-
2
-
-
78751477191
-
Gene silencing by microRNAs: Contributions of translational repression and mRNA decay
-
Huntzinger,E. and Izaurralde,E. (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat. Rev. Genet., 12, 99-110.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 99-110
-
-
Huntzinger, E.1
Izaurralde, E.2
-
3
-
-
80052451056
-
Experimental strategies for microRNA target identification
-
Thomson,D.W., Bracken,C.P. and Goodall,G.J. (2011) Experimental strategies for microRNA target identification. Nucleic Acids Res., 39, 6845-6853.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 6845-6853
-
-
Thomson, D.W.1
Bracken, C.P.2
Goodall, G.J.3
-
4
-
-
84968903135
-
Coming of age: Ten years of next-generation sequencing technologies
-
Goodwin,S., McPherson,J.D. and McCombie,W.R. (2016) Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet., 17, 333-351.
-
(2016)
Nat. Rev. Genet.
, vol.17
, pp. 333-351
-
-
Goodwin, S.1
McPherson, J.D.2
McCombie, W.R.3
-
5
-
-
85032151882
-
Computational challenges and-omics approaches for the identification of miRNAs and targets
-
In: De,Pietri Tonelli D (ed.) Academic Press, Boston
-
Vlachos,I.S., Georgakilas,G., Tastsoglou,S., Paraskevopoulou,M.D., Karagkouni,D. and Hatzigeorgiou,A.G. (2017) Computational challenges and-omics approaches for the identification of miRNAs and targets. In: De,Pietri Tonelli D (ed.) Essentials of Noncoding RNA in Neuroscience. Academic Press, Boston, pp. 39-60.
-
(2017)
Essentials of Noncoding RNA in Neuroscience
, pp. 39-60
-
-
Vlachos, I.S.1
Georgakilas, G.2
Tastsoglou, S.3
Paraskevopoulou, M.D.4
Karagkouni, D.5
Hatzigeorgiou, A.G.6
-
6
-
-
46249103973
-
Stem cell transcriptome profiling via massive-scale mRNA sequencing
-
Cloonan,N., Forrest,A.R., Kolle,G., Gardiner,B.B., Faulkner,G.J., Brown,M.K., Taylor,D.F., Steptoe,A.L., Wani,S. and Bethel,G. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods, 5, 613-619.
-
(2008)
Nat. Methods
, vol.5
, pp. 613-619
-
-
Cloonan, N.1
Forrest, A.R.2
Kolle, G.3
Gardiner, B.B.4
Faulkner, G.J.5
Brown, M.K.6
Taylor, D.F.7
Steptoe, A.L.8
Wani, S.9
Bethel, G.10
-
7
-
-
84922394487
-
MRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues
-
Eichhorn,S.W., Guo,H., McGeary,S.E., Rodriguez-Mias,R.A., Shin,C., Baek,D., Hsu,S.-H., Ghoshal,K., Villen,J. and Bartel,D.P. (2014) mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol. Cell, 56, 104-115.
-
(2014)
Mol. Cell
, vol.56
, pp. 104-115
-
-
Eichhorn, S.W.1
Guo, H.2
McGeary, S.E.3
Rodriguez-Mias, R.A.4
Shin, C.5
Baek, D.6
Hsu, S.-H.7
Ghoshal, K.8
Villen, J.9
Bartel, D.P.10
-
8
-
-
84941087952
-
DIANA-TarBase v7.0: Indexing more than half a million experimentally supported miRNA:mRNA interactions
-
Vlachos,I.S., Paraskevopoulou,M.D., Karagkouni,D., Georgakilas,G., Vergoulis,T., Kanellos,I., Anastasopoulos,I.L., Maniou,S., Karathanou,K., Kalfakakou,D. et al. (2015) DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res., 43, D153-D159.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D153-D159
-
-
Vlachos, I.S.1
Paraskevopoulou, M.D.2
Karagkouni, D.3
Georgakilas, G.4
Vergoulis, T.5
Kanellos, I.6
Anastasopoulos, I.L.7
Maniou, S.8
Karathanou, K.9
Kalfakakou, D.10
-
9
-
-
84948672434
-
MiRNA-target chimeras reveal miRNA 3 [prime]-end pairing as a major determinant of Argonaute target specificity
-
Moore,M.J., Scheel,T.K., Luna,J.M., Park,C.Y., Fak,J.J., Nishiuchi,E., Rice,C.M. and Darnell,R.B. (2015) miRNA-target chimeras reveal miRNA 3 [prime]-end pairing as a major determinant of Argonaute target specificity. Nat. Commun., 6, 8864.
-
(2015)
Nat. Commun.
, vol.6
, pp. 8864
-
-
Moore, M.J.1
Scheel, T.K.2
Luna, J.M.3
Park, C.Y.4
Fak, J.J.5
Nishiuchi, E.6
Rice, C.M.7
Darnell, R.B.8
-
10
-
-
84876935138
-
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
-
Helwak,A., Kudla,G., Dudnakova,T. and Tollervey,D. (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153, 654-665.
-
(2013)
Cell
, vol.153
, pp. 654-665
-
-
Helwak, A.1
Kudla, G.2
Dudnakova, T.3
Tollervey, D.4
-
11
-
-
84976904131
-
MiRTarBase 2016: Updates to the experimentally validated miRNA-target interactions database
-
Chou,C.-H., Chang,N.-W., Shrestha,S., Hsu,S.-D., Lin,Y.-L., Lee,W.-H., Yang,C.-D., Hong,H.-C., Wei,T.-Y. and Tu,S.-J. (2015) miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res., 44, D239-D247.
-
(2015)
Nucleic Acids Res.
, vol.44
, pp. D239-D247
-
-
Chou, C.-H.1
Chang, N.-W.2
Shrestha, S.3
Hsu, S.-D.4
Lin, Y.-L.5
Lee, W.-H.6
Yang, C.-D.7
Hong, H.-C.8
Wei, T.-Y.9
Tu, S.-J.10
-
12
-
-
84884994218
-
The cancer genome atlas pan-cancer analysis project
-
Weinstein,J.N., Collisson,E.A., Mills,G.B., Shaw,K.R.M., Ozenberger,B.A., Ellrott,K., Shmulevich,I., Sander,C., Stuart,J.M. and Network,C.G.A.R. (2013) The cancer genome atlas pan-cancer analysis project. Nat. Genet., 45, 1113-1120.
-
(2013)
Nat. Genet.
, vol.45
, pp. 1113-1120
-
-
Weinstein, J.N.1
Collisson, E.A.2
Mills, G.B.3
Shaw, K.R.M.4
Ozenberger, B.A.5
Ellrott, K.6
Shmulevich, I.7
Sander, C.8
Stuart, J.M.9
Network, C.G.A.R.10
-
13
-
-
58149186499
-
MiRecords: An integrated resource for microRNA-target interactions
-
Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X. and Li,T. (2008) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res., 37, D105-D110.
-
(2008)
Nucleic Acids Res.
, vol.37
, pp. D105-D110
-
-
Xiao, F.1
Zuo, Z.2
Cai, G.3
Kang, S.4
Gao, X.5
Li, T.6
-
14
-
-
58149179989
-
MiR2Disease: A manually curated database for microRNA deregulation in human disease
-
Jiang,Q., Wang,Y., Hao,Y., Juan,L., Teng,M., Zhang,X., Li,M., Wang,G. and Liu,Y. (2008) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res., 37, D98-D104.
-
(2008)
Nucleic Acids Res.
, vol.37
, pp. D98-D104
-
-
Jiang, Q.1
Wang, Y.2
Hao, Y.3
Juan, L.4
Teng, M.5
Zhang, X.6
Li, M.7
Wang, G.8
Liu, Y.9
-
15
-
-
84891818924
-
StarBase v2
-
Li,J.-H., Liu,S., Zhou,H., Qu,L.-H. and Yang,J.-H. (2013) starBase v2. 0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-seq data. Nucleic Acids Res., 42, D92-D97.
-
(2013)
0: Decoding MiRNA-ceRNA, MiRNA-ncRNA and Protein-RNA Interaction Networks from Large-scale CLIP-seq Data. Nucleic Acids Res.
, vol.42
, pp. D92-D97
-
-
Li, J.-H.1
Liu, S.2
Zhou, H.3
Qu, L.-H.4
Yang, J.-H.5
-
16
-
-
78651271270
-
CLIPZ: A database and analysis environment for experimentally determined binding sites of RNA-binding proteins
-
Khorshid,M., Rodak,C. and Zavolan,M. (2010) CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res., 39, D245-D252.
-
(2010)
Nucleic Acids Res.
, vol.39
, pp. D245-D252
-
-
Khorshid, M.1
Rodak, C.2
Zavolan, M.3
-
17
-
-
84874271270
-
NCBI GEO: Archive for functional genomics data sets-update
-
Barrett,T., Wilhite,S.E., Ledoux,P., Evangelista,C., Kim,I.F., Tomashevsky,M., Marshall,K.A., Phillippy,K.H., Sherman,P.M. and Holko,M. (2012) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
-
(2012)
Nucleic Acids Res.
, vol.41
, pp. D991-D995
-
-
Barrett, T.1
Wilhite, S.E.2
Ledoux, P.3
Evangelista, C.4
Kim, I.F.5
Tomashevsky, M.6
Marshall, K.A.7
Phillippy, K.H.8
Sherman, P.M.9
Holko, M.10
-
18
-
-
84862198590
-
The sequence read archive: Explosive growth of sequencing data
-
Kodama,Y., Shumway,M. and Leinonen,R. (2011) The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res., 40, D54-D56.
-
(2011)
Nucleic Acids Res.
, vol.40
, pp. D54-D56
-
-
Kodama, Y.1
Shumway, M.2
Leinonen, R.3
-
19
-
-
85040910916
-
-
R Development Core Team (2016). R: A Language and Environment for Statistical Computing. R Found. Stat. Comp., Vienna
-
R Development Core Team (2016). R: A Language and Environment for Statistical Computing. R Found. Stat. Comp., Vienna.
-
-
-
-
20
-
-
1342288026
-
Affy-analysis of Affymetrix GeneChip data at the probe level
-
Gautier,L., Cope,L., Bolstad,B.M. and Irizarry,R.A. (2004) affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics, 20, 307-315.
-
(2004)
Bioinformatics
, vol.20
, pp. 307-315
-
-
Gautier, L.1
Cope, L.2
Bolstad, B.M.3
Irizarry, R.A.4
-
21
-
-
77957230671
-
A framework for oligonucleotide microarray preprocessing
-
Carvalho,B.S. and Irizarry,R.A. (2010) A framework for oligonucleotide microarray preprocessing. Bioinformatics, 26, 2363-2367.
-
(2010)
Bioinformatics
, vol.26
, pp. 2363-2367
-
-
Carvalho, B.S.1
Irizarry, R.A.2
-
22
-
-
84926507971
-
Limma powers differential expression analyses for RNA-sequencing and microarray studies
-
Ritchie,M.E., Phipson,B., Wu,D., Hu,Y., Law,C.W., Shi,W. and Smyth,G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e47
-
-
Ritchie, M.E.1
Phipson, B.2
Wu, D.3
Hu, Y.4
Law, C.W.5
Shi, W.6
Smyth, G.K.7
-
23
-
-
84858221706
-
Ensembl 2012
-
Flicek,P., Amode,M.R., Barrell,D., Beal,K., Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G., Fairley,S. and Fitzgerald,S. (2011) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
-
(2011)
Nucleic Acids Res.
, vol.40
, pp. D84-D90
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Carvalho-Silva, D.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
-
24
-
-
84961289551
-
Orchestrating high-throughput genomic analysis with Bioconductor
-
Huber,W., Carey,V.J., Gentleman,R., Anders,S., Carlson,M., Carvalho,B.S., Bravo,H.C., Davis,S., Gatto,L., Girke,T. et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods, 12, 115-121.
-
(2015)
Nat. Methods
, vol.12
, pp. 115-121
-
-
Huber, W.1
Carey, V.J.2
Gentleman, R.3
Anders, S.4
Carlson, M.5
Carvalho, B.S.6
Bravo, H.C.7
Davis, S.8
Gatto, L.9
Girke, T.10
-
25
-
-
84903616729
-
Unambiguous identification of miRNA: Target site interactions by different types of ligation reactions
-
Grosswendt,S., Filipchyk,A., Manzano,M., Klironomos,F., Schilling,M., Herzog,M., Gottwein,E. and Rajewsky,N. (2014) Unambiguous identification of miRNA: target site interactions by different types of ligation reactions. Mol. Cell, 54, 1042-1054.
-
(2014)
Mol. Cell
, vol.54
, pp. 1042-1054
-
-
Grosswendt, S.1
Filipchyk, A.2
Manzano, M.3
Klironomos, F.4
Schilling, M.5
Herzog, M.6
Gottwein, E.7
Rajewsky, N.8
-
26
-
-
84891818318
-
MiRBase: Annotating high confidence microRNAs using deep sequencing data
-
Kozomara,A. and Griffiths-Jones,S. (2013) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-D73.
-
(2013)
Nucleic Acids Res.
, vol.42
, pp. D68-D73
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
27
-
-
84883579190
-
DIANA-microT web server v5
-
Paraskevopoulou,M.D., Georgakilas,G., Kostoulas,N., Vlachos,I.S., Vergoulis,T., Reczko,M., Filippidis,C., Dalamagas,T. and Hatzigeorgiou,A.G. (2013) DIANA-microT web server v5. 0: service integration into miRNA functional analysis workflows. Nucleic Acids Res., 41, W169-W173.
-
(2013)
0: Service Integration into MiRNA Functional Analysis Workflows. Nucleic Acids Res.
, vol.41
, pp. W169-W173
-
-
Paraskevopoulou, M.D.1
Georgakilas, G.2
Kostoulas, N.3
Vlachos, I.S.4
Vergoulis, T.5
Reczko, M.6
Filippidis, C.7
Dalamagas, T.8
Hatzigeorgiou, A.G.9
-
28
-
-
84976875164
-
DIANA-LncBase v2: Indexing microRNA targets on non-coding transcripts
-
Paraskevopoulou,M.D., Vlachos,I.S., Karagkouni,D., Georgakilas,G., Kanellos,I., Vergoulis,T., Zagganas,K., Tsanakas,P., Floros,E. and Dalamagas,T. (2016) DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res., 44, D231-D238.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D231-D238
-
-
Paraskevopoulou, M.D.1
Vlachos, I.S.2
Karagkouni, D.3
Georgakilas, G.4
Kanellos, I.5
Vergoulis, T.6
Zagganas, K.7
Tsanakas, P.8
Floros, E.9
Dalamagas, T.10
-
29
-
-
84979854255
-
DIANA-miRPath v3 0: Deciphering microRNA function with experimental support
-
Vlachos,I.S., Zagganas,K., Paraskevopoulou,M.D., Georgakilas,G., Karagkouni,D., Vergoulis,T., Dalamagas,T. and Hatzigeorgiou,A.G. (2015) DIANA-miRPath v3. 0: deciphering microRNA function with experimental support. Nucleic Acids Res., 43, W460-W466.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. W460-W466
-
-
Vlachos, I.S.1
Zagganas, K.2
Paraskevopoulou, M.D.3
Georgakilas, G.4
Karagkouni, D.5
Vergoulis, T.6
Dalamagas, T.7
Hatzigeorgiou, A.G.8
|