-
2
-
-
77951940273
-
Modeling non-uniformity in short-read rates in RNA-Seq data
-
Li J, Jiang H, Wong WH. Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biology. 2010b:11
-
(2010)
Genome Biology
, pp. 11
-
-
Li, J.1
Jiang, H.2
Wong, W.H.3
-
3
-
-
57149085481
-
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
-
e141
-
Hoen PAC, Ariyurek Y, Thygesen HH, et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Research. 2008; 36:e141
-
(2008)
Nucleic Acids Research
, pp. 36
-
-
Hoen, P.A.C.1
Ariyurek, Y.2
Thygesen, H.H.3
-
5
-
-
77950640840
-
Analyzing' omics data using hierarchical models
-
Ji H, Liu XS. Analyzing' omics data using hierarchical models. Nature Biotechnology. 2010
-
(2010)
Nature Biotechnology
-
-
Ji, H.1
Liu, X.S.2
-
6
-
-
77955504378
-
Statistical design and analysis of RNA sequencing data
-
Auer PL, Doerge RW. Statistical design and analysis of RNA sequencing data. The Genetics Society of America. 2010;185:405-16.
-
(2010)
The Genetics Society of America
, vol.185
, pp. 405-416
-
-
Auer, P.L.1
Doerge, R.W.2
-
7
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, Schaefier L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008;5:621-8.
-
(2008)
Nature Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaefier, L.4
Wold, B.5
-
8
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology. 2010;11:3
-
(2010)
Genome Biology
, vol.11
, pp. 3
-
-
Robinson, M.D.1
Oshlack, A.2
-
9
-
-
68849123047
-
Methods for analyzing deep sequencing expression data: Constructing the human and mouse promoterome with deepCAGE data
-
Balwierz PJ, Carninci P, Daub CO, et al. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biology. 2009;10:7
-
(2009)
Genome Biology
, vol.10
, pp. 7
-
-
Balwierz, P.J.1
Carninci, P.2
Daub, C.O.3
-
10
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research. 2008;18:1509-17.
-
(2008)
Genome Research
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
11
-
-
36448981743
-
Moderated statistical tests for assessing differences in tag abundance
-
Robinson MD, Smyth GK. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics. 2007;23(21):2881-7.
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2881-2887
-
-
Robinson, M.D.1
Smyth, G.K.2
-
12
-
-
75249087100
-
edgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-40.
-
(2010)
Bioinformatics
, vol.26
, Issue.1
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
13
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
Bullard JH, Purdom EHKD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010:11
-
(2010)
BMC Bioinformatics
, pp. 11
-
-
Bullard, J.H.1
Purdom, E.H.K.D.2
Dudoit, S.3
-
14
-
-
84891909553
-
Transcript length bias in RNA-seq data confounds systems biology
-
Oshlack A, Wakefield MJ. Transcript length bias in RNA-seq data confounds systems biology. Biology Direct. 2010:4
-
(2010)
Biology Direct
, pp. 4
-
-
Oshlack, A.1
Wakefield, M.J.2
-
16
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biology. 2010;11:10
-
(2010)
Genome Biology
, vol.11
, pp. 10
-
-
Anders, S.1
Huber, W.2
-
18
-
-
78149495055
-
Empirical bayes analysis of sequencing-based transcriptional profiling without replicates
-
Wu Z, Jenkins BD, Rynearson TA, et al. Empirical bayes analysis of sequencing-based transcriptional profiling without replicates. BMC Bioinformatics. 2010:11
-
(2010)
BMC Bioinformatics
, pp. 11
-
-
Wu, Z.1
Jenkins, B.D.2
Rynearson, T.A.3
-
19
-
-
64549119707
-
Statistical inferences for isoform expression in RNASeq
-
Jian H, Wong WH. Statistical inferences for isoform expression in RNASeq. Bioinformatics. 2009;25:1026-32.
-
(2009)
Bioinformatics
, vol.25
, pp. 1026-1032
-
-
Jian, H.1
Wong, W.H.2
-
21
-
-
77949507153
-
RNA-Seq gene expression estimation with read mapping uncertainty
-
Li B, Ruotti V, Stewart R, Thomson J, Dewey C. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 2010a;26: 493-500.
-
(2010)
Bioinformatics
, vol.26
, pp. 493-500
-
-
Li, B.1
Ruotti, V.2
Stewart, R.3
Thomson, J.4
Dewey, C.5
-
22
-
-
62349130698
-
Ultrafast and memory-eficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-eficient alignment of short DNA sequences to the human genome. Genome Biology. 2009;10:R25
-
(2009)
Genome Biology
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
23
-
-
18744410117
-
Applications of beta-mixture models in bioinformatics
-
Ji Y, Wu C, Liu P, Coombes K. Applications of beta-mixture models in bioinformatics. Bioinformatics. 2005;21(9):2118-22.
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2118-2122
-
-
Ji, Y.1
Wu, C.2
Liu, P.3
Coombes, K.4
-
25
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia N, Ghaemmaghami S, Newman J, Weissman J. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324(5924):218-23.
-
(2009)
Science
, vol.324
, Issue.5924
, pp. 218-223
-
-
Ingolia, N.1
Ghaemmaghami, S.2
Newman, J.3
Weissman, J.4
-
27
-
-
4444235995
-
Detecting differential gene expression with a semiparametric hierarchical mixture method
-
Newton MA, Noueiry A, Sarkar D, Ahlquist P. detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics. 2004;5:155-76.
-
(2004)
Biostatistics
, vol.5
, pp. 155-176
-
-
Newton, M.A.1
Noueiry, A.2
Sarkar, D.3
Ahlquist, P.4
-
28
-
-
75249095274
-
DEGseq: An R package for identifying differentially expressed genes from RNA-seq data
-
Wang L, Feng Z, Wang X, Wang X, Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 2009a;26(1):136-8.
-
(2009)
Bioinformatics
, vol.26
, Issue.1
, pp. 136-138
-
-
Wang, L.1
Feng, Z.2
Wang, X.3
Wang, X.4
Zhang, X.5
-
30
-
-
80053590625
-
Incorporating biological information into linear models: A bayesian approach to the selection of pathways and genes
-
Stingo F, Chen Y, Tadesse M, Vannucci M. Incorporating biological information into linear models: a bayesian approach to the selection of pathways and genes. Annals of Applied Statistics. 2011
-
(2011)
Annals of Applied Statistics
-
-
Stingo, F.1
Chen, Y.2
Tadesse, M.3
Vannucci, M.4
-
31
-
-
20144364427
-
Experiments in stochastic computation for high-dimensional graphical models
-
Jones B, Carvalho C, Dobra A, Hans C, Carter C, West M. Experiments in stochastic computation for high-dimensional graphical models. Statistical Science. 2004;20:388-400
-
(2004)
Statistical Science
, vol.20
, pp. 388-400
-
-
Jones, B.1
Carvalho, C.2
Dobra, A.3
Hans, C.4
Carter, C.5
West, M.6
|