-
1
-
-
0037109192
-
Additivity in protein-DNA interactions: how good an approximation is it?
-
Benos P.V., Bulyk M.L., and Stormo G.D. Additivity in protein-DNA interactions: how good an approximation is it?. Nucleic Acids Res. 30 (2002) 4442-4451
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4442-4451
-
-
Benos, P.V.1
Bulyk, M.L.2
Stormo, G.D.3
-
2
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins statistical-mechanical theory and application to operators and promoters
-
Berg O.G., and von Hippel P.H. Selection of DNA binding sites by regulatory proteins statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193 (1987) 723-750
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 723-750
-
-
Berg, O.G.1
von Hippel, P.H.2
-
3
-
-
0023894726
-
Selection of DNA binding sites by regulatory proteins II. The binding specificity of cyclic AMP receptor protein to recognition sites
-
Berg O.G., and von Hippel P.H. Selection of DNA binding sites by regulatory proteins II. The binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol. 200 (1988) 709-723
-
(1988)
J. Mol. Biol.
, vol.200
, pp. 709-723
-
-
Berg, O.G.1
von Hippel, P.H.2
-
4
-
-
0034326362
-
Analysis of canonical and non-canonical splice sites in mammalian genomes
-
Burset M., Seledtsov A., and Solovyeva V.V. Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res. 28 (2000) 4364-4375
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4364-4375
-
-
Burset, M.1
Seledtsov, A.2
Solovyeva, V.V.3
-
5
-
-
17444380495
-
SpliceMachine: predicting splice sites from high-dimensional local context representations
-
Degroeve S., Saeys Y., Baets B.D., Rouzé P., and de Peer Y.V. SpliceMachine: predicting splice sites from high-dimensional local context representations. Bioinformatics 21 (2005) 1332-1338
-
(2005)
Bioinformatics
, vol.21
, pp. 1332-1338
-
-
Degroeve, S.1
Saeys, Y.2
Baets, B.D.3
Rouzé, P.4
de Peer, Y.V.5
-
6
-
-
19944433052
-
Gene and alternative splicing annotation with AIR
-
Florea L., Francesco V.D., Miller J., Turner R., Yao A., et al. Gene and alternative splicing annotation with AIR. Genome Res. 15 (2005) 54-66
-
(2005)
Genome Res.
, vol.15
, pp. 54-66
-
-
Florea, L.1
Francesco, V.D.2
Miller, J.3
Turner, R.4
Yao, A.5
-
7
-
-
0035252410
-
Alternative splicing: increasing diversity in the proteomic world
-
Graveley B.R. Alternative splicing: increasing diversity in the proteomic world. Trends Genet. 17 (2001) 100-107
-
(2001)
Trends Genet.
, vol.17
, pp. 100-107
-
-
Graveley, B.R.1
-
9
-
-
33746634756
-
An approach of encoding for prediction of splice sites using SVM
-
Huang J., Li T., Chen K., and Wu J. An approach of encoding for prediction of splice sites using SVM. Biochimie 88 (2006) 923-929
-
(2006)
Biochimie
, vol.88
, pp. 923-929
-
-
Huang, J.1
Li, T.2
Chen, K.3
Wu, J.4
-
10
-
-
11944266539
-
Information theory and statistical mechanics
-
Jaynes E.T. Information theory and statistical mechanics. Phys. Rev. 106 (1957) 620-630
-
(1957)
Phys. Rev.
, vol.106
, pp. 620-630
-
-
Jaynes, E.T.1
-
11
-
-
0347623371
-
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays
-
Johnson J.M., et al. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302 (2003) 2141-2144
-
(2003)
Science
, vol.302
, pp. 2141-2144
-
-
Johnson, J.M.1
-
12
-
-
0142245713
-
Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged
-
Kazan K. Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends Plant Sci. 8 (2003) 468-471
-
(2003)
Trends Plant Sci.
, vol.8
, pp. 468-471
-
-
Kazan, K.1
-
13
-
-
33846351302
-
Precise physical models of protein-DNA interaction from high-throughput data
-
Kinney J.B., Tkacik G., and Callan C.G. Precise physical models of protein-DNA interaction from high-throughput data. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 501-506
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 501-506
-
-
Kinney, J.B.1
Tkacik, G.2
Callan, C.G.3
-
14
-
-
20444470310
-
Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation
-
Kol G., Lev-Maor G., and Ast G. Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. Hum. Mol. Genet. 14 (2005) 1559-1568
-
(2005)
Hum. Mol. Genet.
, vol.14
, pp. 1559-1568
-
-
Kol, G.1
Lev-Maor, G.2
Ast, G.3
-
15
-
-
38449094866
-
From biophysics to evolutionary genetics: statistical aspects of gene regulation
-
Lässig M. From biophysics to evolutionary genetics: statistical aspects of gene regulation. BMC Bioinformatics 8 Suppl 6 (2007) S7
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 6
-
-
Lässig, M.1
-
16
-
-
35548985891
-
Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns
-
Lezon T.R., Banavar J.R., Cieplak M., Maritan A., and Fedoroff N.V. Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 19033-19038
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, pp. 19033-19038
-
-
Lezon, T.R.1
Banavar, J.R.2
Cieplak, M.3
Maritan, A.4
Fedoroff, N.V.5
-
17
-
-
0035949674
-
A computational analysis of sequence features involved in recognition of short introns
-
Lim L.P., and Burge C.B. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 11193-11198
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 11193-11198
-
-
Lim, L.P.1
Burge, C.B.2
-
18
-
-
0032435862
-
Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation
-
Lopez A.J. Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu. Rev. Genet. 32 (1998) 279-305
-
(1998)
Annu. Rev. Genet.
, vol.32
, pp. 279-305
-
-
Lopez, A.J.1
-
19
-
-
0036009859
-
Defining a 5′ splice site by functional selection in the presence and absence of U1 snRNA 5′ end
-
Lund M., and Kjems J. Defining a 5′ splice site by functional selection in the presence and absence of U1 snRNA 5′ end. RNA 8 (2002) 166-179
-
(2002)
RNA
, vol.8
, pp. 166-179
-
-
Lund, M.1
Kjems, J.2
-
21
-
-
0029058712
-
The maximum information principle and the evolution of nucleotide Sequences
-
Luo L.F., and Bai G.Y. The maximum information principle and the evolution of nucleotide Sequences. J. Theor. Biol. 174 (1995) 131-136
-
(1995)
J. Theor. Biol.
, vol.174
, pp. 131-136
-
-
Luo, L.F.1
Bai, G.Y.2
-
22
-
-
0036337915
-
A genomic view of alternative splicing
-
Modrek B., and Lee C. A genomic view of alternative splicing. Nature Genet. 30 (2002) 13-19
-
(2002)
Nature Genet.
, vol.30
, pp. 13-19
-
-
Modrek, B.1
Lee, C.2
-
23
-
-
0035393343
-
Genome-wide analysis of alternative splicing using human expressed sequence tags
-
Modrek B., Resch A., Grasso C., and Lee C. Genome-wide analysis of alternative splicing using human expressed sequence tags. Nucleic Acids Res. 29 (2001) 2850-2859
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2850-2859
-
-
Modrek, B.1
Resch, A.2
Grasso, C.3
Lee, C.4
-
24
-
-
0034256020
-
Alternative pre-mRNA splicing: the logic of combinatorial control
-
Smith C.W., and Valcárcel J. Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci. 25 (2000) 381-388
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 381-388
-
-
Smith, C.W.1
Valcárcel, J.2
-
25
-
-
42149137369
-
Accurate splice site prediction using support vector machines
-
Sonnenburg S., Schweikert G., Philips P., Behr J., and Rätsch G. Accurate splice site prediction using support vector machines. BMC Bioinformatics 8 Suppl 10 (2007) S7
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 10
-
-
Sonnenburg, S.1
Schweikert, G.2
Philips, P.3
Behr, J.4
Rätsch, G.5
-
26
-
-
0033010430
-
An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p
-
Staley J.P., and Guthrie C. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell 3 (1999) 55-64
-
(1999)
Mol. Cell
, vol.3
, pp. 55-64
-
-
Staley, J.P.1
Guthrie, C.2
-
27
-
-
33644878582
-
ASD: a bioinformatics resource on alternative splicing
-
Stamm S., Riethoven J., Le T.V., Gopalakrishnan C., Kumanduri V., Tang Y., Barbosa-Morais N.L., and Thanaraj T.A. ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res. 34 (2006) D46-D55
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Stamm, S.1
Riethoven, J.2
Le, T.V.3
Gopalakrishnan, C.4
Kumanduri, V.5
Tang, Y.6
Barbosa-Morais, N.L.7
Thanaraj, T.A.8
-
28
-
-
0348122177
-
Prediction and statistical analysis of alternatively splices exons
-
Thanaraj T.A., and Stamm S. Prediction and statistical analysis of alternatively splices exons. Prog. Mol. Subcell. Biol. 31 (2003) 1-31
-
(2003)
Prog. Mol. Subcell. Biol.
, vol.31
, pp. 1-31
-
-
Thanaraj, T.A.1
Stamm, S.2
-
29
-
-
0345865005
-
ASD: the alternative splicing database
-
Thanaraj T.A., Stamm S., Clark F., Riethoven J.J., Le T.V., and Muilu J. ASD: the alternative splicing database. Nucleic Acids Res. 32 (2004) D64-D69
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Thanaraj, T.A.1
Stamm, S.2
Clark, F.3
Riethoven, J.J.4
Le, T.V.5
Muilu, J.6
-
30
-
-
32544456772
-
Characterization and prediction of alternative splice sites
-
Wang M., and Marin A. Characterization and prediction of alternative splice sites. Gene 366 (2006) 219-227
-
(2006)
Gene
, vol.366
, pp. 219-227
-
-
Wang, M.1
Marin, A.2
-
31
-
-
33845660883
-
Identification of alternative 5′/3′ splice sites based on the mechanism of splice site competition
-
Xia H.Y., Bi J.N., and Li Y.D. Identification of alternative 5′/3′ splice sites based on the mechanism of splice site competition. Nucleic Acids Res. 34 (2006) 6305-6313
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 6305-6313
-
-
Xia, H.Y.1
Bi, J.N.2
Li, Y.D.3
-
32
-
-
39549106036
-
One parameter to describe the mechanism of splice sites competition
-
Yang W., and Li Q.Z. One parameter to describe the mechanism of splice sites competition. Biochem. Biophys. Res. Commun. 368 (2008) 379-381
-
(2008)
Biochem. Biophys. Res. Commun.
, vol.368
, pp. 379-381
-
-
Yang, W.1
Li, Q.Z.2
-
33
-
-
2442441507
-
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
-
Yeo G., and Burge C.B. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comp. Biol. 11 (2004) 377-394
-
(2004)
J. Comp. Biol.
, vol.11
, pp. 377-394
-
-
Yeo, G.1
Burge, C.B.2
-
34
-
-
0344874227
-
Splice site prediction with quadratic discriminant analysis using diversity measure
-
Zhang L.R., and Luo L.F. Splice site prediction with quadratic discriminant analysis using diversity measure. Nucleic Acids Res. 31 (2003) 6214-6220
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6214-6220
-
-
Zhang, L.R.1
Luo, L.F.2
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