-
1
-
-
84879408529
-
Alternative cleavage and polyadenylation: Extent, regulation and function
-
Elkon, R., Ugalde, A. P. & Agami, R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet. 14, 496-506 (2013).
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 496-506
-
-
Elkon, R.1
Ugalde, A.P.2
Agami, R.3
-
2
-
-
46249092601
-
Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer microRNA target sites
-
Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. & Burge, C. B. Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer microRNA target sites. Science 320, 1643-1647 (2008).
-
(2008)
Science
, vol.320
, pp. 1643-1647
-
-
Sandberg, R.1
Neilson, J.R.2
Sarma, A.3
Sharp, P.A.4
Burge, C.B.5
-
3
-
-
84861903786
-
A quantitative atlas of polyadenylation in five mammals
-
Derti, A. et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 22, 1173-1183 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1173-1183
-
-
Derti, A.1
-
4
-
-
13744254695
-
A large-scale analysis of mRNA polyadenylation of human and mouse genes
-
Tian, B., Hu, J., Zhang, H. & Lutz, C. S. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33, 201-212 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 201-212
-
-
Tian, B.1
Hu, J.2
Zhang, H.3
Lutz, C.S.4
-
5
-
-
31144448042
-
AU-rich elements and associated factors: Are there unifying principles?
-
Barreau, C., Paillard, L. & Osborne, H. B. AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res. 33, 7138-7150 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 7138-7150
-
-
Barreau, C.1
Paillard, L.2
Osborne, H.B.3
-
6
-
-
84887499256
-
Analysis of microRNA-target interactions across diverse cancer types
-
Jacobsen, A. et al. Analysis of microRNA-target interactions across diverse cancer types. Nat. Struct. Mol. Biol. 20, 1325-1332 (2013).
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 1325-1332
-
-
Jacobsen, A.1
-
7
-
-
0032246188
-
Levels of polyadenylation factor CstF-64 control IgM heavy chain mRNA accumulation and other events associated with B cell differentiation
-
Takagaki, Y. & Manley, J. L. Levels of polyadenylation factor CstF-64 control IgM heavy chain mRNA accumulation and other events associated with B cell differentiation. Mol. Cell 2, 761-771 (1998).
-
(1998)
Mol. Cell
, vol.2
, pp. 761-771
-
-
Takagaki, Y.1
Manley, J.L.2
-
8
-
-
68749113985
-
Widespread shortening of 30 UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells
-
Mayr, C. & Bartel, D. P. Widespread shortening of 30 UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673-684 (2009).
-
(2009)
Cell
, vol.138
, pp. 673-684
-
-
Mayr, C.1
Bartel, D.P.2
-
9
-
-
84863093448
-
E2F mediates enhanced alternative polyadenylation in proliferation
-
Elkon, R. et al. E2F mediates enhanced alternative polyadenylation in proliferation. Genome. Biol. 13, R59 (2012).
-
(2012)
Genome. Biol.
, vol.13
, pp. R59
-
-
Elkon, R.1
-
10
-
-
73649139638
-
Global changes in processing of mRNA 30 untranslated regions characterize clinically distinct cancer subtypes
-
Singh, P. et al. Global changes in processing of mRNA 30 untranslated regions characterize clinically distinct cancer subtypes. Cancer Res. 69, 9422-9430 (2009).
-
(2009)
Cancer Res.
, vol.69
, pp. 9422-9430
-
-
Singh, P.1
-
11
-
-
84866945388
-
Alternative cleavage and polyadenylation during colorectal cancer development
-
Morris, A. R. et al. Alternative cleavage and polyadenylation during colorectal cancer development. Clin. Cancer Res. 18, 5256-5266 (2012).
-
(2012)
Clin. Cancer Res.
, vol.18
, pp. 5256-5266
-
-
Morris, A.R.1
-
12
-
-
66049104920
-
Progressive lengthening of 30 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
-
Ji, Z., Lee, J. Y., Pan, Z., Jiang, B. & Tian, B. Progressive lengthening of 30 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl Acad. Sci. USA 106, 7028-7033 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 7028-7033
-
-
Ji, Z.1
Lee, J.Y.2
Pan, Z.3
Jiang, B.4
Tian, B.5
-
13
-
-
84873405541
-
Analysis of alternative cleavage and polyadenylation by 30 region extraction and deep sequencing
-
Hoque, M. et al. Analysis of alternative cleavage and polyadenylation by 30 region extraction and deep sequencing. Nat. Methods 10, 133-139 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 133-139
-
-
Hoque, M.1
-
14
-
-
84871582070
-
Genome-wide alternative polyadenylation in animals: Insights from high-throughput technologies
-
Sun, Y., Fu, Y., Li, Y. & Xu, A. Genome-wide alternative polyadenylation in animals: insights from high-throughput technologies. J. Mol. Cell Biol. 4, 352-361 (2012).
-
(2012)
J. Mol. Cell Biol.
, vol.4
, pp. 352-361
-
-
Sun, Y.1
Fu, Y.2
Li, Y.3
Xu, A.4
-
15
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing
-
Pickrell, J. K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768-772 (2010).
-
(2010)
Nature
, vol.464
, pp. 768-772
-
-
Pickrell, J.K.1
-
16
-
-
78649714014
-
Analysis and design of RNA sequencing experiments for identifying isoform regulation
-
Katz, Y., Wang, E. T., Airoldi, E. M. & Burge, C. B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009-1015 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 1009-1015
-
-
Katz, Y.1
Wang, E.T.2
Airoldi, E.M.3
Burge, C.B.4
-
17
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
-
18
-
-
84869036699
-
Modelling and simulating generic RNA-Seq experiments with the flux simulator
-
Griebel, T. et al. Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res. 40, 10073-10083 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 10073-10083
-
-
Griebel, T.1
-
19
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
Bullard, J. H., Purdom, E., Hansen, K. D. & Dudoit, S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11, 94 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 94
-
-
Bullard, J.H.1
Purdom, E.2
Hansen, K.D.3
Dudoit, S.4
-
20
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
-
Consortium, M. et al. The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 24, 1151-1161 (2006).
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1151-1161
-
-
Consortium, M.1
-
21
-
-
84877111454
-
Widespread and extensive lengthening of 30 UTRs in the mammalian brain
-
Miura, P., Shenker, S., Andreu-Agullo, C., Westholm, J. O. & Lai, E. C. Widespread and extensive lengthening of 30 UTRs in the mammalian brain. Genome Res. 23, 812-825 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 812-825
-
-
Miura, P.1
Shenker, S.2
Andreu-Agullo, C.3
Westholm, J.O.4
Lai, E.C.5
-
22
-
-
84867163995
-
Extensive alternative polyadenylation during zebrafish development
-
Ulitsky, I. et al. Extensive alternative polyadenylation during zebrafish development. Genome Res. 22, 2054-2066 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 2054-2066
-
-
Ulitsky, I.1
-
23
-
-
13444302775
-
Poly ADB: A database for mammalian mRNA polyadenylation
-
Zhang, H., Hu, J., Recce, M. & Tian, B. PolyA-DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res. 33, D116-D120 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. D116-D120
-
-
Zhang, H.1
Hu, J.2
Recce, M.3
Tian, B.4
-
24
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-W208 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W202-W208
-
-
Bailey, T.L.1
-
25
-
-
0033858202
-
Patterns of variant polyadenylation signal usage in human genes
-
Beaudoing, E., Freier, S., Wyatt, J. R., Claverie, J. M. & Gautheret, D. Patterns of variant polyadenylation signal usage in human genes. Genome Res. 10, 1001-1010 (2000).
-
(2000)
Genome Res.
, vol.10
, pp. 1001-1010
-
-
Beaudoing, E.1
Freier, S.2
Wyatt, J.R.3
Claverie, J.M.4
Gautheret, D.5
-
26
-
-
79958090979
-
DREME: Motif discovery in transcription factor ChIP-seq data
-
Bailey, T. L. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27, 1653-1659 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 1653-1659
-
-
Bailey, T.L.1
-
27
-
-
79953014914
-
Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq
-
Shepard, P. J. et al. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA 17, 761-772 (2011).
-
(2011)
RNA
, vol.17
, pp. 761-772
-
-
Shepard, P.J.1
-
28
-
-
84892833777
-
Discovery and saturation analysis of cancer genes across 21 tumour types
-
Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495-501 (2014).
-
(2014)
Nature
, vol.505
, pp. 495-501
-
-
Lawrence, M.S.1
-
29
-
-
0001646484
-
Cox's regression model for counting processes: A large sample study
-
Andersen, P. K. & Gill, R. D. Cox's regression model for counting processes: a large sample study. Ann. Statist. 1100-1120 (1982).
-
(1982)
Ann. Statist.
, pp. 1100-1120
-
-
Andersen, P.K.1
Gill, R.D.2
-
30
-
-
52649107626
-
Cancer cell metabolism: Warburg and beyond
-
Hsu, P. P. & Sabatini, D. M. Cancer cell metabolism: Warburg and beyond. Cell 134, 703-707 (2008).
-
(2008)
Cell
, vol.134
, pp. 703-707
-
-
Hsu, P.P.1
Sabatini, D.M.2
-
31
-
-
84856374900
-
Mitochondrial localization and structure-based phosphate activation mechanism of Glutaminase C with implications for cancer metabolism
-
Cassago, A. et al. Mitochondrial localization and structure-based phosphate activation mechanism of Glutaminase C with implications for cancer metabolism. Proc. Natl Acad. Sci. USA 109, 1092-1097 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 1092-1097
-
-
Cassago, A.1
-
32
-
-
0033661413
-
Identification of two human glutaminase loci and tissue-specific expression of the two related genes
-
Aledo, J. C., Gomez-Fabre, P. M., Olalla, L. & Marquez, J. Identification of two human glutaminase loci and tissue-specific expression of the two related genes. Mamm. Genome 11, 1107-1110 (2000).
-
(2000)
Mamm. Genome
, vol.11
, pp. 1107-1110
-
-
Aledo, J.C.1
Gomez-Fabre, P.M.2
Olalla, L.3
Marquez, J.4
-
33
-
-
64949158435
-
A novel glutaminase isoform in mammalian tissues
-
de la Rosa, V. et al. A novel glutaminase isoform in mammalian tissues. Neurochem. Int. 55, 76-84 (2009).
-
(2009)
Neurochem. Int.
, vol.55
, pp. 76-84
-
-
De La Rosa, V.1
-
34
-
-
0033620972
-
Cloning and analysis of unique human glutaminase isoforms generated by tissue-specific alternative splicing
-
Elgadi, K. M., Meguid, R. A., Qian, M., Souba, W. W. & Abcouwer, S. F. Cloning and analysis of unique human glutaminase isoforms generated by tissue-specific alternative splicing. Physiol. Genomics 1, 51-62 (1999).
-
(1999)
Physiol. Genomics
, vol.1
, pp. 51-62
-
-
Elgadi, K.M.1
Meguid, R.A.2
Qian, M.3
Souba, W.W.4
Abcouwer, S.F.5
-
35
-
-
64749116346
-
C-Myc suppression of miR-23a/b enhances mitochondrial glutaminase expression and glutamine metabolism
-
Gao, P. et al. c-Myc suppression of miR-23a/b enhances mitochondrial glutaminase expression and glutamine metabolism. Nature 458, 762-765 (2009).
-
(2009)
Nature
, vol.458
, pp. 762-765
-
-
Gao, P.1
-
36
-
-
84867130104
-
Analysis of glutamine dependency in non-small cell lung cancer: GLS1 splice variant GAC is essential for cancer cell growth
-
van den Heuvel, A. P., Jing, J., Wooster, R. F. & Bachman, K. E. Analysis of glutamine dependency in non-small cell lung cancer: GLS1 splice variant GAC is essential for cancer cell growth. Cancer Biol. Ther. 13, 1185-1194 (2012).
-
(2012)
Cancer Biol. Ther.
, vol.13
, pp. 1185-1194
-
-
Van Den Heuvel, A.P.1
Jing, J.2
Wooster, R.F.3
Bachman, K.E.4
-
37
-
-
80055009292
-
A germline variant in the TP53 polyadenylation signal confers cancer susceptibility
-
Stacey, S. N. et al. A germline variant in the TP53 polyadenylation signal confers cancer susceptibility. Nat. Genet. 43, 1098-1103 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 1098-1103
-
-
Stacey, S.N.1
-
38
-
-
34249723211
-
Point mutations and genomic deletions in CCND1 create stable truncated cyclin D1 mRNAs that are associated with increased proliferation rate and shorter survival
-
Wiestner, A. et al. Point mutations and genomic deletions in CCND1 create stable truncated cyclin D1 mRNAs that are associated with increased proliferation rate and shorter survival. Blood 109, 4599-4606 (2007).
-
(2007)
Blood
, vol.109
, pp. 4599-4606
-
-
Wiestner, A.1
-
39
-
-
80052979140
-
Mechanisms and consequences of alternative polyadenylation
-
Di Giammartino, D. C., Nishida, K. & Manley, J. L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853-866 (2011).
-
(2011)
Mol. Cell
, vol.43
, pp. 853-866
-
-
Di Giammartino, D.C.1
Nishida, K.2
Manley, J.L.3
-
40
-
-
84869765539
-
Alternative polyadenylation: New insights from global analyses
-
Shi, Y. Alternative polyadenylation: new insights from global analyses. RNA 18, 2105-2117 (2012).
-
(2012)
RNA
, vol.18
, pp. 2105-2117
-
-
Shi, Y.1
-
41
-
-
59649122202
-
Molecular architecture of the human pre-mRNA 30 processing complex
-
Shi, Y. et al. Molecular architecture of the human pre-mRNA 30 processing complex. Mol. Cell 33, 365-376 (2009).
-
(2009)
Mol. Cell
, vol.33
, pp. 365-376
-
-
Shi, Y.1
-
42
-
-
84863093884
-
Genome-wide analysis of pre-mRNA 30 end processing reveals a decisive role of human cleavage factor i in the regulation of 30 UTR length
-
Martin, G., Gruber, A. R., Keller, W. & Zavolan, M. Genome-wide analysis of pre-mRNA 30 end processing reveals a decisive role of human cleavage factor I in the regulation of 30 UTR length. Cell Rep. 1, 753-763 (2012).
-
(2012)
Cell Rep.
, vol.1
, pp. 753-763
-
-
Martin, G.1
Gruber, A.R.2
Keller, W.3
Zavolan, M.4
-
43
-
-
84869228761
-
Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation
-
Yao, C. et al. Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc. Natl Acad. Sci. USA 109, 18773-18778 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 18773-18778
-
-
Yao, C.1
-
44
-
-
84905004288
-
A change-point model for identifying 30 UTR switching by next-generation RNA sequencing
-
Wang, W., Wei, Z. & Li, H. A change-point model for identifying 30 UTR switching by next-generation RNA sequencing. Bioinformatics 30, 2162-2170 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2162-2170
-
-
Wang, W.1
Wei, Z.2
Li, H.3
-
45
-
-
84866910243
-
An in-depth map of polyadenylation sites in cancer
-
Lin, Y. et al. An in-depth map of polyadenylation sites in cancer. Nucleic Acids Res. 40, 8460-8471 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 8460-8471
-
-
Lin, Y.1
-
46
-
-
84887084951
-
Network-based stratification of tumor mutations
-
Hofree, M., Shen, J. P., Carter, H., Gross, A. & Ideker, T. Network-based stratification of tumor mutations. Nat. Methods 10, 1108-1115 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1108-1115
-
-
Hofree, M.1
Shen, J.P.2
Carter, H.3
Gross, A.4
Ideker, T.5
-
47
-
-
84903129276
-
CFIm25 links alternative polyadenylation to glioblastoma tumour suppression
-
Masamha, C. P. et al. CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature 509, 412-416 (2014).
-
(2014)
Nature
, vol.509
, pp. 412-416
-
-
Masamha, C.P.1
-
48
-
-
84875490185
-
Cancer genome landscapes
-
Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558 (2013).
-
(2013)
Science
, vol.339
, pp. 1546-1558
-
-
Vogelstein, B.1
-
49
-
-
77954302477
-
R Quant.web: A tool for RNA-Seq-based transcript quantitation
-
Bohnert, R. & Ratsch, G. rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res. 38, W348-W351 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W348-W351
-
-
Bohnert, R.1
Ratsch, G.2
-
50
-
-
77951940273
-
Modeling non-uniformity in short-read rates in RNA-Seq data
-
Li, J., Jiang, H. & Wong, W. H. Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol. 11, R50 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R50
-
-
Li, J.1
Jiang, H.2
Wong, W.H.3
-
51
-
-
77950537175
-
Regularization paths for generalized linear models via coordinate descent
-
Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33, 1-22 (2010).
-
(2010)
J. Stat. Softw.
, vol.33
, pp. 1-22
-
-
Friedman, J.1
Hastie, T.2
Tibshirani, R.3
-
52
-
-
34250805982
-
MicroRNA targeting specificity in mammals: Determinants beyond seed pairing
-
Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91-105 (2007).
-
(2007)
Mol. Cell
, vol.27
, pp. 91-105
-
-
Grimson, A.1
-
53
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005).
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
54
-
-
14044251458
-
Human MicroRNA targets
-
John, B. et al. Human MicroRNA targets. PLoS Biol. 2, e363 (2004).
-
(2004)
PLoS Biol.
, vol.2
, pp. e363
-
-
John, B.1
-
55
-
-
75249087100
-
Edge R: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
|