 319-392.
-
(2009)
J. R. Stat. Soc. Ser. B: Stat. Methodol.
, vol.71
, pp. 319-392
-
-
Rue, H.V.1
Martino, S.2
Chopin, N.3
-
31
-
-
84873680686
-
-
in press
-
Martins, T.G., Simpson, D., Lindgren, F. and Rue, H. (2012) Bayesian computing with INLA: new features, in press .
-
(2012)
Bayesian Computing with INLA: New Features
-
-
Martins, T.G.1
Simpson, D.2
Lindgren, F.3
Rue, H.4
-
32
-
-
1542784653
-
Empirical Bayes analysis of a microarray experiment
-
Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001) Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc., 96, 1151-1160.
-
(2001)
J. Am. Stat. Assoc.
, vol.96
, pp. 1151-1160
-
-
Efron, B.1
Tibshirani, R.2
Storey, J.D.3
Tusher, V.4
-
33
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B: Methodol., 57, 289-300.
-
(1995)
J. R. Stat. Soc. Ser. B: Methodol.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
35
-
-
84858068675
-
Removing technical variability in RNA-seq data using conditional quantile normalization
-
Hansen, K.D., Irizarry, R.A. and Wu, Z. (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.3
-
36
-
-
75649102520
-
Sex-specific and lineage-specific alternative splicing in primates
-
Blekhman, R., Marioni, J.C., Zumbo, P., Stephens, M. and Gilad, Y. (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res., 20, 180-189.
-
(2010)
Genome Res.
, vol.20
, pp. 180-189
-
-
Blekhman, R.1
Marioni, J.C.2
Zumbo, P.3
Stephens, M.4
Gilad, Y.5
-
37
-
-
84903168376
-
Tissue inhibitor of metalloproteinase-1 and-2 RNA expression in rat and human liver fibrosis
-
Herbst, H., Wege, T., Milani, S., Pellegrini, G., Orzechowski, H., Bechstein, W., Neuhaus, P. and Schuppan, D. (1997) Tissue inhibitor of metalloproteinase-1 and-2 RNA expression in rat and human liver fibrosis. Am. Soc. Invest. Pathol., 150, 51647-51659.
-
(1997)
Am. Soc. Invest. Pathol.
, vol.150
, pp. 51647-51659
-
-
Herbst, H.1
Wege, T.2
Milani, S.3
Pellegrini, G.4
Orzechowski, H.5
Bechstein, W.6
Neuhaus, P.7
Schuppan, D.8
-
38
-
-
28844464258
-
Liver gene expression signature of mild fibrosis in patients with chronic hepatitis C
-
Asselah, T., Bìeche, I., Laurendeau, I., Paradis, V., Vidaud, D., Degott, C., Martinot, M., Bedossa, P., Valla, D., Vidaud, M. et al. (2005) Liver gene expression signature of mild fibrosis in patients with chronic hepatitis C. Gastroenterology, 129, 2064-2075.
-
(2005)
Gastroenterology
, vol.129
, pp. 2064-2075
-
-
Asselah, T.1
Bìeche, I.2
Laurendeau, I.3
Paradis, V.4
Vidaud, D.5
Degott, C.6
Martinot, M.7
Bedossa, P.8
Valla, D.9
Vidaud, M.10
-
39
-
-
84885962211
-
Evaluating statistical analysis models for RNA sequencing experiments
-
Reeb, P. and Steibel, J. (2013) Evaluating statistical analysis models for RNA sequencing experiments. Front. Genet., 4, 178 .
-
(2013)
Front. Genet.
, vol.4
, pp. 178
-
-
Reeb, P.1
Steibel, J.2
-
40
-
-
84879225342
-
Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data
-
Di, Y., Sarah, C.E., Daniel, W.S., Kimbrel, J.A. and Chang, J.H. (2013) Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data.Stat. App. Genet. Mol. Biol., 12 , 49-70 .
-
(2013)
Stat. App. Genet. Mol. Biol.
, vol.12
, pp. 49-70
-
-
Di, Y.1
Sarah, C.E.2
Daniel, W.S.3
Kimbrel, J.A.4
Chang, J.H.5
|