-
1
-
-
84861694712
-
Differential GC content between exons and introns establishes distinct strategies of splice-site recognition
-
Amit,M. et al. (2012) Differential GC content between exons and introns establishes distinct strategies of splice-site recognition. Cell Reports, 1, 543-556.
-
(2012)
Cell Reports
, vol.1
, pp. 543-556
-
-
Amit, M.1
-
2
-
-
84861963461
-
DoRiNA: A database of RNA interactions in post-transcriptional regulation
-
Anders,G. et al. (2012) doRiNA: A database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res., 40, D180-D186.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D180-D186
-
-
Anders, G.1
-
3
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
Ashburner,M. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
4
-
-
48949103996
-
A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation
-
Aznarez,I. et al. (2008) A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res., 18, 1247-1258.
-
(2008)
Genome Res.
, vol.18
, pp. 1247-1258
-
-
Aznarez, I.1
-
5
-
-
84892821162
-
Transcriptome-wide discovery of microRNA binding sites in human brain
-
Boudreau,R.L. et al. (2014) Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron, 81, 294-305.
-
(2014)
Neuron
, vol.81
, pp. 294-305
-
-
Boudreau, R.L.1
-
6
-
-
1642529511
-
Metagenes and molecular pattern discovery using matrix factorization
-
Brunet,J.P. et al. (2004) Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. U.S.A., 101, 4164-4169.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 4164-4169
-
-
Brunet, J.P.1
-
7
-
-
33645794993
-
Biclustering of gene expression data by nonsmooth non-negative matrix factorization
-
Carmona-Saez, P. et al. (2006) Biclustering of gene expression data by nonsmooth non-negative matrix factorization. BMC Bioinf, 7, 1-18.
-
(2006)
BMC Bioinf
, vol.7
, pp. 1-18
-
-
Carmona-Saez, P.1
-
8
-
-
84861969926
-
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins
-
Castello,A. et al. (2012) Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell, 149, 1393-1406.
-
(2012)
Cell
, vol.149
, pp. 1393-1406
-
-
Castello, A.1
-
9
-
-
84922392412
-
CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3 processing
-
Chan,S.L. et al. (2014) CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3 processing. Genes Dev., 28, 2370-2380.
-
(2014)
Genes Dev.
, vol.28
, pp. 2370-2380
-
-
Chan, S.L.1
-
10
-
-
0003729218
-
-
John Wiley & Sons, Inc., Hoboken, New Jersey 07030-075774, USA
-
Chatterjee,S. et al. (2015). Regression Analysis by Example. John Wiley & Sons, Inc., Hoboken, New Jersey, 07030-5774 USA.
-
(2015)
Regression Analysis by Example
-
-
Chatterjee, S.1
-
11
-
-
84873723387
-
Predictions of protein-RNA interactions
-
Cirillo,D. et al. (2013) Predictions of protein-RNA interactions. Comp. Mol. Sci., 3, 161-175.
-
(2013)
Comp. Mol. Sci.
, vol.3
, pp. 161-175
-
-
Cirillo, D.1
-
12
-
-
84880312659
-
RNA protein interaction in neurons
-
Darnell,R.B. (2013) RNA protein interaction in neurons. Annu. Rev. Neurosci., 36, 243-270.
-
(2013)
Annu. Rev. Neurosci.
, vol.36
, pp. 243-270
-
-
Darnell, R.B.1
-
13
-
-
29644438050
-
Statistical comparisons of classifiers over multiple data sets
-
Demšar,J. (2006) Statistical comparisons of classifiers over multiple data sets. J. Mach. Learn. Res, 7, 1-30.
-
(2006)
J. Mach. Learn. Res
, vol.7
, pp. 1-30
-
-
Demšar, J.1
-
14
-
-
0027330888
-
Using RNAFOLD to predict the activity of small catalytic RNAs
-
Denman,R.B. (1993) Using RNAFOLD to predict the activity of small catalytic RNAs. BioTechniques, 15, 1090-1095.
-
(1993)
BioTechniques
, vol.15
, pp. 1090-1095
-
-
Denman, R.B.1
-
15
-
-
84871429429
-
Computational biology of RNA interactions
-
Dieterich,C. et al. (2013) Computational biology of RNA interactions. Wiley Interdisc. Rev. RNA, 4, 107-120.
-
(2013)
Wiley Interdisc. Rev. RNA
, vol.4
, pp. 107-120
-
-
Dieterich, C.1
-
16
-
-
33749575326
-
Orthogonal nonnegative matrix t-factorizations for clustering
-
Ding, C. et al. (2006). Orthogonal nonnegative matrix t-factorizations for clustering. In: Proceedings of the 12th ACM SIGKDD.
-
(2006)
Proceedings of the 12th ACM SIGKDD
-
-
Ding, C.1
-
17
-
-
84871617105
-
Convex and semi-nonnegative matrix factorizations
-
Ding,C. et al. (2010) Convex and semi-nonnegative matrix factorizations. IEEE Trans. Pattern Anal. Mach. Intell., 32, 45-55.
-
(2010)
IEEE Trans. Pattern Anal. Mach. Intell.
, vol.32
, pp. 45-55
-
-
Ding, C.1
-
18
-
-
27744601822
-
Improving molecular cancer class discovery through sparse non-negative matrix factorization
-
Gao,Y. et al. (2005) Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics, 21, 3970-3975.
-
(2005)
Bioinformatics
, vol.21
, pp. 3970-3975
-
-
Gao, Y.1
-
19
-
-
84865442402
-
Online nonnegative matrix factorization with robust stochastic approximation
-
Guan,N. et al. (2012) Online nonnegative matrix factorization with robust stochastic approximation. IEEE Trans. Neural Netw. Learn. Syst., 23, 1087-1099.
-
(2012)
IEEE Trans. Neural Netw. Learn. Syst.
, vol.23
, pp. 1087-1099
-
-
Guan, N.1
-
20
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner,M. et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 141, 129-141.
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
-
21
-
-
82955236089
-
RNA targets of wild-type and mutant FET family proteins
-
Hoell,J.I. et al. (2011) RNA targets of wild-type and mutant FET family proteins. Nat. Struct. Mol. Biol., 18, 1428-1431.
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 1428-1431
-
-
Hoell, J.I.1
-
22
-
-
84900510076
-
Non-negative matrix factorization with sparseness constraints
-
Hoyer,P.O. (2004) Non-negative matrix factorization with sparseness constraints. J. Mach. Learn. Res, 5, 1457-1469.
-
(2004)
J. Mach. Learn. Res
, vol.5
, pp. 1457-1469
-
-
Hoyer, P.O.1
-
23
-
-
18444402182
-
The Ensembl genome database project
-
Hubbard,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 38-41
-
-
Hubbard, T.1
-
24
-
-
84880791572
-
NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs
-
Hussain,S. et al. (2013) NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep., 4, 255-261.
-
(2013)
Cell Rep.
, vol.4
, pp. 255-261
-
-
Hussain, S.1
-
25
-
-
56649100783
-
Position-dependent motif characterization using non-negative matrix factorization
-
Hutchins,L.N. et al. (2008) Position-dependent motif characterization using non-negative matrix factorization. Bioinformatics, 24, 2684-2690.
-
(2008)
Bioinformatics
, vol.24
, pp. 2684-2690
-
-
Hutchins, L.N.1
-
26
-
-
84924330592
-
Competition between target sites of regulators shapes post-transcriptional gene regulation
-
Jens,M. et al. (2015) Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat. Rev. Genet., 16, 113-126.
-
(2015)
Nat. Rev. Genet.
, vol.16
, pp. 113-126
-
-
Jens, M.1
-
28
-
-
78049275913
-
RNAcontext: A new method for learning the sequence and structure binding preferences of RNA-binding proteins
-
1-10
-
Kazan,H. et al. (2010) RNAcontext: A new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput. Biol., 6, e1000832: 1-10.
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. e1000832
-
-
Kazan, H.1
-
29
-
-
34547844077
-
Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis
-
Kim,H. et al. (2007) Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis. Bioinformatics, 23, 1495-1502.
-
(2007)
Bioinformatics
, vol.23
, pp. 1495-1502
-
-
Kim, H.1
-
30
-
-
79959813870
-
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins
-
Kishore,S. et al. (2011) A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat. Methods, 8, 559-564.
-
(2011)
Nat. Methods
, vol.8
, pp. 559-564
-
-
Kishore, S.1
-
31
-
-
84901297233
-
The cleverSuite approach for protein characterization: Predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities
-
Klus,P. et al. (2014) The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities. Bioinformatics, 30, 1601-1608.
-
(2014)
Bioinformatics
, vol.30
, pp. 1601-1608
-
-
Klus, P.1
-
32
-
-
77954387023
-
ICLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
-
König,J. et al. (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol., 17, 909-915.
-
(2010)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 909-915
-
-
König, J.1
-
33
-
-
84898964201
-
Algorithms for non-negative matrix factorization
-
Lee,D.D.D. et al. (2001) Algorithms for non-negative matrix factorization. Adv. NIPS, 548-562.
-
(2001)
Adv. NIPS
, pp. 548-562
-
-
Lee, D.D.D.1
-
34
-
-
77952687104
-
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure
-
Li,X. et al. (2010) Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA, 1096-1107. pages
-
(2010)
RNA
, pp. 1096-1107
-
-
Li, X.1
-
35
-
-
35548969471
-
Projected gradient methods for nonnegative matrix factorization
-
Lin,C.J. (2007) Projected gradient methods for nonnegative matrix factorization. Neural Comput., 19, 2756-2779.
-
(2007)
Neural Comput.
, vol.19
, pp. 2756-2779
-
-
Lin, C.J.1
-
36
-
-
84900394210
-
Protein-specific prediction of mRNA binding using RNA sequences, bindingmotifs and pred. Secondary structures
-
Livi,C. et al. (2014) Protein-specific prediction of mRNA binding using RNA sequences, bindingmotifs and pred. secondary structures.BMC Bioinf., 15, 123.
-
(2014)
BMC Bioinf.
, vol.15
, pp. 123
-
-
Livi, C.1
-
37
-
-
84892636681
-
GraphProt: Modeling binding preferences of RNAbinding proteins
-
Maticzka,D. et al. (2014) GraphProt: modeling binding preferences of RNAbinding proteins. Genome Biol., 15, R17.
-
(2014)
Genome Biol.
, vol.15
, pp. R17
-
-
Maticzka, D.1
-
38
-
-
67650770061
-
Predictor correlation impacts machine learning algorithms: Implications for genomic studies
-
Nicodemus,K.K. et al. (2009) Predictor correlation impacts machine learning algorithms: implications for genomic studies. Bioinformatics, 25, 1884-1890.
-
(2009)
Bioinformatics
, vol.25
, pp. 1884-1890
-
-
Nicodemus, K.K.1
-
39
-
-
84865194573
-
Computational methods for prediction of protein-RNA interactions
-
Puton,T. et al. (2012) Computational methods for prediction of protein-RNA interactions. J. Struct. Biol., 179, 261-268.
-
(2012)
J. Struct. Biol.
, vol.179
, pp. 261-268
-
-
Puton, T.1
-
40
-
-
84880427394
-
A compendium of RNA-binding motifs for decoding gene regulation
-
Ray,D. et al. (2013) A compendium of RNA-binding motifs for decoding gene regulation. Nature, 499, 172-177.
-
(2013)
Nature
, vol.499
, pp. 172-177
-
-
Ray, D.1
-
41
-
-
84896885113
-
Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L
-
Rossbach,O. et al. (2014) Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. RNA Biol., 11, 146-155.
-
(2014)
RNA Biol.
, vol.11
, pp. 146-155
-
-
Rossbach, O.1
-
42
-
-
61849139645
-
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
-
Sanford,J.R. et al. (2009) Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res., 19, 381-394.
-
(2009)
Genome Res.
, vol.19
, pp. 381-394
-
-
Sanford, J.R.1
-
43
-
-
84869087484
-
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex
-
Saulière,J. et al. (2012) CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. Nat. Struct. Mol. Biol., 19, 1124-1131.
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 1124-1131
-
-
Saulière, J.1
-
44
-
-
84869071915
-
Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data
-
Sievers,C. et al. (2012) Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data. Nucleic Acids Res., 40, e160-e160.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e160-e160
-
-
Sievers, C.1
-
45
-
-
84936744064
-
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
-
Sugimoto,Y. et al. (2012) Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol., 13, R67.
-
(2012)
Genome Biol.
, vol.13
, pp. R67
-
-
Sugimoto, Y.1
-
46
-
-
79953180492
-
Characterizing the RNA targets and position-dependent splicing regulation by TDP-43
-
Tollervey,J.R. et al. (2011) Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat. Neurosci., 14, 452-U180.
-
(2011)
Nat. Neurosci.
, vol.14
, pp. U452-U4180
-
-
Tollervey, J.R.1
-
47
-
-
84876235880
-
Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization
-
Wang,H. et al. (2013) Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization. J. Comput. Biol., 20, 344-358.
-
(2013)
J. Comput. Biol.
, vol.20
, pp. 344-358
-
-
Wang, H.1
-
48
-
-
78149393552
-
ICLIP predicts the dual splicing effects of TIA-RNA interactions
-
Wang,Z. et al. (2010) iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions. PLoS Biol., 8, e1000530.
-
(2010)
PLoS Biol.
, vol.8
, pp. e1000530
-
-
Wang, Z.1
-
49
-
-
70549083928
-
Weighted nonnegative matrix co-tri-factorization for collaborative prediction
-
Yoo, J. et al. (2009) Weighted nonnegative matrix co-tri-factorization for collaborative prediction. Adv. Mach. Learn., 5828, 396-411.
-
(2009)
Adv. Mach. Learn.
, vol.5828
, pp. 396-411
-
-
Yoo, J.1
-
50
-
-
84873323035
-
Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements
-
Zarnack,K. et al. (2013) Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell, 152, 453-466.
-
(2013)
Cell
, vol.152
, pp. 453-466
-
-
Zarnack, K.1
-
51
-
-
85014098635
-
Non-negative matrix factorization with quasi-Newton optimization
-
Zdunek,R. et al. (2006) Non-negative matrix factorization with quasi-newton optimization. Artif. Intell. Soft Comput., 87, 870-879.
-
(2006)
Artif. Intell. Soft Comput.
, vol.87
, pp. 870-879
-
-
Zdunek, R.1
-
52
-
-
77954838957
-
Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls
-
Zhang,C. et al. (2010) Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science, 329, 439-443.
-
(2010)
Science
, vol.329
, pp. 439-443
-
-
Zhang, C.1
-
53
-
-
79959448071
-
A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules
-
Zhang,S. et al. (2011) A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinformatics, 27, i401-i409.
-
(2011)
Bioinformatics
, vol.27
, pp. i401-i409
-
-
Zhang, S.1
-
54
-
-
84868152524
-
Discovery of multi-dimensional modules by integrative analysis of cancer genomic data
-
Zhang,S. et al. (2012) Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Res., 40, 9379-9391.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 9379-9391
-
-
Zhang, S.1
-
55
-
-
84881493949
-
Prediction of clustered RNA-binding protein motif sites in the mammalian genome
-
Zhang,C. et al. (2013) Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res., 41, 6793-6807.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 6793-6807
-
-
Zhang, C.1
-
56
-
-
80052119372
-
Functional matrix factorizations for cold-start recommendation
-
Zhou,K. et al. (2011). Functional matrix factorizations for cold-start recommendation. In: Proceedings of the 34th International ACM SIGIR, p. 315.
-
(2011)
Proceedings of the 34th International ACM SIGIR
, pp. 315
-
-
Zhou, K.1
|