-
1
-
-
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
-
2
-
-
48549086654
-
Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study
-
Arikawa, E. et al. (2008) Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study. BMC Genomics, 9, 328.
-
(2008)
BMC Genomics
, vol.9
, pp. 328
-
-
Arikawa, E.1
-
3
-
-
79958115654
-
A two-stage Poisson model for testing RNA-seq data
-
Auer, P. and Doerge, R. (2011) A two-stage Poisson model for testing RNA-seq data. Stat. Appl. Genet. Mol. Biol., 10, 1-26.
-
(2011)
Stat. Appl. Genet. Mol. Biol.
, vol.10
, pp. 1-26
-
-
Auer, P.1
Doerge, R.2
-
4
-
-
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. B, 57, 289-300.
-
(1995)
J. R Stat. Soc. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
5
-
-
79953034289
-
Evaluating Gene Expression in C57BL/6J and DBA/2J mouse striatum using RNA-seq and microarrays
-
Bottomly, D. et al. (2011) Evaluating Gene Expression in C57BL/6J and DBA/2J mouse striatum using RNA-seq and microarrays. PloS One, 6, e17820.
-
(2011)
PloS One
, vol.6
-
-
Bottomly, D.1
-
6
-
-
84878001429
-
Extended moment series and the parameters of the negative binomial distribution
-
Bowman, K. (1984) Extended moment series and the parameters of the negative binomial distribution. Biometrics, 40, 249-252.
-
(1984)
Biometrics
, vol.40
, pp. 249-252
-
-
Bowman, K.1
-
7
-
-
79551584794
-
Conservation of an RNA regulatory map between Drosophila and mammals
-
Brooks, A. et al. (2011) Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res., 21, 193-202.
-
(2011)
Genome Res.
, vol.21
, pp. 193-202
-
-
Brooks, A.1
-
8
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments
-
Bullard, J. et al. (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.1
-
9
-
-
0003121342
-
Regression Analysis of Count Data
-
Cambridge University Press, Cambridge, UK
-
Cameron, A. and Trivedi, P. (1998) Regression Analysis of Count Data, Econometric Society Monograph (No. 30). Cambridge University Press, Cambridge, UK.
-
(1998)
Econometric Society Monograph (No. 30)
-
-
Cameron, A.1
Trivedi, P.2
-
10
-
-
0024601101
-
Estimation of the negative binomial parameter K by maximum quasi-likelihood
-
Clark, S. and Perry, J. (1989) Estimation of the negative binomial parameter K by maximum quasi-likelihood. Biometrics, 45, 309-316.
-
(1989)
Biometrics
, vol.45
, pp. 309-316
-
-
Clark, S.1
Perry, J.2
-
11
-
-
0041954178
-
-
National Institute of Standards and Technology 15 April 2013, date last accessed
-
Croarkin, C. and Tobias, P. (2006) NIST/SEMATECH e-Handbook of Statistical Methods. National Institute of Standards and Technology. http://www.itl.nist. gov/div898/handbook/(15 April 2013, date last accessed).
-
(2006)
NIST/SEMATECH E-Handbook of Statistical Methods
-
-
Croarkin, C.1
Tobias, P.2
-
12
-
-
81055124271
-
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets
-
Frazee, A. et al. (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.1
-
13
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber, M. et al. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods, 8, 469-477.
-
(2011)
Nat. Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
-
14
-
-
77957663917
-
Alternative expression analysis by RNA sequencing
-
Griffith, M. et al. (2010) Alternative expression analysis by RNA sequencing. Nature Methods, 7, 843-847.
-
(2010)
Nature Methods
, vol.7
, pp. 843-847
-
-
Griffith, M.1
-
15
-
-
77953018202
-
MRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain
-
Hammer, P. et al. (2010) mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain. Genome Res., 20, 847-860.
-
(2010)
Genome Res.
, vol.20
, pp. 847-860
-
-
Hammer, P.1
-
17
-
-
77955298482
-
BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
-
Hardcastle, T. andKelly, K. (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.1
Kelly, K.2
-
18
-
-
0001486499
-
Estimation with quadratic loss
-
University of California, June 20-July 30, 1960. University of California Press
-
James, W. and Stein, C. (1961) Estimation with quadratic loss. In: Proceedings of the fourth Berkeley Symposium on Mathematical Statistics and Probability Held at the Statistical Laboratory, University of California, June 20-July 30, 1960. University of California Press, p. 361.
-
(1961)
Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability Held at the Statistical Laboratory
, pp. 361
-
-
James, W.1
Stein, C.2
-
20
-
-
84863562292
-
Normalization, testing, and false discovery rate estimation for RNA-sequencing data
-
Li, J. et al. (2011) Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics, 13, 523-538.
-
(2011)
Biostatistics
, vol.13
, pp. 523-538
-
-
Li, J.1
-
21
-
-
84886557480
-
Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-seq data
-
Epub ahead of print, doi: 10.1177/0962280211428386, November 28, 2011]
-
Li, J. and Tibshirani, R. (2011) Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-seq data. Stat. Methods Med. Res., [Epub ahead of print, doi: 10.1177/0962280211428386, November 28, 2011].
-
(2011)
Stat. Methods Med. Res
-
-
Li, J.1
Tibshirani, R.2
-
22
-
-
34250370287
-
Maximum likelihood estimation of the negative binomial dispersion parameter for highly overdispersed data, with applications to infectious diseases
-
Lloyd-Smith, J. (2007) Maximum likelihood estimation of the negative binomial dispersion parameter for highly overdispersed data, with applications to infectious diseases. PLoS One, 2, e180.
-
(2007)
PLoS One
, vol.2
-
-
Lloyd-Smith, J.1
-
23
-
-
32344448950
-
Statistical practice in high-throughput screening data analysis
-
Malo, N. et al. (2006) Statistical practice in high-throughput screening data analysis. Nat. Biotechnol., 24, 167-175.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 167-175
-
-
Malo, N.1
-
24
-
-
52949096084
-
Next-generation DNA sequencing methods
-
Mardis, E. (2008) Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet., 9, 387-402.
-
(2008)
Annu. Rev. Genomics Hum. Genet.
, vol.9
, pp. 387-402
-
-
Mardis, E.1
-
25
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni, J. et al. (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.1
-
26
-
-
77649213364
-
How to understand the cell by breaking it: Network analysis of gene perturbation screens
-
Markowetz, F. (2010) How to understand the cell by breaking it: network analysis of gene perturbation screens. PLoS Comput. Biol., 6, e1000655.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Markowetz, F.1
-
27
-
-
84858041341
-
Differential expression analysis of multifactor RNA-seq experiments with respect to biological variation
-
McCarthy, D. et al. (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.1
-
29
-
-
72849144434
-
Sequencing technologies: The next generation
-
Metzker, M. (2009) Sequencing technologies: The next generation. Nat. Rev. Genetics, 11, 31-46.
-
(2009)
Nat. Rev. Genetics
, vol.11
, pp. 31-46
-
-
Metzker, M.1
-
30
-
-
78650539308
-
From RNA-seq reads to differential expression results
-
Oshlack, A. et al. (2010) From RNA-seq reads to differential expression results. Genome Biol., 11, 220.
-
(2010)
Genome Biol.
, vol.11
, pp. 220
-
-
Oshlack, A.1
-
31
-
-
33748491718
-
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project.Nat
-
Patterson, T. et al. (2006) Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project.Nat. Biotechnol., 24, 1140-1150.
-
(2006)
Biotechnol.
, vol.24
, pp. 1140-1150
-
-
Patterson, T.1
-
32
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
Pepke, S. et al. (2009) Computation for ChIP-seq and RNA-seq studies. Nat. Methods, 6, S22-S32.
-
(2009)
Nat. Methods
, vol.6
-
-
Pepke, S.1
-
33
-
-
0025047727
-
Maximum likelihood estimation for the negative binomial dispersion parameter
-
Piegorsch, W. (1990) Maximum likelihood estimation for the negative binomial dispersion parameter. Biometrics, 46, 863-867.
-
(1990)
Biometrics
, vol.46
, pp. 863-867
-
-
Piegorsch, W.1
-
35
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. et al. (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.1
-
36
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson, M. 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.1
Oshlack, A.2
-
37
-
-
36448981743
-
Moderated statistical tests for assessing differences in tag abundance
-
Robinson, M. and Smyth, G. (2007) Moderated statistical tests for assessing differences in tag abundance. Bioinformatics, 23, 2881-2887.
-
(2007)
Bioinformatics
, vol.23
, pp. 2881-2887
-
-
Robinson, M.1
Smyth, G.2
-
38
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements
-
Shi, L. et al. (2006) The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements. Nat. Biotechnol., 24, 1151-1161.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1151-1161
-
-
Shi, L.1
-
39
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Smyth, G. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, 3.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
, pp. 3
-
-
Smyth, G.1
-
41
-
-
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
-
42
-
-
0000813561
-
Inadmissibility of the usual estimator for the mean of a multivariate Normal distribution
-
University of California Press, Berkeley
-
Stein, C. (1956) Inadmissibility of the usual estimator for the mean of a multivariate Normal distribution. In: Proceedings of the Third Berkeley symposium on mathematical statistics and probability. Vol. 1, University of California Press, Berkeley, pp. 197-206.
-
(1956)
Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability.
, vol.1
, pp. 197-206
-
-
Stein, C.1
-
43
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
Sultan, M. et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321, 956-960.
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
-
44
-
-
20544477743
-
The Gamma-Poisson model as a statistical method to determine if micro-organisms are randomly distributed in a food matrix
-
Toft, N. et al. (2006) The Gamma-Poisson model as a statistical method to determine if micro-organisms are randomly distributed in a food matrix. Food Microbiol., 23, 90-94.
-
(2006)
Food Microbiol.
, vol.23
, pp. 90-94
-
-
Toft, N.1
-
45
-
-
77949536719
-
Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations
-
Tuch, B. et al. (2010) Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. PloS One, 5, e9317.
-
(2010)
PloS One
, vol.5
-
-
Tuch, B.1
-
46
-
-
75249095274
-
DEGseq: An R package for identifying differentially expressed genes from RNA-seq data
-
Wang, L. et al. (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.1
-
47
-
-
57749195712
-
RNA-seq: A revolutionary tool for transcriptomics
-
Wang, Z. et al. (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
-
48
-
-
0021612706
-
Multistage estimation compared with fixed-sample-size estimation of the negative binomial parameter k
-
Willson, L. et al. (1984) Multistage estimation compared with fixed-sample-size estimation of the negative binomial parameter k. Biometrics, 40, 109-117.
-
(1984)
Biometrics
, vol.40
, pp. 109-117
-
-
Willson, L.1
-
49
-
-
77957723086
-
Evaluation of gene expression data generated from expired Affymetrix GeneChip microarrays using MAQC reference RNA samples
-
Zhining, W. et al. (2010) Evaluation of gene expression data generated from expired Affymetrix GeneChip microarrays using MAQC reference RNA samples. BMC Bioinformatics, 11 (Suppl. 6), S10.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 6
-
-
Zhining, W.1
-
50
-
-
80053451880
-
A powerful and flexible approach to the analysis of RNA sequence count data
-
Zhou, Y. et al. (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.1
|