-
1
-
-
0036176773
-
RNA-protein interactions that regulate pre-mRNA splicing
-
Singh, R. RNA-protein interactions that regulate pre-mRNA splicing. Gene Expr 2002;10:79-92.
-
(2002)
Gene Expr
, vol.10
, pp. 79-92
-
-
Singh, R.1
-
2
-
-
48949115091
-
RNA-binding proteins in human genetic disease
-
Lukong KE, Chang KW, Khandjian EW, et al. RNA-binding proteins in human genetic disease. Trends Genet 2008;24(8): 416-25.
-
(2008)
Trends Genet
, vol.24
, Issue.8
, pp. 416-425
-
-
Lukong, K.E.1
Chang, K.W.2
Khandjian, E.W.3
-
3
-
-
79954989654
-
Deciphering the role of RNAbinding proteins in the post-transcriptional control of gene expression
-
Kishore S, Luber S, Zavolan M. Deciphering the role of RNAbinding proteins in the post-transcriptional control of gene expression. Brief Funct Genomics 2010;9:391-404.
-
(2010)
Brief Funct Genomics
, vol.9
, pp. 391-404
-
-
Kishore, S.1
Luber, S.2
Zavolan, M.3
-
4
-
-
72849106592
-
RNA processing and its regulation: Global insights into biological networks
-
Licatalosi DD, Darnell RB. RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 2010; 11:75-87.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 75-87
-
-
Licatalosi, D.D.1
Darnell, R.B.2
-
5
-
-
84884953564
-
Function of lncRNAs and approaches to lncRNA-protein interactions
-
Zhu J, Fu H, Wu Y, et al. Function of lncRNAs and approaches to lncRNA-protein interactions. Sci China Life Sci 2013;56:876- 85.
-
(2013)
Sci China Life Sci
, vol.56
, pp. 876-885
-
-
Zhu, J.1
Fu, H.2
Wu, Y.3
-
6
-
-
46649093597
-
Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
-
Wang X, Arai S, Song X, et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008;454:126-30.
-
(2008)
Nature
, vol.454
, pp. 126-130
-
-
Wang, X.1
Arai, S.2
Song, X.3
-
7
-
-
84886252113
-
RNA in unexpected places: Long non-coding RNA functions in diverse cellular contexts
-
Geisler S, Coller J. RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 2013;14(11):699-712.
-
(2013)
Nat Rev Mol Cell Biol
, vol.14
, Issue.11
, pp. 699-712
-
-
Geisler, S.1
Coller, J.2
-
8
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
-
Rinn JL, Kertesz M, Wang JK, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007;129:1311-23.
-
(2007)
Cell
, vol.129
, pp. 1311-1323
-
-
Rinn, J.L.1
Kertesz, M.2
Wang, J.K.3
-
9
-
-
80054715378
-
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA
-
Cesana M, Cacchiarelli D, Legnini I, et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 2011;147:358-69.
-
(2011)
Cell
, vol.147
, pp. 358-369
-
-
Cesana, M.1
Cacchiarelli, D.2
Legnini, I.3
-
10
-
-
79953748673
-
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
-
Wang KC, Yang YW, Liu B, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011;472:120-24.
-
(2011)
Nature
, vol.472
, pp. 120-124
-
-
Wang, K.C.1
Yang, Y.W.2
Liu, B.3
-
11
-
-
84869088820
-
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
-
Carrieri C, Cimatti L, Biagioli M, et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 2012;491:454-57.
-
(2012)
Nature
, vol.491
, pp. 454-457
-
-
Carrieri, C.1
Cimatti, L.2
Biagioli, M.3
-
12
-
-
77956927823
-
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation
-
Tripathi V, Ellis JD, Shen Z, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010;39: 925-38.
-
(2010)
Mol Cell
, vol.39
, pp. 925-938
-
-
Tripathi, V.1
Ellis, J.D.2
Shen, Z.3
-
13
-
-
84876806808
-
RNA-binding proteins in Mendelian disease
-
Castello A, Fischer B, Hentze MW, et al. RNA-binding proteins in Mendelian disease. Trends Genet 2013;29(5):318-27.
-
(2013)
Trends Genet
, vol.29
, Issue.5
, pp. 318-327
-
-
Castello, A.1
Fischer, B.2
Hentze, M.W.3
-
14
-
-
10344250458
-
Components of the DNA methylation system of chromatin control are RNA-binding proteins
-
Jeffery L, Nakielny S. Components of the DNA methylation system of chromatin control are RNA-binding proteins. J Biol Chem 2004;279(47):49479-87.
-
(2004)
J Biol Chem
, vol.279
, Issue.47
, pp. 49479-49487
-
-
Jeffery, L.1
Nakielny, S.2
-
15
-
-
23044437498
-
RNA meets chromatin
-
Bernstein E, Allis CD. RNA meets chromatin. Genes Dev 2005; 19(14):1635-55.
-
(2005)
Genes Dev
, vol.19
, Issue.14
, pp. 1635-1655
-
-
Bernstein, E.1
Allis, C.D.2
-
16
-
-
38949188739
-
Non-coding RNAs regulating the transcriptional machinery
-
Barrandon C, Spiluttini B, Bensaude O. Non-coding RNAs regulating the transcriptional machinery. Biol Cell 2008;100(2):83-95.
-
(2008)
Biol Cell
, vol.100
, Issue.2
, pp. 83-95
-
-
Barrandon, C.1
Spiluttini, B.2
Bensaude, O.3
-
17
-
-
84892402537
-
Dissecting the expression landscape of RNA-binding proteins in human cancers
-
Kechavarzi B, Janga SC. Dissecting the expression landscape of RNA-binding proteins in human cancers. Genome Biol 2014;15(1):R14.
-
(2014)
Genome Biol
, vol.15
, Issue.1
, pp. R14
-
-
Kechavarzi, B.1
Janga, S.C.2
-
18
-
-
84921029014
-
Long noncoding RNA HOTAIR involvement in cancer
-
Wu Y, Zhang L, Wang Y, et al. Long noncoding RNA HOTAIR involvement in cancer. Tumour Biol 2014;35(10):9531-38.
-
(2014)
Tumour Biol
, vol.35
, Issue.10
, pp. 9531-9538
-
-
Wu, Y.1
Zhang, L.2
Wang, Y.3
-
19
-
-
84904385428
-
HOTAIR: A cancer-related long non-coding RNA
-
Cai B, Song XQ, Cai JP, et al. HOTAIR: a cancer-related long non-coding RNA. Neoplasma 2014;61(4):379-91.
-
(2014)
Neoplasma
, vol.61
, Issue.4
, pp. 379-391
-
-
Cai, B.1
Song, X.Q.2
Cai, J.P.3
-
20
-
-
84862883971
-
RNA-protein interactions in vivo: Global gets specific
-
Ankö ML, Neugebauer KM. RNA-protein interactions in vivo: global gets specific. Trends Biochem Sci 2012;37(7):255-62
-
(2012)
Trends Biochem Sci
, vol.37
, Issue.7
, pp. 255-262
-
-
Ankö, M.L.1
Neugebauer, K.M.2
-
21
-
-
80053613296
-
Promoter-associated long noncoding RNAs repress transcription through a RNA binding protein TLS
-
Kurokawa R. Promoter-associated long noncoding RNAs repress transcription through a RNA binding protein TLS. Adv Exp Med Biol 2011;722:196-208.
-
(2011)
Adv Exp Med Biol
, vol.722
, pp. 196-208
-
-
Kurokawa, R.1
-
22
-
-
77953096072
-
Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a
-
Yap KL, Li S, Muñ oz-Cabello AM, et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 2010;38(5):662-74.
-
(2010)
Mol Cell
, vol.38
, Issue.5
, pp. 662-674
-
-
Yap, K.L.1
Li, S.2
Muñ oz-Cabello, A.M.3
-
23
-
-
78651397147
-
Large non-coding RNAs: Missing links in cancer?
-
Huarte M, Rinn JL. Large non-coding RNAs: missing links in cancer? Hum Mol Genet 2010;19(R2):R152-61.
-
(2010)
Hum Mol Genet
, vol.19
, Issue.R2
, pp. R152-R161
-
-
Huarte, M.1
Rinn, J.L.2
-
24
-
-
79953888460
-
The functional role of long noncoding RNA in human carcinomas
-
Gibb EA, Brown CJ, Lam WL. The functional role of long noncoding RNA in human carcinomas. Mol Cancer 2011;10:38.
-
(2011)
Mol Cancer
, vol.10
, pp. 38
-
-
Gibb, E.A.1
Brown, C.J.2
Lam, W.L.3
-
25
-
-
82155186923
-
The emergence of lncRNAs in cancer biology
-
Prensner JR, Chinnaiyan AM. The emergence of lncRNAs in cancer biology. Cancer Discov 2011;1(5):391-407.
-
(2011)
Cancer Discov
, vol.1
, Issue.5
, pp. 391-407
-
-
Prensner, J.R.1
Chinnaiyan, A.M.2
-
26
-
-
78651390167
-
Long intergenic noncoding RNAs: New links in cancer progression
-
Tsai MC, Spitale RC, Chang HY. Long intergenic noncoding RNAs: new links in cancer progression. Cancer Res 2011;71(1): 3-7.
-
(2011)
Cancer Res
, vol.71
, Issue.1
, pp. 3-7
-
-
Tsai, M.C.1
Spitale, R.C.2
Chang, H.Y.3
-
27
-
-
84860119507
-
Long non-coding RNAs: Versatile master regulators of gene expression and crucial players in cancer
-
Nie L, Wu HJ, Hsu JM, et al. Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. Am J Transl Res 2012;4(2):127-50.
-
(2012)
Am J Transl Res
, vol.4
, Issue.2
, pp. 127-150
-
-
Nie, L.1
Wu, H.J.2
Hsu, J.M.3
-
28
-
-
34548169696
-
Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions
-
Hellman LM, Fried MG. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2007;2:1849-1861.
-
(2007)
Nat Protoc
, vol.2
, pp. 1849-1861
-
-
Hellman, L.M.1
Fried, M.G.2
-
29
-
-
0034657686
-
HuR regulates cyclin A and cyclin B1 mRNA stability during cell proliferation
-
Wang W, Caldwell MC, Lin S, et al. HuR regulates cyclin A and cyclin B1 mRNA stability during cell proliferation. EMBO J 2000;19:2340-50.
-
(2000)
EMBO J
, vol.19
, pp. 2340-2350
-
-
Wang, W.1
Caldwell, M.C.2
Lin, S.3
-
30
-
-
0036354951
-
Analysis of RNA-protein complexes by oligonucleotide-targeted RNase H digestion
-
Gü nzl A, Palfi Z, Bindereif A. Analysis of RNA-protein complexes by oligonucleotide-targeted RNase H digestion. Methods 2002;26:162-69.
-
(2002)
Methods
, vol.26
, pp. 162-169
-
-
Gü nzl, A.1
Palfi, Z.2
Bindereif, A.3
-
31
-
-
80053186141
-
Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA
-
Shih JD, Waks Z, Kedersha N, et al. Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA. Nucleic Acids Res 2011;39: 7740-49.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 7740-7749
-
-
Shih, J.D.1
Waks, Z.2
Kedersha, N.3
-
32
-
-
54949148332
-
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
-
Hogan DJ, Riordan DP, Gerber AP, et al. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol 2008;6(10): e255.
-
(2008)
PLoS Biol
, vol.6
, Issue.10
, pp. e255
-
-
Hogan, D.J.1
Riordan, D.P.2
Gerber, A.P.3
-
33
-
-
84907272104
-
Ribonomic approaches to study the RNAbinding proteome
-
Faoro C, Ataide SF. Ribonomic approaches to study the RNAbinding proteome. FEBS Lett 2014;588(20):3649-64.
-
(2014)
FEBS Lett
, vol.588
, Issue.20
, pp. 3649-3664
-
-
Faoro, C.1
Ataide, S.F.2
-
34
-
-
84892999996
-
Methods for comprehensive experimental identification of RNA-protein interactions
-
McHugh CA, Russell P, Guttman M. Methods for comprehensive experimental identification of RNA-protein interactions. Genome Biol 2014;15(1):203
-
(2014)
Genome Biol
, vol.15
, Issue.1
, pp. 203
-
-
McHugh, C.A.1
Russell, P.2
Guttman, M.3
-
35
-
-
84922454174
-
High-throughput characterization of protein-RNA interactions
-
Cook KB, Hughes TR, Morris QD. High-throughput characterization of protein-RNA interactions. Brief Funct Genomics 2015;14(1):74-89.
-
(2015)
Brief Funct Genomics
, vol.14
, Issue.1
, pp. 74-89
-
-
Cook, K.B.1
Hughes, T.R.2
Morris, Q.D.3
-
36
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990;249(4968):505-10.
-
(1990)
Science
, vol.249
, Issue.4968
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
37
-
-
0025074907
-
In vitro selection of RNA molecules that bind specific ligands
-
Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature 1990;346(6287):818-22.
-
(1990)
Nature
, vol.346
, Issue.6287
, pp. 818-822
-
-
Ellington, A.D.1
Szostak, J.W.2
-
38
-
-
74549209548
-
Inferring binding energies from selected binding sites
-
Zhao Y, Granas D, Stormo GD. Inferring binding energies from selected binding sites. PLoS Comput Biol 2009;5(12): e1000590.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.12
-
-
Zhao, Y.1
Granas, D.2
Stormo, G.D.3
-
39
-
-
84861705421
-
Cooperativity in RNA-protein interactions: Global analysis of RNA binding specificity
-
Campbell ZT, Bhimsaria D, Valley CT, et al. Cooperativity in RNA-protein interactions: global analysis of RNA binding specificity. Cell Rep 2012;1(5):570-81.
-
(2012)
Cell Rep
, vol.1
, Issue.5
, pp. 570-581
-
-
Campbell, Z.T.1
Bhimsaria, D.2
Valley, C.T.3
-
41
-
-
67650484984
-
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
-
Ray D, Kazan H, Chan ET, et al. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol 2009;27(7):667-70.
-
(2009)
Nat Biotechnol
, vol.27
, Issue.7
, pp. 667-670
-
-
Ray, D.1
Kazan, H.2
Chan, E.T.3
-
42
-
-
84901913783
-
RNA Bind-n-Seq: Quantitative assessment of the sequence and structural binding specificity of RNA binding proteins
-
Lambert N, Robertson A, Jangi M, et al. RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol Cell 2014;54(5):887-900.
-
(2014)
Mol Cell
, vol.54
, Issue.5
, pp. 887-900
-
-
Lambert, N.1
Robertson, A.2
Jangi, M.3
-
43
-
-
84901804745
-
Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes
-
Buenrostro JD, Araya CL, Chircus LM, et al. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nat Biotechnol 2014;32(6):562-8.
-
(2014)
Nat Biotechnol
, vol.32
, Issue.6
, pp. 562-568
-
-
Buenrostro, J.D.1
Araya, C.L.2
Chircus, L.M.3
-
44
-
-
34047187080
-
Genomic systematic evolution of ligands by exponential enrichment (Genomic SELEX) for the identification of protein-binding RNAs independent of their expression levels
-
Lorenz C, von Pelchrzim F, Schroeder R. Genomic systematic evolution of ligands by exponential enrichment (Genomic SELEX) for the identification of protein-binding RNAs independent of their expression levels. Nat Protoc 2006;1(5): 2204-12.
-
(2006)
Nat Protoc
, vol.1
, Issue.5
, pp. 2204-2212
-
-
Lorenz, C.1
von Pelchrzim, F.2
Schroeder, R.3
-
45
-
-
77957143552
-
Genomic SELEX: A discovery tool for genomic aptamers
-
Zimmermann B, Bilusic I, Lorenz C, et al. Genomic SELEX: a discovery tool for genomic aptamers. Methods 2010;52(2): 125-32.
-
(2010)
Methods
, vol.52
, Issue.2
, pp. 125-132
-
-
Zimmermann, B.1
Bilusic, I.2
Lorenz, C.3
-
46
-
-
84873631335
-
Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity
-
Bannikova O, Zywicki M, Marquez Y, et al. Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity. Nucleic Acids Res 2013;41(3):1783-96.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.3
, pp. 1783-1796
-
-
Bannikova, O.1
Zywicki, M.2
Marquez, Y.3
-
47
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994;2:28-36.
-
(1994)
Proc Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
48
-
-
44949239504
-
Discovering sequence motifs with arbitrary insertions and deletions
-
Frith MC, Saunders NF, Kobe B, et al. Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol 2008;4(4):e1000071.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.4
-
-
Frith, M.C.1
Saunders, N.F.2
Kobe, B.3
-
49
-
-
33750212480
-
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions
-
Hiller M, Pudimat R, Busch A, et al. Using RNA secondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res 2006;34(17):e117.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.17
, pp. e117
-
-
Hiller, M.1
Pudimat, R.2
Busch, A.3
-
50
-
-
84863528670
-
Identification of sequence- structure RNA binding motifs for SELEX-derived aptamers
-
Hoinka J, Zotenko E, Friedman A, et al. Identification of sequence- structure RNA binding motifs for SELEX-derived aptamers. Bioinformatics 2012;28(12):i215-23.
-
(2012)
Bioinformatics
, vol.28
, Issue.12
-
-
Hoinka, J.1
Zotenko, E.2
Friedman, A.3
-
51
-
-
84876814241
-
The non-coding RNA llme23 drives the malignant property of human melanoma cells
-
Wu CF, Tan GH, Ma CC, et al. The non-coding RNA llme23 drives the malignant property of human melanoma cells. J Genet Genomics 2013;40(4):179-88.
-
(2013)
J Genet Genomics
, vol.40
, Issue.4
, pp. 179-188
-
-
Wu, C.F.1
Tan, G.H.2
Ma, C.C.3
-
52
-
-
77954378224
-
Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts
-
Lorenz C, Gesell T, Zimmermann B, et al. Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res 2010;38(11): 3794-808.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.11
, pp. 3794-3808
-
-
Lorenz, C.1
Gesell, T.2
Zimmermann, B.3
-
53
-
-
78651308986
-
RBPDB: A database of RNA-binding specificities
-
Cook KB, Kazan H, Zuberi K, et al. RBPDB: a database of RNA-binding specificities. Nucleic Acids Res 2011; 39:D301-8.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D301-D308
-
-
Cook, K.B.1
Kazan, H.2
Zuberi, K.3
-
54
-
-
84880427394
-
A compendium of RNAbinding motifs for decoding gene regulation
-
Ray D, Kazan H, Cook KB, et al. A compendium of RNAbinding motifs for decoding gene regulation. Nature 2013; 499(7457):172-77.
-
(2013)
Nature
, vol.499
, Issue.7457
, pp. 172-177
-
-
Ray, D.1
Kazan, H.2
Cook, K.B.3
-
55
-
-
33845275018
-
RIP-Chip: The isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
-
Keene JD, Komisarow JM, Friedersdorf MB. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 2006;1:302-07.
-
(2006)
Nat Protoc
, vol.1
, pp. 302-307
-
-
Keene, J.D.1
Komisarow, J.M.2
Friedersdorf, M.B.3
-
56
-
-
78650253763
-
Genome-wide identification of polycomb-associated RNAs by RIP-seq
-
Zhao J, Ohsumi TK, Kung JT, et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 2010; 40:939-53.
-
(2010)
Mol Cell
, vol.40
, pp. 939-953
-
-
Zhao, J.1
Ohsumi, T.K.2
Kung, J.T.3
-
57
-
-
79960918737
-
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability
-
Mukherjee N, Corcoran DL, Nusbaum JD, et al. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell 2010;43(3):327-39.
-
(2010)
Mol Cell
, vol.43
, Issue.3
, pp. 327-339
-
-
Mukherjee, N.1
Corcoran, D.L.2
Nusbaum, J.D.3
-
58
-
-
84879172698
-
Analysis of long non-coding RNA expression profiles in gastric cancer
-
Cao WJ, Wu HL, He BS, et al. Analysis of long non-coding RNA expression profiles in gastric cancer. World J Gastroenterol 2013;19:3658-64.
-
(2013)
World J Gastroenterol
, vol.19
, pp. 3658-3664
-
-
Cao, W.J.1
Wu, H.L.2
He, B.S.3
-
59
-
-
27944508215
-
CLIP: A method for identifying protein-RNA interaction sites in living cells
-
Ule J, Jensen K, Mele A, et al. CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 2005; 37:376-386.
-
(2005)
Methods
, vol.37
, pp. 376-386
-
-
Ule, J.1
Jensen, K.2
Mele, A.3
-
60
-
-
56549105330
-
HITS-CLIP yields genomewide insights into brain alternative RNA processing
-
Licatalosi DD, Mele A, Fak JJ, et al. HITS-CLIP yields genomewide insights into brain alternative RNA processing. Nature 2008;456:464-69.
-
(2008)
Nature
, vol.456
, pp. 464-469
-
-
Licatalosi, D.D.1
Mele, A.2
Fak, J.J.3
-
61
-
-
79960230895
-
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
-
Zhang C, Darnell RB. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 2011;29:607-14.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 607-614
-
-
Zhang, C.1
Darnell, R.B.2
-
62
-
-
80055101895
-
PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins
-
Hafner M, Landthaler M, Burger L, et al. PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp 2010;41:2034.
-
(2010)
J Vis Exp
, vol.41
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
-
63
-
-
80455179726
-
iCLIP-transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution
-
Konig J, Zarnack K, Rot G, et al. iCLIP-transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp 2011;50:2638.
-
(2011)
J Vis Exp
, vol.50
-
-
Konig, J.1
Zarnack, K.2
Rot, G.3
-
64
-
-
67649854477
-
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV crosslinking and high-throughput analysis of cDNAs
-
Granneman S, Kudla G, Petfalski E, et al. Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV crosslinking and high-throughput analysis of cDNAs. Proc Natl Acad Sci USA 2009;106(24):9613-18.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.24
, pp. 9613-9618
-
-
Granneman, S.1
Kudla, G.2
Petfalski, E.3
-
65
-
-
84960151955
-
Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation
-
pii:elu020.
-
Kloetgen A, Mü nch PC, Borkhardt A, et al. Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief Funct Genomics 2014;pii:elu020.
-
(2014)
Brief Funct Genomics
-
-
Kloetgen, A.1
Mü nch, P.C.2
Borkhardt, A.3
-
66
-
-
84920574625
-
A computational approach for identifying microRNA-target interactions using highthroughput CLIP and PAR-CLIP sequencing
-
Chou CH, Lin FM, Chou MT, et al. A computational approach for identifying microRNA-target interactions using highthroughput CLIP and PAR-CLIP sequencing. BMC Genomics 2013;14 (Suppl 1), S2.
-
(2013)
BMC Genomics
, vol.14
, pp. S2
-
-
Chou, C.H.1
Lin, F.M.2
Chou, M.T.3
-
67
-
-
80051786284
-
PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data
-
Corcoran DL, Georgiev S, Mukherjee N, et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol 2011;12:R79.
-
(2011)
Genome Biol
, vol.12
, pp. R79
-
-
Corcoran, D.L.1
Georgiev, S.2
Mukherjee, N.3
-
68
-
-
84870471564
-
Site identification in high-throughput RNA-protein interaction data
-
Uren PJ, Bahrami-Samani E, Burns SC, et al. Site identification in high-throughput RNA-protein interaction data. Bioinformatics 2012;28(23):3013-20.
-
(2012)
Bioinformatics
, vol.28
, Issue.23
, pp. 3013-3020
-
-
Uren, P.J.1
Bahrami-Samani, E.2
Burns, S.C.3
-
69
-
-
84869071915
-
Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data
-
Sievers C, Schlumpf T, Sawarkar R, et al. Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data. Nucleic Acids Res 2012;40(20):e160.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.20
, pp. e160
-
-
Sievers, C.1
Schlumpf, T.2
Sawarkar, R.3
-
70
-
-
84877291550
-
RIPSeeker: A statistical package for identifying protein-associated transcripts from RIP-seq experiments
-
Li Y, Zhao DY, Greenblatt JF, et al. RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Res 2013; 41(8):e94.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.8
, pp. e94
-
-
Li, Y.1
Zhao, D.Y.2
Greenblatt, J.F.3
-
71
-
-
84899497034
-
A model-based approach to identify binding sites in CLIP-Seq data
-
Wang T, Chen B, Kim M, et al. A model-based approach to identify binding sites in CLIP-Seq data. PLoS One 2014;9: e93248.
-
(2014)
PLoS One
, vol.9
-
-
Wang, T.1
Chen, B.2
Kim, M.3
-
72
-
-
84892665507
-
PIPE-CLIP: A comprehensive online tool for CLIP-seq data analysis
-
Chen B, Yun J, Kim MS, et al. PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. Genome Biol 2014;15(1): R18.
-
(2014)
Genome Biol
, vol.15
, Issue.1
, pp. R18
-
-
Chen, B.1
Yun, J.2
Kim, M.S.3
-
73
-
-
83255194564
-
Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data
-
Althammer S, Gonzá lez-Vallinas J, Ballaré C, et al. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics 2011;27(24):3333-40.
-
(2011)
Bioinformatics
, vol.27
, Issue.24
, pp. 3333-3340
-
-
Althammer, S.1
Gonzá lez-Vallinas, J.2
Ballaré, C.3
-
74
-
-
84865727393
-
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
-
Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012;22(9): 1775-89.
-
(2012)
Genome Res
, vol.22
, Issue.9
, pp. 1775-1789
-
-
Derrien, T.1
Johnson, R.2
Bussotti, G.3
-
75
-
-
84891798006
-
NONCODEv4: Exploring the world of long non-coding RNA genes
-
Xie C, Yuan J, Li H, et al. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 2014:42:D98- 103.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D98-D103
-
-
Xie, C.1
Yuan, J.2
Li, H.3
-
76
-
-
84946086288
-
An update on LNCipedia: A database for annotated human lncRNA sequences
-
Volders PJ, Verheggen K, Menschaert G, et al. An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res 2015;43:D174-80
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D174-D180
-
-
Volders, P.J.1
Verheggen, K.2
Menschaert, G.3
-
77
-
-
78651325932
-
lncRNAdb: A reference database for long noncoding RNAs
-
Amaral PP, Clark MB, Gascoigne DK, et al. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011;39:D146-51.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D146-D151
-
-
Amaral, P.P.1
Clark, M.B.2
Gascoigne, D.K.3
-
78
-
-
58149177177
-
NRED: A database of long noncoding RNA expression
-
Dinger ME, Pang KC, Mercer TR, et al. NRED: a database of long noncoding RNA expression. Nucleic Acids Res 2009;37: D122-6.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D122-D126
-
-
Dinger, M.E.1
Pang, K.C.2
Mercer, T.R.3
-
80
-
-
0030992812
-
The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo
-
Buckanovich RJ, Darnell RB. The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo. Mol Cell Biol 1997;17:3194-201.
-
(1997)
Mol Cell Biol
, vol.17
, pp. 3194-3201
-
-
Buckanovich, R.J.1
Darnell, R.B.2
-
81
-
-
13444305211
-
The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: A quantitative model
-
Hackermü ller J, Meisner NC, Auer M, et al. The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. Gene 2005;345:3- 12.
-
(2005)
Gene
, vol.345
, pp. 3-12
-
-
Hackermü ller, J.1
Meisner, N.C.2
Auer, M.3
-
82
-
-
0032864042
-
RNA-protein complexes
-
Cusack S. RNA-protein complexes. Curr Opin Struct Biol 1999; 9:66-73.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 66-73
-
-
Cusack, S.1
-
83
-
-
84890294599
-
Finding the target sites of RNA-binding proteins
-
Li X, Kazan H, Lipshitz HD, et al. Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA 2014;5(1): 111-30.
-
(2014)
Wiley Interdiscip Rev RNA
, vol.5
, Issue.1
, pp. 111-130
-
-
Li, X.1
Kazan, H.2
Lipshitz, H.D.3
-
84
-
-
32544452741
-
CMfinder-a covariance model based RNA motif finding algorithm
-
Yao Z, Weinberg Z, Ruzzo WL. CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics 2006;22(4):445-52.
-
(2006)
Bioinformatics
, vol.22
, Issue.4
, pp. 445-452
-
-
Yao, Z.1
Weinberg, Z.2
Ruzzo, W.L.3
-
85
-
-
54449097862
-
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes
-
Rabani M, Kertesz M, Segal E. Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci USA 2008;105(39):14885- 90.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.39
, pp. 14885-14890
-
-
Rabani, M.1
Kertesz, M.2
Segal, E.3
-
86
-
-
66249108559
-
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs
-
Foat BC, Stormo GD. Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. Mol Syst Biol 2009;5:268.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 268
-
-
Foat, B.C.1
Stormo, G.D.2
-
87
-
-
77952687104
-
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure
-
Li X, Quon G, Lipshitz HD, et al. Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA 2010;16(6):1096-107.
-
(2010)
RNA
, vol.16
, Issue.6
, pp. 1096-1107
-
-
Li, X.1
Quon, G.2
Lipshitz, H.D.3
-
88
-
-
78049275913
-
RNAcontext: A new method for learning the sequence and structure binding preferences of RNA-binding proteins
-
Kazan H, Ray D, Chan ET, et al. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol 2010;6:e1000832.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Kazan, H.1
Ray, D.2
Chan, E.T.3
-
89
-
-
84883592184
-
RBPmotif: A web server for the discovery of sequence and structure preferences of RNA-binding proteins
-
Kazan H, Morris Q. RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. Nucleic Acids Res 2013;41:W180-6.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. W180-W186
-
-
Kazan, H.1
Morris, Q.2
-
90
-
-
84892636681
-
GraphProt: Modeling binding preferences of RNA-binding proteins
-
Maticzka D, Lange SJ, Costa F, et al. GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol 2014;15(1):R17.
-
(2014)
Genome Biol
, vol.15
, Issue.1
, pp. R17
-
-
Maticzka, D.1
Lange, S.J.2
Costa, F.3
-
91
-
-
84941068123
-
Leveraging cross-link modification events in CLIP-seq for motif discovery
-
Bahrami-Samani E, Penalva LO, Smith AD, et al. Leveraging cross-link modification events in CLIP-seq for motif discovery. Nucleic Acids Res 2015;43(1):95-103.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.1
, pp. 95-103
-
-
Bahrami-Samani, E.1
Penalva, L.O.2
Smith, A.D.3
-
92
-
-
84864688599
-
DGCR8 HITS-CLIP reveals novel functions for the Microprocessor
-
Macias S, Plass M, Stajuda A, et al. DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nat Struct Mol Biol 2012;19(8):760-6.
-
(2012)
Nat Struct Mol Biol
, vol.19
, Issue.8
, pp. 760-766
-
-
Macias, S.1
Plass, M.2
Stajuda, A.3
-
93
-
-
84948614436
-
PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity
-
Yoon JH, De S, Srikantan S, et al. PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. Nat Commun 2014;5:5248.
-
(2014)
Nat Commun
, vol.5
-
-
Yoon, J.H.1
De, S.2
Srikantan, S.3
-
94
-
-
79953180492
-
Characterizing the RNA targets and position-dependent splicing regulation by TDP- 43
-
Tollervey JR, Curk T, Rogelj B, et al. Characterizing the RNA targets and position-dependent splicing regulation by TDP- 43. Nat Neurosci 2011;14(4):452-8.
-
(2011)
Nat Neurosci
, vol.14
, Issue.4
, pp. 452-458
-
-
Tollervey, J.R.1
Curk, T.2
Rogelj, B.3
-
95
-
-
84883377142
-
A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs
-
Tuck AC, Tollervey D. A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell 2013;154(5):996-1009.
-
(2013)
Cell
, vol.154
, Issue.5
, pp. 996-1009
-
-
Tuck, A.C.1
Tollervey, D.2
-
96
-
-
84892889808
-
Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin
-
Kaneko S, Bonasio R, Saldañ a-Meyer R, et al. Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin. Mol Cell 2014;53(2):290-300.
-
(2014)
Mol Cell
, vol.53
, Issue.2
, pp. 290-300
-
-
Kaneko, S.1
Bonasio, R.2
Saldañ a-Meyer, R.3
-
97
-
-
84888057006
-
DNMT1-interacting RNAs block gene-specific DNA methylation
-
Di Ruscio A, Ebralidze AK, Benoukraf T, et al. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 2013;503(7476):371-6.
-
(2013)
Nature
, vol.503
, Issue.7476
, pp. 371-376
-
-
Di Ruscio, A.1
Ebralidze, A.K.2
Benoukraf, T.3
-
98
-
-
84869990948
-
Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes
-
Gong C, Popp MW, Maquat LE. Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes. Methods 2012;58(2):88-93.
-
(2012)
Methods
, vol.58
, Issue.2
, pp. 88-93
-
-
Gong, C.1
Popp, M.W.2
Maquat, L.E.3
-
99
-
-
84885852048
-
Identification of a long noncoding RNA-associated RNP complex regulating metastasis at the translational step
-
Gumireddy K, Li A, Yan J, et al. Identification of a long noncoding RNA-associated RNP complex regulating metastasis at the translational step. EMBO J 2013;32(20):2672-84.
-
(2013)
EMBO J
, vol.32
, Issue.20
, pp. 2672-2684
-
-
Gumireddy, K.1
Li, A.2
Yan, J.3
-
100
-
-
84890458330
-
Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators
-
Scheibe M, Arnoult N, Kappei D, et al. Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators. Genome Res 2013;23(12):2149-57.
-
(2013)
Genome Res
, vol.23
, Issue.12
, pp. 2149-2157
-
-
Scheibe, M.1
Arnoult, N.2
Kappei, D.3
-
101
-
-
84910068881
-
The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells
-
Mazar J, Zhao W, Khalil AM, et al. The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells. Oncotarget 2014;5(19):8959-69.
-
(2014)
Oncotarget
, vol.5
, Issue.19
, pp. 8959-8969
-
-
Mazar, J.1
Zhao, W.2
Khalil, A.M.3
-
102
-
-
84887020835
-
Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1)
-
Hämmerle M, Gutschner T, Uckelmann H, et al. Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1). Hepatology 2013;58(5):1703-12.
-
(2013)
Hepatology
, vol.58
, Issue.5
, pp. 1703-1712
-
-
Hämmerle, M.1
Gutschner, T.2
Uckelmann, H.3
-
103
-
-
84861969926
-
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins
-
Castello A, Fischer B, Eichelbaum K, et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012;149(6):1393-406.
-
(2012)
Cell
, vol.149
, Issue.6
, pp. 1393-1406
-
-
Castello, A.1
Fischer, B.2
Eichelbaum, K.3
-
104
-
-
84861997955
-
The mRNAbound proteome and its global occupancy profile on protein- coding transcripts
-
Baltz AG, Munschauer M, Schwanhsser B, et al. The mRNAbound proteome and its global occupancy profile on protein- coding transcripts. Mol Cell 2012;46(5):674-90.
-
(2012)
Mol Cell
, vol.46
, Issue.5
, pp. 674-690
-
-
Baltz, A.G.1
Munschauer, M.2
Schwanhsser, B.3
-
105
-
-
84883741725
-
The RNA-binding protein repertoire of embryonic stem cells
-
Kwon SC, Yi H, Eichelbaum K, et al. The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol 2013; 20(9):1122-30.
-
(2013)
Nat Struct Mol Biol
, vol.20
, Issue.9
, pp. 1122-1130
-
-
Kwon, S.C.1
Yi, H.2
Eichelbaum, K.3
-
107
-
-
84055185205
-
Predicting RNA-protein interactions using only sequence information
-
Muppirala UK, Honavar VG, Dobbs D. Predicting RNA-protein interactions using only sequence information. BMC Bioinformatics 2011;12:489.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 489
-
-
Muppirala, U.K.1
Honavar, V.G.2
Dobbs, D.3
-
108
-
-
79957840868
-
Predicting protein associations with long noncoding RNAs
-
Bellucci M, Agostini F, Masin M, et al. Predicting protein associations with long noncoding RNAs. Nat Methods 2011;8(6): 444-5.
-
(2011)
Nat Methods
, vol.8
, Issue.6
, pp. 444-445
-
-
Bellucci, M.1
Agostini, F.2
Masin, M.3
-
109
-
-
84874453404
-
De novo prediction of RNA-protein interactions from sequence information
-
Wang Y, Chen X, Liu ZP, et al. De novo prediction of RNA-protein interactions from sequence information. Mol Biosyst 2013;9(1):133-42.
-
(2013)
Mol Biosyst
, vol.9
, Issue.1
, pp. 133-142
-
-
Wang, Y.1
Chen, X.2
Liu, Z.P.3
-
110
-
-
84884837017
-
Computational prediction of associations between long non-coding RNAs and proteins
-
Lu Q, Ren S, Lu M, et al. Computational prediction of associations between long non-coding RNAs and proteins. BMC Genomics 2013;14:651.
-
(2013)
BMC Genomics
, vol.14
, pp. 651
-
-
Lu, Q.1
Ren, S.2
Lu, M.3
-
111
-
-
84936100998
-
RPI-Pred: Predicting ncRNAprotein interaction using sequence and structural information
-
Suresh V, Liu L, Adjeroh D, et al. RPI-Pred: predicting ncRNAprotein interaction using sequence and structural information. Nucleic Acids Res 2015;43(3):1370-9.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.3
, pp. 1370-1379
-
-
Suresh, V.1
Liu, L.2
Adjeroh, D.3
-
112
-
-
84929516625
-
Computationally predicting protein- RNA interactions using only positive and unlabeled examples
-
Cheng Z, Zhou S, Guan J. Computationally predicting protein- RNA interactions using only positive and unlabeled examples. J Bioinform Comput Biol 2015;1541005.
-
(2015)
J Bioinform Comput Biol
-
-
Cheng, Z.1
Zhou, S.2
Guan, J.3
-
113
-
-
84900394210
-
Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures
-
Livi CM, Blanzieri E. Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures. BMC Bioinformatics 2014;15:123.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 123
-
-
Livi, C.M.1
Blanzieri, E.2
-
114
-
-
80051711205
-
In silico characterization and prediction of global protein-mRNA interactions in yeast
-
Pancaldi V, Bä hler J. In silico characterization and prediction of global protein-mRNA interactions in yeast. Nucleic Acids Res 2011;39(14):5826-36.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.14
, pp. 5826-5836
-
-
Pancaldi, V.1
Bä hler, J.2
-
115
-
-
84891773261
-
NPInter v2.0: An updated database of ncRNA interactions
-
Yuan J, Wu W, Xie C, et al. NPInter v2.0: an updated database of ncRNA interactions. Nucleic Acids Res 2014;42:D104-8
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D104-D108
-
-
Yuan, J.1
Wu, W.2
Xie, C.3
-
116
-
-
84879574789
-
linc-UBC1 physically associates with polycomb repressive complex 2 (PRC2) and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer
-
He W, Cai Q, Sun F, et al. linc-UBC1 physically associates with polycomb repressive complex 2 (PRC2) and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer. Biochim Biophys Acta 2013;1832( 10):1528-37.
-
(2013)
Biochim Biophys Acta
, vol.1832
, Issue.10
, pp. 1528-1537
-
-
He, W.1
Cai, Q.2
Sun, F.3
-
117
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali S, Davis CA, Merkel A, et al. Landscape of transcription in human cells. Nature 2012;489(7414):101-8.
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
-
118
-
-
84874271270
-
NCBI GEO: Archive for functional genomics data sets-update
-
Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res 2013;41:D991-5.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D991-D995
-
-
Barrett, T.1
Wilhite, S.E.2
Ledoux, P.3
-
119
-
-
84941103248
-
Array Express update- simplifying data submissions
-
Kolesnikov N, Hastings E, Keays M, et al. ArrayExpress update- simplifying data submissions. Nucleic Acids Res 2015:43: D1113-6
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D1113-D1116
-
-
Kolesnikov, N.1
Hastings, E.2
Keays, M.3
-
120
-
-
84941102569
-
DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation
-
Blin K, Dieterich C,Wurmus R, et al. DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res 2015:43:D160-7.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D160-D167
-
-
Blin, K.1
Dieterich, C.2
Wurmus, R.3
-
121
-
-
78651271270
-
CLIPZ: A database and analysis environment for experimentally determined binding sites of RNA-binding proteins
-
Khorshid M, Rodak C, Zavolan M. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res 2011;39: D245-52.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D245-D252
-
-
Khorshid, M.1
Rodak, C.2
Zavolan, M.3
-
122
-
-
84891818924
-
starBase v2.0: Decoding miRNAceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
-
Li JH, Liu S, Zhou H, et al. starBase v2.0: decoding miRNAceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 2014; 42:D92-7.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D92-D97
-
-
Li, J.H.1
Liu, S.2
Zhou, H.3
-
123
-
-
84904820636
-
RBPmap: A web server for mapping binding sites of RNA-binding proteins
-
Paz I, Kosti I, Ares M Jr, et al. RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res 2014;42:W361-7.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. W361-W367
-
-
Paz, I.1
Kosti, I.2
Ares, M.3
-
124
-
-
84934922535
-
Comprehensive reconstruction and visualization of non-coding regulatory networks in human
-
Bonnici V, Russo F, Bombieri N, et al. Comprehensive reconstruction and visualization of non-coding regulatory networks in human. Front Bioeng Biotechnol 2014:2:69.
-
(2014)
Front Bioeng Biotechnol
, vol.2
, pp. 69
-
-
Bonnici, V.1
Russo, F.2
Bombieri, N.3
-
125
-
-
84921514976
-
A global view of network of lncRNAs and their binding proteins
-
Shang D, Yang H, Xu Y, et al. A global view of network of lncRNAs and their binding proteins. Mol Biosyst 2015;11(2): 656-63.
-
(2015)
Mol Biosyst
, vol.11
, Issue.2
, pp. 656-663
-
-
Shang, D.1
Yang, H.2
Xu, Y.3
-
126
-
-
84876566914
-
ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data
-
Yang JH, Li JH, Jiang S, et al. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res 2013;41:D177-87
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D177-D187
-
-
Yang, J.H.1
Li, J.H.2
Jiang, S.3
-
127
-
-
85117313432
-
Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNASeq Datasets
-
Li JH, Liu S, Zheng LL, et al. Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNASeq Datasets. Front Bioeng Biotechnol 2015;2:88.
-
(2015)
Front Bioeng Biotechnol
, vol.2
, pp. 88
-
-
Li, J.H.1
Liu, S.2
Zheng, L.L.3
-
128
-
-
84868100738
-
Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions
-
Scheibe M, Butter F, Hafner M, et al. Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. Nucleic Acids Res 2012;40(19):9897-902.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.19
, pp. 9897-9902
-
-
Scheibe, M.1
Butter, F.2
Hafner, M.3
-
129
-
-
80054756754
-
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions
-
Chu C, Qu K, Zhong FL, et al. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 2011;44(4):667-78.
-
(2011)
Mol Cell
, vol.44
, Issue.4
, pp. 667-678
-
-
Chu, C.1
Qu, K.2
Zhong, F.L.3
-
131
-
-
84921767267
-
RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin
-
Engreitz J, Lander ES, Guttman M. RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin. Methods Mol Biol 2015;1262:183-97.
-
(2015)
Methods Mol Biol
, vol.1262
, pp. 183-197
-
-
Engreitz, J.1
Lander, E.S.2
Guttman, M.3
-
132
-
-
84925283052
-
Technologies to probe functions and mechanisms of long noncoding RNAs
-
Chu C, Spitale RC, Chang HY. Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol 2015;22(1):29-35.
-
(2015)
Nat Struct Mol Biol
, vol.22
, Issue.1
, pp. 29-35
-
-
Chu, C.1
Spitale, R.C.2
Chang, H.Y.3
-
133
-
-
79959946169
-
Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast
-
Kudla G, Granneman S, Hahn D, et al. Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast. Proc Natl Acad Sci USA 2011;108(24):10010-5.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.24
, pp. 10010-10015
-
-
Kudla, G.1
Granneman, S.2
Hahn, D.3
-
134
-
-
84876935138
-
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
-
Helwak A, Kudla G, Dudnakova T, et al. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 2013;153(3):654-65.
-
(2013)
Cell
, vol.153
, Issue.3
, pp. 654-665
-
-
Helwak, A.1
Kudla, G.2
Dudnakova, T.3
-
135
-
-
84903148507
-
A novel approach to represent and compare RNA secondary structures
-
Mattei E, Ausiello G, Ferrè F, et al. A novel approach to represent and compare RNA secondary structures. Nucleic Acids Res 2014;42(10):6146-57.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.10
, pp. 6146-6157
-
-
Mattei, E.1
Ausiello, G.2
Ferrè, F.3
|