-
1
-
-
12344250822
-
Function of alternative splicing
-
Stamm, S., Ben-Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T.A. and Soreq, H. (2005) Function of alternative splicing. Gene, 344, 1-20.
-
(2005)
Gene
, vol.344
, pp. 1-20
-
-
Stamm, S.1
Ben-Ari, S.2
Rafalska, I.3
Tang, Y.4
Zhang, Z.5
Toiber, D.6
Thanaraj, T.A.7
Soreq, H.8
-
2
-
-
69049116283
-
Stochastic noise in splicing machinery
-
Melamud, E. and Moult, J. (2009) Stochastic noise in splicing machinery. Nucleic Acids Res., 37, 4873-4886.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4873-4886
-
-
Melamud, E.1
Moult, J.2
-
3
-
-
78650689920
-
Noisy splicing drives mRNA isoform diversity in human cells
-
Pickrell, J.K., Pai, A.A., Gilad, Y. and Pritchard, J.K. (2010) Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet., 6, e1001236.
-
(2010)
PLoS Genet.
, vol.6
-
-
Pickrell, J.K.1
Pai, A.A.2
Gilad, Y.3
Pritchard, J.K.4
-
4
-
-
80053027909
-
Functional consequences of developmentally regulated alternative splicing
-
Kalsotra, A. and Cooper, T.A. (2011) Functional consequences of developmentally regulated alternative splicing. Nat. Rev. Genet., 12, 715-729.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 715-729
-
-
Kalsotra, A.1
Cooper, T.A.2
-
5
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan, Q., Shai, O., Lee, L.J., Frey, B.J. and Blencowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
-
(2008)
Nat. Genet.
, vol.40
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.J.3
Frey, B.J.4
Blencowe, B.J.5
-
6
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P. and Burge, C.B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.F.7
Schroth, G.P.8
Burge, C.B.9
-
7
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber, M., Grabherr, M.G., Guttman, M. and Trapnell, C. (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
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
8
-
-
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
-
9
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
10
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J. and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
11
-
-
77954127002
-
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
-
Richard, H., Schulz, M., Sultan, M., Nürnberger, A., Schrinner, S., Balzereit, D., Dagand, E., Rasche, A., Lehrach, H., Vingron, M. et al. (2010) Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res., 38, e112.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Richard, H.1
Schulz, M.2
Sultan, M.3
Nürnberger, A.4
Schrinner, S.5
Balzereit, D.6
Dagand, E.7
Rasche, A.8
Lehrach, H.9
Vingron, M.10
-
12
-
-
84865527768
-
Detecting differential usage of exons from RNA-seq data
-
Anders, S., Reyes, A. and Huber, W. (2012) Detecting differential usage of exons from RNA-seq data. Genome Res., 22, 2008-2017.
-
(2012)
Genome Res.
, vol.22
, pp. 2008-2017
-
-
Anders, S.1
Reyes, A.2
Huber, W.3
-
13
-
-
78649714014
-
Analysis and design of RNA sequencing experiments for identifying isoform regulation
-
Katz, Y., Wang, E.T., Airoldi, E.M. and Burge, C.B. (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods, 7, 1009-1015.
-
(2010)
Nat. Methods
, vol.7
, pp. 1009-1015
-
-
Katz, Y.1
Wang, E.T.2
Airoldi, E.M.3
Burge, C.B.4
-
14
-
-
84860385776
-
MATS: A Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data
-
Shen, S., Park, J.W., Huang, J., Dittmar, K.A., Lu, Z.X., Zhou, Q., Carstens, R.P. and Xing, Y. (2012) MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res., 40, e61.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Shen, S.1
Park, J.W.2
Huang, J.3
Dittmar, K.A.4
Lu, Z.X.5
Zhou, Q.6
Carstens, R.P.7
Xing, Y.8
-
15
-
-
77957663917
-
Alternative expression analysis by RNA sequencing
-
Griffith, M., Griffith, O.L., Mwenifumbo, J., Goya, R., Morrissy, A.S., Morin, R.D., Corbett, R., Tang, M.J., Hou, Y.C., Pugh, T.J. et al. (2010) Alternative expression analysis by RNA sequencing. Nat. Methods, 7, 843-847.
-
(2010)
Nat. Methods
, vol.7
, pp. 843-847
-
-
Griffith, M.1
Griffith, O.L.2
Mwenifumbo, J.3
Goya, R.4
Morrissy, A.S.5
Morin, R.D.6
Corbett, R.7
Tang, M.J.8
Hou, Y.C.9
Pugh, T.J.10
-
16
-
-
27944446829
-
Detection and measurement of alternative splicing using splicing-sensitive microarrays
-
Srinivasan, K., Shiue, L., Hayes, J.D., Centers, R., Fitzwater, S., Loewen, R., Edmondson, L.R., Bryant, J., Smith, M., Rommelfanger, C. et al. (2005) Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods, 37, 345-359.
-
(2005)
Methods
, vol.37
, pp. 345-359
-
-
Srinivasan, K.1
Shiue, L.2
Hayes, J.D.3
Centers, R.4
Fitzwater, S.5
Loewen, R.6
Edmondson, L.R.7
Bryant, J.8
Smith, M.9
Rommelfanger, C.10
-
17
-
-
62249205133
-
Identifying differential exon splicing using linear models and correlation coefficients
-
Shah, S.H. and Pallas, J.A. (2009) Identifying differential exon splicing using linear models and correlation coefficients. BMC Bioinformatics, 10, 26.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 26
-
-
Shah, S.H.1
Pallas, J.A.2
-
18
-
-
75249101203
-
ARH: Predicting splice variants from genome-wide data with modified entropy
-
Rasche, A. and Herwig, R. (2009) ARH: predicting splice variants from genome-wide data with modified entropy. Bioinformatics, 26, 84-90.
-
(2009)
Bioinformatics
, vol.26
, pp. 84-90
-
-
Rasche, A.1
Herwig, R.2
-
19
-
-
84863203049
-
TGF-beta drives epithelial-mesenchymal transition through deltaEF1-mediated downregulation of ESRP
-
Horiguchi, K., Sakamoto, K., Koinuma, D., Semba, K., Inoue, A., Inoue, S., Fujii, H., Yamaguchi, A., Miyazawa, K., Miyazono, K. et al. (2012) TGF-beta drives epithelial-mesenchymal transition through deltaEF1-mediated downregulation of ESRP. Oncogene, 31, 3190-3201.
-
(2012)
Oncogene
, vol.31
, pp. 3190-3201
-
-
Horiguchi, K.1
Sakamoto, K.2
Koinuma, D.3
Semba, K.4
Inoue, A.5
Inoue, S.6
Fujii, H.7
Yamaguchi, A.8
Miyazawa, K.9
Miyazono, K.10
-
20
-
-
34547632484
-
Discovery of tissue-specific exons using comprehensive human exon microarrays
-
Clark, T.A., Schweitzer, A.C., Chen, T.X., Staples, M.K., Lu, G., Wang, H., Williams, A. and Blume, J.E. (2007) Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol., 8, R64.
-
(2007)
Genome Biol.
, vol.8
-
-
Clark, T.A.1
Schweitzer, A.C.2
Chen, T.X.3
Staples, M.K.4
Lu, G.5
Wang, H.6
Williams, A.7
Blume, J.E.8
-
21
-
-
34547922009
-
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing
-
Das, D., Clark, T.A., Schweitzer, A., Yamamoto, M., Marr, H., Arribere, J., Minovitsky, S., Poliakov, A., Dubchak, I., Blume, J.E. et al. (2007) A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res., 35, 4845-4857.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 4845-4857
-
-
Das, D.1
Clark, T.A.2
Schweitzer, A.3
Yamamoto, M.4
Marr, H.5
Arribere, J.6
Minovitsky, S.7
Poliakov, A.8
Dubchak, I.9
Blume, J.E.10
-
22
-
-
0034533608
-
An alternative-exon database and its statistical analysis
-
Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O. and Zhang, M.Q. (2000) An alternative-exon database and its statistical analysis. DNA Cell Biol., 19, 739-756.
-
(2000)
DNA Cell Biol.
, vol.19
, pp. 739-756
-
-
Stamm, S.1
Zhu, J.2
Nakai, K.3
Stoilov, P.4
Stoss, O.5
Zhang, M.Q.6
-
23
-
-
12344280017
-
Summaries of Affymetrix GeneChip probe level data
-
Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B. and Speed, T.P. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res., 31, e15.
-
(2003)
Nucleic Acids Res.
, vol.31
-
-
Irizarry, R.A.1
Bolstad, B.M.2
Collin, F.3
Cope, L.M.4
Hobbs, B.5
Speed, T.P.6
-
24
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
Shi, L., Reid, L.H., Jones, W.D., Shippy, R., Warrington, J.A., Baker, S.C., Collins, P.J., de Longueville, F., Kawasaki, E.S., Lee, K.Y. et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol., 24, 1151-1161.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1151-1161
-
-
Shi, L.1
Reid, L.H.2
Jones, W.D.3
Shippy, R.4
Warrington, J.A.5
Baker, S.C.6
Collins, P.J.7
De Longueville, F.8
Kawasaki, E.S.9
Lee, K.Y.10
-
25
-
-
75549089967
-
The UCSC Genome Browser database: Update 2010
-
Rhead, B., Karolchik, D., Kuhn, R.M., Hinrichs, A.S., Zweig, A.S., Fujita, P.A., Diekhans, M., Smith, K.E., Rosenbloom, K.R., Raney, B.J. et al. (2010) The UCSC Genome Browser database: update 2010. Nucleic Acids Res., 38, D613-D619.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Rhead, B.1
Karolchik, D.2
Kuhn, R.M.3
Hinrichs, A.S.4
Zweig, A.S.5
Fujita, P.A.6
Diekhans, M.7
Smith, K.E.8
Rosenbloom, K.R.9
Raney, B.J.10
-
26
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
27
-
-
77955443472
-
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
-
Au, K.F., Jiang, H., Lin, L., Xing, Y. and Wong, W.H. (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res., 38, 4570-4578.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 4570-4578
-
-
Au, K.F.1
Jiang, H.2
Lin, L.3
Xing, Y.4
Wong, W.H.5
-
28
-
-
78649345104
-
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
-
Wang, K., Singh, D., Zeng, Z., Coleman, S.J., Huang, Y., Savich, G.L., He, X., Mieczkowski, P., Grimm, S.A., Perou, C.M. et al. (2011) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res., 38, e178.
-
(2011)
Nucleic Acids Res.
, vol.38
-
-
Wang, K.1
Singh, D.2
Zeng, Z.3
Coleman, S.J.4
Huang, Y.5
Savich, G.L.6
He, X.7
Mieczkowski, P.8
Grimm, S.A.9
Perou, C.M.10
-
29
-
-
33644876924
-
Ensembl 2006
-
Birney, E., Andrews, D., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T. et al. (2006) Ensembl 2006. Nucleic Acids Res., 34, D556-D561.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Birney, E.1
Andrews, D.2
Caccamo, M.3
Chen, Y.4
Clarke, L.5
Coates, G.6
Cox, T.7
Cunningham, F.8
Curwen, V.9
Cutts, T.10
-
30
-
-
24044522270
-
BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis
-
Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., Moor, B.D., Brazma, A. and Huber, W. (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics, 21, 3439-3440.
-
(2005)
Bioinformatics
, vol.21
, pp. 3439-3440
-
-
Durinck, S.1
Moreau, Y.2
Kasprzyk, A.3
Davis, S.4
Moor, B.D.5
Brazma, A.6
Huber, W.7
-
31
-
-
9144269670
-
EnsMart: A generic system for fast and flexible access to biological data
-
Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T. and Birney, E. (2004) EnsMart: a generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.
-
(2004)
Genome Res.
, vol.14
, pp. 160-169
-
-
Kasprzyk, A.1
Keefe, D.2
Smedley, D.3
London, D.4
Spooner, W.5
Melsopp, C.6
Hammond, M.7
Rocca-Serra, P.8
Cox, T.9
Birney, E.10
-
32
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628.
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
33
-
-
84893488015
-
Fitdistrplus: Help to fit of a parametric distribution to non-censored or censored data
-
Delignette-Muller, M.L., Pouillot, R., Denis, J.-B. and Dutang, C. (2010) fitdistrplus: help to fit of a parametric distribution to non-censored or censored data. R package.
-
(2010)
R Package
-
-
Delignette-Muller, M.L.1
Pouillot, R.2
Denis, J.-B.3
Dutang, C.4
-
34
-
-
84906234545
-
Alternative transcript analysis methods for Exon Arrays v1.1
-
Affymetrix Inc.
-
Affymetrix, Inc. (2005)Alternative Transcript Analysis Methods for Exon Arrays v1.1, Technical Report.
-
(2005)
Technical Report
-
-
-
35
-
-
60049093585
-
ASTD: The alternative splicing and transcript diversity database
-
Koscielny, G., Texier, V.L., Gopalakrishnan, C., Kumanduri, V., Riethoven, J.-J., Nardone, F., Stanley, E., Fallsehr, C., Hofmann, O., Kull, M. et al. (2009) ASTD: the alternative splicing and transcript diversity database. Genomics, 93, 213-220.
-
(2009)
Genomics
, vol.93
, pp. 213-220
-
-
Koscielny, G.1
Texier, V.L.2
Gopalakrishnan, C.3
Kumanduri, V.4
Riethoven, J.-J.5
Nardone, F.6
Stanley, E.7
Fallsehr, C.8
Hofmann, O.9
Kull, M.10
-
36
-
-
0036798006
-
Signals and their transduction pathways regulating alternative splicing: A new dimension of the human genome
-
Stamm, S. (2002) Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome. Hum. Mol. Genet., 11, 2409-2416.
-
(2002)
Hum. Mol. Genet.
, vol.11
, pp. 2409-2416
-
-
Stamm, S.1
-
37
-
-
80052745094
-
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
-
Grant, G.R., Farkas, M.H., Pizarro, A.D., Lahens, N.F., Schug, J., Brunk, B.P., Stoeckert, C.J., Hogenesch, J.B. and Pierce, E.A. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics, 27, 2518-2528.
-
(2011)
Bioinformatics
, vol.27
, pp. 2518-2528
-
-
Grant, G.R.1
Farkas, M.H.2
Pizarro, A.D.3
Lahens, N.F.4
Schug, J.5
Brunk, B.P.6
Stoeckert, C.J.7
Hogenesch, J.B.8
Pierce, E.A.9
-
38
-
-
79959709133
-
Mason - A read simulator for second generation sequencing data
-
Holtgrewe, M. (2010) Mason-a read simulator for second generation sequencing data. Technical Report, FU Berlin.
-
(2010)
Technical Report, FU Berlin
-
-
Holtgrewe, M.1
-
39
-
-
27544491192
-
ROCR: Visualizing classifier performance in R
-
Sing, T., Sander, O., Beerenwinkel, N. and Lengauer, T. (2005) ROCR: visualizing classifier performance in R. Bioinformatics, 21, 3940-3941.
-
(2005)
Bioinformatics
, vol.21
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
40
-
-
0037453249
-
Identification of a variant form of PZR lacking immunoreceptor tyrosine-based inhibitory motifs
-
Zhao, R. and Zhao, Z.J. (2003) Identification of a variant form of PZR lacking immunoreceptor tyrosine-based inhibitory motifs. Biochem. Biophys. Res. Commun., 303, 1028-1033.
-
(2003)
Biochem. Biophys. Res. Commun.
, vol.303
, pp. 1028-1033
-
-
Zhao, R.1
Zhao, Z.J.2
-
41
-
-
0030681260
-
The significance of digital gene expression profiles
-
Audic, S. and Claverie, J.M. (1997) The significance of digital gene expression profiles. Genome Res., 7, 986-995.
-
(1997)
Genome Res.
, vol.7
, pp. 986-995
-
-
Audic, S.1
Claverie, J.M.2
-
42
-
-
41249097678
-
Experimental comparison and evaluation of the Affymetrix exon and U133Plus2 GeneChip arrays
-
Abdueva, D., Wing, M.R., Schaub, B. and Triche, T.J. (2007) Experimental comparison and evaluation of the Affymetrix exon and U133Plus2 GeneChip arrays. PLoS One, 2, e913.
-
(2007)
PLoS One
, vol.2
-
-
Abdueva, D.1
Wing, M.R.2
Schaub, B.3
Triche, T.J.4
|