-
1
-
-
84898618335
-
Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells
-
S. Zhao, W.-P. Fung-Leung, A. Bittner, K. Ngo, and X. Liu, "Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells", PLoS ONE, vol. 9, no. 1, Article ID e78644, 2014.
-
(2014)
PLoS ONE
, vol.9
, Issue.1
-
-
Zhao, S.1
Fung-Leung, W.-P.2
Bittner, A.3
Ngo, K.4
Liu, X.5
-
2
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
E. T. Wang, R. Sandberg, S. Luo et al., "Alternative isoform regulation in human tissue transcriptomes", Nature, vol. 456, no. 7221, pp. 470-476, 2008.
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
-
3
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Q. Pan, O. Shai, L. J. Lee, B. J. Frey, and B. J. Blencowe, "Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing", Nature Genetics, vol. 40, no. 12, pp. 1413-1415, 2008.
-
(2008)
Nature Genetics
, vol.40
, Issue.12
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.J.3
Frey, B.J.4
Blencowe, B.J.5
-
4
-
-
84892599763
-
Dispersion estimation and its effect on test performance in RNA-seq data analysis: A simulationbased comparison ofmethods
-
W. M. Landau and P. Liu, "Dispersion estimation and its effect on test performance in RNA-seq data analysis: a simulationbased comparison ofmethods", PLoS ONE, vol. 8, no. 12, Article ID e81415, 2013.
-
(2013)
PLoS ONE
, vol.8
, Issue.12
-
-
Landau, W.M.1
Liu, P.2
-
5
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, "Mapping and quantifying mammalian transcriptomes by RNA-Seq", Nature Methods, vol. 5, no. 7, pp. 621-628, 2008.
-
(2008)
Nature Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
6
-
-
65649126066
-
Transcript length bias in RNAseq data confounds systems biology
-
A. Oshlack and M. J. Wakefield, "Transcript length bias in RNAseq data confounds systems biology", Biology Direct, vol. 4, article 14, 2009.
-
(2009)
Biology Direct
, vol.4
-
-
Oshlack, A.1
Wakefield, M.J.2
-
7
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing
-
J. K. Pickrell, J. C. Marioni, A. A. Pai et al., "Understanding mechanisms underlying human gene expression variation with RNA sequencing", Nature, vol. 464, no. 7289, pp. 768-772, 2010.
-
(2010)
Nature
, vol.464
, Issue.7289
, pp. 768-772
-
-
Pickrell, J.K.1
Marioni, J.C.2
Pai, A.A.3
-
8
-
-
84934297887
-
-
Tech. Rep, Division of Biostatistics, University of California, Berkeley
-
D. Risso, K. Schwartz, G. Sherlock et al., "GC-content normalization for RNA-seq", Tech. Rep. 291, Division of Biostatistics, University of California, Berkeley, 2011.
-
(2011)
GC-content Normalization for RNA-seq
-
-
Risso, D.1
Schwartz, K.2
Sherlock, G.3
-
9
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in highthroughput data
-
J. T. Leek, R. B. Scharpf, H. C. Bravo et al., "Tackling the widespread and critical impact of batch effects in highthroughput data", Nature Reviews Genetics, vol. 11, no. 10, pp. 733-739, 2010.
-
(2010)
Nature Reviews Genetics
, vol.11
, Issue.10
, pp. 733-739
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
-
10
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
J. H. Bullard, E. Purdom, K. D. Hansen, and S. Dudoit, "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", BMC Bioinformatics, vol. 11, article 94, 2010.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Bullard, J.H.1
Purdom, E.2
Hansen, K.D.3
Dudoit, S.4
-
11
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
M. D. Robinson and A. Oshlack, "A scaling normalization method for differential expression analysis of RNA-seq data", Genome Biology, vol. 11, no. 3, article r25, 2010.
-
(2010)
Genome Biology
, vol.11
, Issue.3
-
-
Robinson, M.D.1
Oshlack, A.2
-
12
-
-
75249087100
-
EdgeR: A bioconductor package for differential expression analysis of digital gene expression data
-
M. D. Robinson, D. J. McCarthy, and G. K. Smyth, "EdgeR: a bioconductor package for differential expression analysis of digital gene expression data", Bioinformatics, vol. 26, no. 1, pp. 139-140, 2010.
-
(2010)
Bioinformatics
, vol.26
, Issue.1
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
13
-
-
77958471357
-
Differential expression analysis for sequence count data
-
S. Anders and W. Huber, "Differential expression analysis for sequence count data", Genome Biology, vol. 11, no. 10, article R106, 2010.
-
(2010)
Genome Biology
, vol.11
, Issue.10
-
-
Anders, S.1
Huber, W.2
-
14
-
-
84875593544
-
-
Tech. Rep, University of Wisconsin
-
N. Leng, J. Dawson, J. Thomson et al., "EBSeq: an empirical bayes hierarchical model for inference in RNA-seq experiments", Tech. Rep. 226, University of Wisconsin, 2012.
-
(2012)
EBSeq: An Empirical Bayes Hierarchical Model for Inference in RNA-seq Experiments
-
-
Leng, N.1
Dawson, J.2
Thomson, J.3
-
15
-
-
84863562292
-
Normalization, testing, and false discovery rate estimation for RNA-sequencing data
-
J. Li, D. M. Witten, I. M. Johnstone, and R. Tibshirani, "Normalization, testing, and false discovery rate estimation for RNA-sequencing data", Biostatistics, vol. 13, no. 3, pp. 523-538, 2012.
-
(2012)
Biostatistics
, vol.13
, Issue.3
, pp. 523-538
-
-
Li, J.1
Witten, D.M.2
Johnstone, I.M.3
Tibshirani, R.4
-
16
-
-
84860117771
-
Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer
-
Y. W. Asmann, B. M. Necela, K. R. Kalari et al., "Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer", Cancer Research, vol. 72, no. 8, pp. 1921-1928, 2012.
-
(2012)
Cancer Research
, vol.72
, Issue.8
, pp. 1921-1928
-
-
Asmann, Y.W.1
Necela, B.M.2
Kalari, K.R.3
-
17
-
-
77957920003
-
Polymorphic cisand Trans-Regulation of human gene expression
-
V. G. Cheung, R. R. Nayak, I. X. Wang et al., "Polymorphic cisand Trans-Regulation of human gene expression", PLoS Biology, vol. 8, no. 9, Article IDe1000480, 2010.
-
(2010)
PLoS Biology
, vol.8
, Issue.9
-
-
Cheung, V.G.1
Nayak, R.R.2
Wang, I.X.3
-
18
-
-
81055124271
-
Recount: A multiexperiment resource of analysis-ready RNA-seq gene count datasets
-
A. C. Frazee, B. Langmead, and J. T. Leek, "Recount: a multiexperiment resource of analysis-ready RNA-seq gene count datasets", BMC Bioinformatics, vol. 12, article 449, 2011.
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Frazee, A.C.1
Langmead, B.2
Leek, J.T.3
-
19
-
-
33645756842
-
Operational criteria for selecting a cDNA microarray data normalization algorithm
-
C. Argyropoulos, A. A. Chatziioannou, G. Nikiforidis, A. Moustakas, G. Kollias, and V. Aidinis, "Operational criteria for selecting a cDNA microarray data normalization algorithm", Oncology Reports, vol. 15, no. 4, pp. 983-996, 2006.
-
(2006)
Oncology Reports
, vol.15
, Issue.4
, pp. 983-996
-
-
Argyropoulos, C.1
Chatziioannou, A.A.2
Nikiforidis, G.3
Moustakas, A.4
Kollias, G.5
Aidinis, V.6
-
20
-
-
84880396139
-
Analysis of boutique arrays: A universal method for the selection of the optimal data normalization procedure
-
B. Uszczynska, J. Zyprych-Walczak, L. Handschuh et al., "Analysis of boutique arrays: a universal method for the selection of the optimal data normalization procedure", International Journal of Molecular Medicine, vol. 32, no. 3, pp. 668-684, 2013.
-
(2013)
International Journal of Molecular Medicine
, vol.32
, Issue.3
, pp. 668-684
-
-
Uszczynska, B.1
Zyprych-Walczak, J.2
Handschuh, L.3
-
21
-
-
27744557285
-
Selecting genes by test statistics
-
D. Chen, Z. Liu, X. Ma, and D. Hua, "Selecting genes by test statistics", Journal of Biomedicine and Biotechnology, vol. 2005, no. 2, pp. 132-138, 2005.
-
(2005)
Journal of Biomedicine and Biotechnology
, vol.2005
, Issue.2
, pp. 132-138
-
-
Chen, D.1
Liu, Z.2
Ma, X.3
Hua, D.4
-
22
-
-
84863304598
-
-
R Foundation for Statistical Computing, Vienna, Austria
-
R Development Core Team, R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, 2011.
-
(2011)
R: A Language and Environment for Statistical Computing
-
-
-
23
-
-
84899949862
-
Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues
-
M. Goswami, N. Hensel, B. D. Smith et al., "Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues", Leukemia, vol. 28, no. 5, pp. 1167-1170, 2014.
-
(2014)
Leukemia
, vol.28
, Issue.5
, pp. 1167-1170
-
-
Goswami, M.1
Hensel, N.2
Smith, B.D.3
-
24
-
-
84884416048
-
Human housekeeping genes, revisited
-
E. Eisenberg and E. Y. Levanon, "Human housekeeping genes, revisited", Trends in Genetics, vol. 29, no. 10, pp. 569-574, 2013.
-
(2013)
Trends in Genetics
, vol.29
, Issue.10
, pp. 569-574
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
25
-
-
84928199480
-
Comparison of software packages for detecting differential expression in RNAseq studies
-
F. Seyednasrollah, A. Laiho, and L. L. Elo, "Comparison of software packages for detecting differential expression in RNAseq studies", Briefings in Bioinformatics, vol. 16, no. 1, pp. 59-70, 2015.
-
(2015)
Briefings in Bioinformatics
, vol.16
, Issue.1
, pp. 59-70
-
-
Seyednasrollah, F.1
Laiho, A.2
Elo, L.L.3
-
26
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
-
M.-A. Dillies, A. Rau, J. Aubert et al., "A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis", Briefings in Bioinformatics, vol. 14, no. 6, pp. 671-683, 2013.
-
(2013)
Briefings in Bioinformatics
, vol.14
, Issue.6
, pp. 671-683
-
-
Dillies, M.-A.1
Rau, A.2
Aubert, J.3
-
27
-
-
84894069977
-
Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes
-
E. Maza, P. Frasse, P. Senin, M. Bouzayen, and M. Zouine, "Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: a matter of relative size of studied transcriptomes", Communicative & Integrative Biology, vol. 6, no. 6, Article ID e25849, 2013.
-
(2013)
Communicative & Integrative Biology
, vol.6
, Issue.6
-
-
Maza, E.1
Frasse, P.2
Senin, P.3
Bouzayen, M.4
Zouine, M.5
|