-
1
-
-
67649876421
-
Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies
-
Ahmed, F. et al. (2009) Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies. In Silico Biol., 9, 135-148.
-
(2009)
Silico Biol.
, vol.9
, pp. 135-148
-
-
Ahmed, F.1
-
2
-
-
78349239707
-
Polyar, a new computer program for prediction of poly (A) sites in human sequences
-
Akhtar, M.N. et al. (2010) POLYAR, a new computer program for prediction of poly (A) sites in human sequences. BMC Genomics, 11, 646.
-
(2010)
BMC Genomics
, vol.11
, pp. 646
-
-
Akhtar, M.N.1
-
3
-
-
69549135202
-
To localize or not to localize: NRNA fate is in 30UTR ends
-
Andreassi, C. and Riccio, A. (2009) To localize or not to localize: NRNA fate is in 30UTR ends. Trends Cell Biol., 19, 465-474.
-
(2009)
Trends Cell Biol.
, vol.19
, pp. 465-474
-
-
Andreassi, C.1
Riccio, A.2
-
4
-
-
0034834248
-
Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data
-
Beaudoing, E. and Gautheret, D. (2001) Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res., 11, 1520-1526.
-
(2001)
Genome Res.
, vol.11
, pp. 1520-1526
-
-
Beaudoing, E.1
Gautheret, D.2
-
5
-
-
0033858202
-
Patterns of variant polyadenylation signal usage in human genes
-
Beaudoing, E., D et al. (2000) Patterns of variant polyadenylation signal usage in human genes. Genome Res., 10, 1001-10.
-
(2000)
Genome Res.
, vol.10
, pp. 1001-1010
-
-
Beaudoing, E.D.1
-
6
-
-
55449125185
-
Support vector machines and kernels for computational biology
-
Ben-Hur, A. et al. (2008) Support vector machines and kernels for computational biology. PLoS Comput. Biol., 4, e1000173.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Ben-Hur, A.1
-
7
-
-
75649102520
-
Sex-specific and lineage-specific alternative splicing in primates
-
Blekhman, R. et al. (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res., 20, 180-189.
-
(2010)
Genome Res.
, vol.20
, pp. 180-189
-
-
Blekhman, R.1
-
8
-
-
79955622645
-
Characterization and prediction of mRNA polyadenylation sites in human genes
-
Chang, T. et al. (2011) Characterization and prediction of mRNA polyadenylation sites in human genes. Med. Biol. Eng. Comput., 49, 1-10.
-
(2011)
Med. Biol. Eng. Comput.
, vol.49
, pp. 1-10
-
-
Chang, T.1
-
9
-
-
0029120391
-
Cleavage site determinants min the mammalian polydenylation signal
-
Chen, F. et al. (1995) Cleavage site determinants min the mammalian polydenylation signal. Nucleic Acids Res., 23, 2614-2620.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 2614-2620
-
-
Chen, F.1
-
10
-
-
33749997848
-
Prediction of mRNA polyadenylation sites by support vector machine
-
Cheng, Y. et al. (2006) Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics, 22, 2320-2325.
-
(2006)
Bioinformatics
, vol.22
, pp. 2320-2325
-
-
Cheng, Y.1
-
11
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks, G. et al. (2004) WebLogo: A sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.1
-
12
-
-
33645785104
-
A high-resolution map of transcription in the yeast genome
-
David, L. et al. (2006) A high-resolution map of transcription in the yeast genome. Proc. Natl Acad. Sci. USA, 103, 5320-5325.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 5320-5325
-
-
David, L.1
-
13
-
-
84861903786
-
A quantitative atlas of polyadenylation in five mammals
-
Derti, A. et al. (2012) A quantitative atlas of polyadenylation in five mammals. Genome Res., 22, 1173-1183.
-
(2012)
Genome Res.
, vol.22
, pp. 1173-1183
-
-
Derti, A.1
-
14
-
-
79955554179
-
Differential genome-wide profiling of tandem 30 UTRs among human breast cancer and normal cells by high-throughput sequencing
-
Fu, Y. et al. (2011) Differential genome-wide profiling of tandem 30 UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res., 21, 741-747.
-
(2011)
Genome Res.
, vol.21
, pp. 741-747
-
-
Fu, Y.1
-
15
-
-
3242672609
-
A probabilistic model of 30 end formation in caenorhabditis elegans
-
Hajarnavis, A. et al. (2004) A probabilistic model of 30 end formation in caenorhabditis elegans. Nucleic Acids Res., 32, 3392-3399.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3392-3399
-
-
Hajarnavis, A.1
-
16
-
-
25844497003
-
Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation
-
Hu, J. et al. (2005) Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA, 11, 1485-1493.
-
(2005)
RNA
, vol.11
, pp. 1485-1493
-
-
Hu, J.1
-
17
-
-
78650972252
-
Formation, regulation and evolution of caenorhabditis elegans 30 UTRs
-
Jan, C. et al. (2010) Formation, regulation and evolution of caenorhabditis elegans 30 UTRs. Nature, 469, 97-101.
-
(2010)
Nature
, vol.469
, pp. 97-101
-
-
Jan, C.1
-
18
-
-
77949538391
-
Reprogramming of 30 untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types
-
Ji, Z. and Tian, B. (2009) Reprogramming of 30 untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One, 4, 8419.
-
(2009)
PLoS One
, vol.4
, pp. 8419
-
-
Ji, Z.1
Tian, B.2
-
19
-
-
84855183279
-
Dragon polya spotter: Predictor of poly (A) motifs within human genomic DNA sequences
-
Kalkatawi, M. et al. (2012) Dragon polya spotter: Predictor of poly (A) motifs within human genomic DNA sequences. Bioinformatics, 28, 127-129.
-
(2012)
Bioinformatics
, vol.28
, pp. 127-129
-
-
Kalkatawi, M.1
-
20
-
-
0242292336
-
Sequence determinants in human polyadenylation site selection
-
Legendre, M. and Gautheret, D. (2003) Sequence determinants in human polyadenylation site selection. BMC Genomics, 4, 7.
-
(2003)
BMC Genomics
, vol.4
, pp. 7
-
-
Legendre, M.1
Gautheret, D.2
-
21
-
-
0036358995
-
The spectrum kernel: A string kernel for SVM protein classification
-
Leslie, C. et al. (2002) The spectrum kernel: A string kernel for SVM protein classification. Pac. Symp. Biocomput., 575, 564-575.
-
(2002)
Pac. Symp. Biocomput.
, vol.575
, pp. 564-575
-
-
Leslie, C.1
-
22
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
23
-
-
10044280127
-
An in-silico method for prediction of polyadenylation signals in human sequences
-
Liu, H. et al. (2003) An in-silico method for prediction of polyadenylation signals in human sequences. Genome Inform., 14, 84-93.
-
(2003)
Genome Inform.
, vol.14
, pp. 84-93
-
-
Liu, H.1
-
24
-
-
34347393301
-
Spatial preferences of microRNA targets in 30 untranslated regions
-
Majoros, W. and Ohler, U. (2007) Spatial preferences of microRNA targets in 30 untranslated regions. BMC Genomics, 8, 152.
-
(2007)
BMC Genomics
, vol.8
, pp. 152
-
-
Majoros, W.1
Ohler, U.2
-
25
-
-
77954847055
-
The landscape of C
-
Mangone, M. et al. (2010) The landscape of C. elegans 30 UTRs. Science, 329, 432-435.
-
(2010)
Elegans 30 UTRs. Science
, vol.329
, pp. 432-435
-
-
Mangone, M.1
-
26
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni, J. et al. (2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res., 18, 1509-1517.
-
(2008)
Genome Res.
, vol.18
, pp. 1509-1517
-
-
Marioni, J.1
-
27
-
-
68749113985
-
Widespread shortening of 30UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells
-
Mayr, C. and Bartel, D. (2009) Widespread shortening of 30UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell, 138, 673-684.
-
(2009)
Cell
, vol.138
, pp. 673-684
-
-
Mayr, C.1
Bartel, D.2
-
28
-
-
24644502657
-
From birth to death: The complex lives of eukaryotic mRNAs
-
Moore, M. (2005) From birth to death: The complex lives of eukaryotic mRNAs. Science, 309, 1514-1518.
-
(2005)
Science
, vol.309
, pp. 1514-1518
-
-
Moore, M.1
-
29
-
-
77954716355
-
A paired-end sequencing strategy to map the complex landscape of transcription initiation
-
Ni, T. et al. (2010) A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat. Methods, 7, 521-527.
-
(2010)
Nat. Methods
, vol.7
, pp. 521-527
-
-
Ni, T.1
-
30
-
-
77951977370
-
A functional human poly (a) site requires only a potent DSE and an a-rich upstream sequence
-
Nunes, N. et al. (2010) A functional human poly (a) site requires only a potent DSE and an a-rich upstream sequence. EMBO J., 29, 1523-1536.
-
(2010)
EMBO J.
, vol.29
, pp. 1523-1536
-
-
Nunes, N.1
-
31
-
-
78649910014
-
Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation
-
Ozsolak, F. et al. (2010) Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell, 143, 1018-1029.
-
(2010)
Cell
, vol.143
, pp. 1018-1029
-
-
Ozsolak, F.1
-
32
-
-
84861202208
-
The R development core team 2011 nlme: Linear and nonlinear mixed effects models R package version 3.1-102
-
Pinheiro, J. et al. (2011) The R development core team 2011 nlme: Linear and nonlinear mixed effects models. R package version 3.1-102. R Foundation for Statistical Computing, Vienna, Austria. http://cran.r-project.org/web/packages/ nlme/index.html.
-
(2011)
R Foundation for Statistical Computing, Vienna, Austria.
-
-
Pinheiro, J.1
-
34
-
-
29144512262
-
Rase: Recognition of alternatively spliced exons in C. elegans
-
Rätsch, G. et al. (2005) RASE: Recognition of alternatively spliced exons in C. elegans. Bioinformatics, 21 (Suppl. 1), i369-i377.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL.1
-
-
Rätsch, G.1
-
35
-
-
0030932502
-
Recognition of 30-processing sites of human mRNA precursors
-
Salamov, A. and Solovyev, V. (1997) Recognition of 30-processing sites of human mRNA precursors. Comp. Appl. Biosci., 13, 23-28.
-
(1997)
Comp. Appl. Biosci.
, vol.13
, pp. 23-28
-
-
Salamov, A.1
Solovyev, V.2
-
36
-
-
46249092601
-
Proliferating cells express mRNAs with shortened 30untranslated regions and fewer microRNA target sites
-
Sandberg, R. et al. (2008) Proliferating cells express mRNAs with shortened 30untranslated regions and fewer microRNA target sites. Science, 320, 1643-1647.
-
(2008)
Science
, vol.320
, pp. 1643-1647
-
-
Sandberg, R.1
-
37
-
-
32044442759
-
Promoter features related to tissue specificity as measured by shannon entropy
-
Schug, J. et al. (2005) Promoter features related to tissue specificity as measured by shannon entropy. Genome Biol., 6, R33.
-
(2005)
Genome Biol.
, vol.6
-
-
Schug, J.1
-
39
-
-
79953014914
-
Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq
-
Shepard, P. et al. (2011) Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA, 17, 761-772.
-
(2011)
RNA
, vol.17
, pp. 761-772
-
-
Shepard, P.1
-
40
-
-
59649122202
-
Molecular architecture of the human pre-mRNA 30 processing complex
-
Shi, Y. et al. (2009) Molecular architecture of the human pre-mRNA 30 processing complex. Mol. Cell, 33, 365-376.
-
(2009)
Mol. Cell
, vol.33
, pp. 365-376
-
-
Shi, Y.1
-
41
-
-
27544491192
-
Rocr: Visualizing classifier performance in r
-
Sing, T. et al. (2005) Rocr: Visualizing classifier performance in r. Bioinformatics, 21, 3940-3941.
-
(2005)
Bioinformatics
, vol.21
, pp. 3940-3941
-
-
Sing, T.1
-
42
-
-
33747871991
-
Arts: Accurate recognition of transcription starts in human
-
Sonnenburg, S. et al. (2006) Arts: Accurate recognition of transcription starts in human. Bioinformatics, 22, e472.
-
(2006)
Bioinformatics
, vol.22
-
-
Sonnenburg, S.1
-
43
-
-
42149137369
-
Accurate splice site prediction using support vector machines
-
Sonnenburg, S. et al. (2007) Accurate splice site prediction using support vector machines. BMC Bioinformatics, 8 (Suppl. 10), S7.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL.10
-
-
Sonnenburg, S.1
-
44
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey, JD. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
45
-
-
0033614456
-
Detection of polyadenylation signals in human DNA sequences
-
Tabaska, J. and Zhang, M. (1999) Detection of polyadenylation signals in human DNA sequences. Gene, 231, 77-86.
-
(1999)
Gene
, vol.231
, pp. 77-86
-
-
Tabaska, J.1
Zhang, M.2
-
46
-
-
84862526272
-
Signals for pre-mRNA cleavage and polyadenylation
-
Tian, B. and Graber, JH. (2012) Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip. Rev. RNA, 3, 385-396.
-
(2012)
Wiley Interdiscip Rev. RNA
, vol.3
, pp. 385-396
-
-
Tian, B.1
Graber, J.H.2
-
47
-
-
13744254695
-
A large-scale analysis of mRNA polyadenylation of human and mouse genes
-
Tian, B. et al. (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res., 33, 201-212.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 201-212
-
-
Tian, B.1
-
48
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang, E. et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.1
-
49
-
-
0037335613
-
Downstream elements of mammalian pre-mRNA polyadenylation signals: Primary, secondary and higher-order structures
-
Zarudnaya, M. et al. (2003) Downstream elements of mammalian pre-mRNA polyadenylation signals: Primary, secondary and higher-order structures. Nucleic Acids Res., 31, 1375-1386.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1375-1386
-
-
Zarudnaya, M.1
-
50
-
-
33646950851
-
Biased alternative polyadenylation in human tissues
-
Zhang, H. et al. (2005) Biased alternative polyadenylation in human tissues. Genome Biol., 6, R100.
-
(2005)
Genome Biol.
, vol.6
-
-
Zhang, H.1
-
51
-
-
13444302775
-
PolyA-DB: A database for mammalian mRNA polyadenylation
-
Zhang, H. et al. (2005) PolyA-DB: A database for mammalian mRNA polyadenylation. Nucleic Acids Res., 33 (Suppl. 1), D116-D120.
-
(2005)
Nucleic Acids Res.
, vol.33
, Issue.SUPPL.1
-
-
Zhang, H.1
|