-
1
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Meth 5, 621-628 (2008).
-
(2008)
Nat Meth
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
2
-
-
78650539308
-
From RNA-seq reads to differential expression results
-
Oshlack, A., Robinson, M., Young, M. From RNA-seq reads to differential expression results. Genome Biol 11, 220 (2010).
-
(2010)
Genome Biol
, vol.11
, pp. 220
-
-
Oshlack, A.1
Robinson, M.2
Young, M.3
-
3
-
-
84888861753
-
Systematic evaluation of spliced alignment programs for RNA-seq data
-
Engström, P. G. et al. Systematic evaluation of spliced alignment programs for RNA-seq data. Nat. Methods 10, 1185-1191 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1185-1191
-
-
Engström, P.G.1
-
4
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956-960 (2008).
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
-
5
-
-
83855165105
-
Repetitive DNA and next-generation sequencing: Computational challenges and solutions
-
Treangen, T. J., Salzberg, S. L. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet. 13, 36-46 (2012).
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 36-46
-
-
Treangen, T.J.1
Salzberg, S.L.2
-
6
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure, J., Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145 (2008).
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
7
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber, M., Grabherr, M. G., Guttman, M., Trapnell, C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 8, 469-477 (2011).
-
(2011)
Nat. Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
8
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R36
-
-
Kim, D.1
-
9
-
-
77951820899
-
Fast and SNP-tolerant detection of complex variants and splicing in short reads
-
Wu, T. D., Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 873-881
-
-
Wu, T.D.1
Nacu, S.2
-
10
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H., Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinforma. Oxf. Engl. 25, 1754-1760 (2009).
-
(2009)
Bioinforma. Oxf. Engl.
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
11
-
-
78649345104
-
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
-
Wang, K. et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 38, e178-e178 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e178-e178
-
-
Wang, K.1
-
12
-
-
84940041597
-
-
(eds Baxevanis A. D. et al.) John Wiley & Sons
-
Jean, G., Kahles, A., Sreedharan, V. T., Bona, F. D., Rätsch, G. RNA-Seq Read Alignments with PALMapper in Current Protocols in Bioinformatics (eds Baxevanis, A. D. et al.) 11.6.1-11.6.37 (John Wiley & Sons, 2010).
-
(2010)
RNA-Seq Read Alignments with PALMapper in Current Protocols in Bioinformatics
, pp. 1161-11637
-
-
Jean, G.1
Kahles, A.2
Sreedharan, V.T.3
Bona, F.D.4
Rätsch, G.5
-
13
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
-
14
-
-
84870822864
-
Tools for mapping high-throughput sequencing data
-
Fonseca, N. A., Rung, J., Brazma, A., Marioni, J. C. Tools for mapping high-throughput sequencing data. Bioinformatics 28, 3169-3177 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 3169-3177
-
-
Fonseca, N.A.1
Rung, J.2
Brazma, A.3
Marioni, J.C.4
-
15
-
-
84869014474
-
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: A case study in Saccharomyces cerevisiae
-
Nookaew, I. et al. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res (2012). doi: 10.1093/nar/gks804
-
(2012)
Nucleic Acids Res
-
-
Nookaew, I.1
-
16
-
-
84891363223
-
Specificity control for read alignments using an artificial reference genome-guided false discovery rate
-
Giese, S. H., Zickmann, F., Renard, B. Y. Specificity control for read alignments using an artificial reference genome-guided false discovery rate. Bioinformatics 30, 9-16 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 9-16
-
-
Giese, S.H.1
Zickmann, F.2
Renard, B.Y.3
-
17
-
-
84908698716
-
Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses by RNA sequencing
-
Hoang, T., Raj Kumar, P. K., Sutharzan, S., Tsonis, P. A., Liang, C., Robinson, M. L. Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses by RNA sequencing. Mol. Vis. 20, 1491-1517 (2014).
-
(2014)
Mol. Vis.
, vol.20
, pp. 1491-1517
-
-
Hoang, T.1
Raj Kumar, P.K.2
Sutharzan, S.3
Tsonis, P.A.4
Liang, C.5
Robinson, M.L.6
-
18
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S., Huber, W. Differential expression analysis for sequence count data. Genome Biol 11, R106 (2010).
-
(2010)
Genome Biol
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
19
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014).
-
(2014)
Genome Biol
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
20
-
-
84872198346
-
Differential analysis of gene regulation at transcript resolution with RNA-seq
-
Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol 31, 46-53 (2013).
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 46-53
-
-
Trapnell, C.1
-
21
-
-
84862777104
-
RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings
-
Ren, S. et al. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Res. 22, 806-821 (2012).
-
(2012)
Cell Res.
, vol.22
, pp. 806-821
-
-
Ren, S.1
-
22
-
-
79961071855
-
Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes
-
Rowley, J. W. et al. Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes. Blood 118, e101-e111 (2011).
-
(2011)
Blood
, vol.118
, pp. e101-e111
-
-
Rowley, J.W.1
-
23
-
-
84964203940
-
Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy
-
Efron, B. Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Stat. Sci. 1, 54-75 (1986).
-
(1986)
Stat. Sci.
, vol.1
, pp. 54-75
-
-
Efron, B.1
-
24
-
-
84875391572
-
Ensembl 2013
-
Flicek, P. et al. Ensembl 2013. Nucleic Acids Res. 41, D48-D55 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D48-D55
-
-
Flicek, P.1
-
25
-
-
84860756398
-
Performance comparison of benchtop high-throughput sequencing platforms
-
Loman, N. J. et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol 30, 434-439 (2012).
-
(2012)
Nat. Biotechnol
, vol.30
, pp. 434-439
-
-
Loman, N.J.1
-
26
-
-
84875578097
-
Using Tablet for visual exploration of second-generation sequencing data
-
Milne, I. et al. Using Tablet for visual exploration of second-generation sequencing data. Brief. Bioinform. 14, 193-202 (2013).
-
(2013)
Brief. Bioinform.
, vol.14
, pp. 193-202
-
-
Milne, I.1
-
27
-
-
78651271733
-
Integrative genomics viewer
-
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24-26 (2011).
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
-
28
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
29
-
-
79952422304
-
Quality control and preprocessing of metagenomic datasets
-
Schmieder, R., Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 863-864
-
-
Schmieder, R.1
Edwards, R.2
|