-
1
-
-
4644309196
-
The functions of animal microRNAs
-
Ambros,V. (2004) The functions of animal microRNAs. Nature, 431 350-355.
-
(2004)
Nature
, vol.431
, pp. 350-355
-
-
Ambros, V.1
-
2
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel,D.P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
3
-
-
28044455435
-
microPrimer: The biogenesis and function of microRNA
-
Du,T. and Zamore,P.D. (2005) microPrimer: The biogenesis and function of microRNA. Development, 132, 4645-4652.
-
(2005)
Development
, vol.132
, pp. 4645-4652
-
-
Du, T.1
Zamore, P.D.2
-
4
-
-
33750370444
-
MicroRNA sigNatures in human cancers
-
Calin,G.A. and Croce,C.M. (2006) MicroRNA sigNatures in human cancers. Nat. Rev. Cancer, 6, 857-866.
-
(2006)
Nat. Rev. Cancer
, vol.6
, pp. 857-866
-
-
Calin, G.A.1
Croce, C.M.2
-
5
-
-
33846188098
-
microRNAs as oncogenes and tumor suppressors
-
Zhang,B., Pan,X., Cobb,G.P. and Anderson,T.A. (2007) microRNAs as oncogenes and tumor suppressors. Dev. Biol., 302, 1-12.
-
(2007)
Dev. Biol
, vol.302
, pp. 1-12
-
-
Zhang, B.1
Pan, X.2
Cobb, G.P.3
Anderson, T.A.4
-
6
-
-
38749083425
-
MicroRNAs and cancer: Profile, profile, profile
-
Barbarotto,E., Schmittgen,T.D. and Calin,G.A. (2008) MicroRNAs and cancer: Profile, profile, profile. Int. J. Cancer, 122, 969-977.
-
(2008)
Int. J. Cancer
, vol.122
, pp. 969-977
-
-
Barbarotto, E.1
Schmittgen, T.D.2
Calin, G.A.3
-
7
-
-
38549150275
-
miRBase: Tools for microRNA genomics
-
Griffiths-Jones,S., Saini,H.K., van Dongen,S. and Enright,A.J. (2008) miRBase: Tools for microRNA genomics. Nucleic Acids Res., 36 D154-D158.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Griffiths-Jones, S.1
Saini, H.K.2
van Dongen, S.3
Enright, A.J.4
-
8
-
-
33748587841
-
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
-
Miranda,K.C., Huynh,T., Tay,Y., Ang,Y.S., Tam,W.L., Thomson,A.M., Lim,B. and Rigoutsos,I. (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203-1217.
-
(2006)
Cell
, vol.126
, pp. 1203-1217
-
-
Miranda, K.C.1
Huynh, T.2
Tay, Y.3
Ang, Y.S.4
Tam, W.L.5
Thomson, A.M.6
Lim, B.7
Rigoutsos, I.8
-
9
-
-
33749377869
-
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
-
Berezikov,E., van Tetering,G., Verheul,M., van de Belt,J., van Laake,L., Vos,J., Verloop,R., van de Wetering,M., Guryev,V., Takada,S. et al. (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res., 16, 1289-1298.
-
(2006)
Genome Res
, vol.16
, pp. 1289-1298
-
-
Berezikov, E.1
van Tetering, G.2
Verheul, M.3
van de Belt, J.4
van Laake, L.5
Vos, J.6
Verloop, R.7
van de Wetering, M.8
Guryev, V.9
Takada, S.10
-
10
-
-
33344477448
-
Genomics of microRNA
-
Kim,V.N. and Nam,J.W. (2006) Genomics of microRNA. Trends Genet., 22, 165-173.
-
(2006)
Trends Genet
, vol.22
, pp. 165-173
-
-
Kim, V.N.1
Nam, J.W.2
-
11
-
-
26944443861
-
Identification and characterization of small RNAs involved in RNA silencing
-
Aravin,A. and Tuschl,T. (2005) Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett., 579, 5830-5840.
-
(2005)
FEBS Lett
, vol.579
, pp. 5830-5840
-
-
Aravin, A.1
Tuschl, T.2
-
12
-
-
22844440427
-
Identification of hundreds of conserved and nonconserved human microRNAs
-
Bentwich,I., Avniel,A., Karov,Y., Aharonov,R., Gilad,S., Barad,O., Barzilai,A., Einat,P., Einav,U., Meiri,E. et al. (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet., 37, 766-770.
-
(2005)
Nat. Genet
, vol.37
, pp. 766-770
-
-
Bentwich, I.1
Avniel, A.2
Karov, Y.3
Aharonov, R.4
Gilad, S.5
Barad, O.6
Barzilai, A.7
Einat, P.8
Einav, U.9
Meiri, E.10
-
13
-
-
0037447334
-
The microRNAs of Caenorhabditis elegans
-
Lim,L.P., Lau,N.C., Weinstein,E.G., Abdelhakim,A., Yekta,S., Rhoades,M.W., Burge,C.B. and Bartel,D.P. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev., 17, 991-1008.
-
(2003)
Genes Dev
, vol.17
, pp. 991-1008
-
-
Lim, L.P.1
Lau, N.C.2
Weinstein, E.G.3
Abdelhakim, A.4
Yekta, S.5
Rhoades, M.W.6
Burge, C.B.7
Bartel, D.P.8
-
14
-
-
0037423845
-
Vertebrate microRNA genes
-
Lim,L.P., Glasner,M.E., Yekta,S., Burge,C.B. and Bartel,D.P. (2003) Vertebrate microRNA genes. Science, 299, 1540.
-
(2003)
Science
, vol.299
, pp. 1540
-
-
Lim, L.P.1
Glasner, M.E.2
Yekta, S.3
Burge, C.B.4
Bartel, D.P.5
-
15
-
-
0038054470
-
Computational and experimental identification of C. elegans microRNAs
-
Grad,Y., Aach,J., Hayes,G.D., Reinhart,B.J., Church,G.M., Ruvkun,G. and Kim,J. (2003) Computational and experimental identification of C. elegans microRNAs. Mol. Cell, 11, 1253-1263.
-
(2003)
Mol. Cell
, vol.11
, pp. 1253-1263
-
-
Grad, Y.1
Aach, J.2
Hayes, G.D.3
Reinhart, B.J.4
Church, G.M.5
Ruvkun, G.6
Kim, J.7
-
16
-
-
0038825783
-
Computational identification of Drosophila microRNA genes
-
Lai,E.C., Tomancak,P., Williams,R.W. and Rubin,G.M. (2003) Computational identification of Drosophila microRNA genes. Genome Biol., 4 R42.
-
(2003)
Genome Biol
, vol.4
-
-
Lai, E.C.1
Tomancak, P.2
Williams, R.W.3
Rubin, G.M.4
-
17
-
-
0242418246
-
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
-
Boffelli,D., McAuliffe,J., Ovcharenko,D., Lewis,K.D., Ovcharenko,I., Pachter,L. and Rubin,E.M. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science, 299, 1391-1394.
-
(2003)
Science
, vol.299
, pp. 1391-1394
-
-
Boffelli, D.1
McAuliffe, J.2
Ovcharenko, D.3
Lewis, K.D.4
Ovcharenko, I.5
Pachter, L.6
Rubin, E.M.7
-
18
-
-
11844262661
-
Phylogenetic shadowing and computational identification of human microRNA genes
-
Berezikov,E., Guryev,V., van de Belt,J., Wienholds,E., Plasterk,R.H. and Cuppen,E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell, 120, 21-24.
-
(2005)
Cell
, vol.120
, pp. 21-24
-
-
Berezikov, E.1
Guryev, V.2
van de Belt, J.3
Wienholds, E.4
Plasterk, R.H.5
Cuppen, E.6
-
19
-
-
0346094457
-
Prediction of mammalian microRNA targets
-
Lewis,B.P., Shih,I.H., Jones-Rhoades,M.W., Bartel,D.P. and Burge,C.B. (2003) Prediction of mammalian microRNA targets. Cell, 115, 787-798.
-
(2003)
Cell
, vol.115
, pp. 787-798
-
-
Lewis, B.P.1
Shih, I.H.2
Jones-Rhoades, M.W.3
Bartel, D.P.4
Burge, C.B.5
-
20
-
-
1642374097
-
Specificity of microRNA target selection in translational repression
-
Doench,J.G. and Sharp,P.A. (2004) Specificity of microRNA target selection in translational repression. Genes Dev., 18, 504-511.
-
(2004)
Genes Dev
, vol.18
, pp. 504-511
-
-
Doench, J.G.1
Sharp, P.A.2
-
21
-
-
18044377963
-
Principles of microRNA-target recognition
-
Brennecke,J., Stark,A., Russell,R.B. and Cohen,S.M. (2005) Principles of microRNA-target recognition. PLoS Biol., 3, e85.
-
(2005)
PLoS Biol
, vol.3
-
-
Brennecke, J.1
Stark, A.2
Russell, R.B.3
Cohen, S.M.4
-
22
-
-
4243170045
-
Identification of Drosophila MicroRNA targets
-
Stark,A., Brennecke,J., Russell,R.B. and Cohen,S.M. (2003) Identification of Drosophila MicroRNA targets. PLoS Biol., 1 E60.
-
(2003)
PLoS Biol
, vol.1
-
-
Stark, A.1
Brennecke, J.2
Russell, R.B.3
Cohen, S.M.4
-
23
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
-
Xie,X., Lu,J., Kulbokas,E.J., Golub,T.R., Mootha,V., Lindblad-Toh,K., Lander,E.S. and Kellis,M. (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature, 434, 338-345.
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
24
-
-
39549097946
-
Computational and transcriptional evidence for microRNAs in the honey bee genome
-
Weaver,D.B., Anzola,J.M., Evans,J.D., Reid,J.G., Reese,J.T., Childs,K.L., Zdobnov,E.M., Samanta,M.P., Miller,J. and Elsik,C.G. (2007) Computational and transcriptional evidence for microRNAs in the honey bee genome. Genome Biol., 8, R97.
-
(2007)
Genome Biol
, vol.8
-
-
Weaver, D.B.1
Anzola, J.M.2
Evans, J.D.3
Reid, J.G.4
Reese, J.T.5
Childs, K.L.6
Zdobnov, E.M.7
Samanta, M.P.8
Miller, J.9
Elsik, C.G.10
-
25
-
-
10244243802
-
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
-
Bonnet,E., Wuyts,J., Rouze,P. and Van de Peer,Y. (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics, 20, 2911-2917.
-
(2004)
Bioinformatics
, vol.20
, pp. 2911-2917
-
-
Bonnet, E.1
Wuyts, J.2
Rouze, P.3
Van de Peer, Y.4
-
26
-
-
14044272835
-
Fast and reliable prediction of noncoding RNAs
-
Washietl,S., Hofacker,I.L. and Stadler,P.F. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102 2454-2459.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 2454-2459
-
-
Washietl, S.1
Hofacker, I.L.2
Stadler, P.F.3
-
27
-
-
27844508214
-
Identification of clustered microRNAs using an ab initio prediction method
-
Sewer,A., Paul,N., Landgraf,P., Aravin,A., Pfeffer,S., Brownstein,M.J., Tuschl,T., van Nimwegen,E. and Zavolan,M. (2005) Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics, 6, 267.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 267
-
-
Sewer, A.1
Paul, N.2
Landgraf, P.3
Aravin, A.4
Pfeffer, S.5
Brownstein, M.J.6
Tuschl, T.7
van Nimwegen, E.8
Zavolan, M.9
-
28
-
-
30344447264
-
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
-
Xue,C., Li,F., He,T., Liu,G.P., Li,Y. and Zhang,X. (2005) Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics, 6, 310.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 310
-
-
Xue, C.1
Li, F.2
He, T.3
Liu, G.P.4
Li, Y.5
Zhang, X.6
-
29
-
-
33747814183
-
ProMiR II: A web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
-
Nam,J.W., Kim,J., Kim,S.K. and Zhang,B.T. (2006) ProMiR II: A web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs. Nucleic Acids Res., 34, W455-W458.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Nam, J.W.1
Kim, J.2
Kim, S.K.3
Zhang, B.T.4
-
30
-
-
33846650507
-
Reliable prediction of Drosha processing sites improves microRNA gene prediction
-
Helvik,S.A., Snove,O. Jr. and Saetrom,P. (2007) Reliable prediction of Drosha processing sites improves microRNA gene prediction. Bioinformatics, 23, 142-149.
-
(2007)
Bioinformatics
, vol.23
, pp. 142-149
-
-
Helvik, S.A.1
Snove Jr., O.2
Saetrom, P.3
-
31
-
-
34447309058
-
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
-
Ng,K.L. and Mishra,S.K. (2007) De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics, 23, 1321-1330.
-
(2007)
Bioinformatics
, vol.23
, pp. 1321-1330
-
-
Ng, K.L.1
Mishra, S.K.2
-
32
-
-
34547596338
-
MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features
-
Jiang,P., Wu,H., Wang,W., Ma,W., Sun,X. and Lu,Z. (2007) MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 35, W339-W344.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Jiang, P.1
Wu, H.2
Wang, W.3
Ma, W.4
Sun, X.5
Lu, Z.6
-
33
-
-
1042304206
-
Prediction of locally stable RNA secondary structures for genome-wide surveys
-
Hofacker,I.L., Priwitzer,B. and Stadler,P.F. (2004) Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics, 20, 186-190.
-
(2004)
Bioinformatics
, vol.20
, pp. 186-190
-
-
Hofacker, I.L.1
Priwitzer, B.2
Stadler, P.F.3
-
34
-
-
30744468557
-
Evidence that miRNAs are different from other RNAs
-
Zhang,B.H., Pan,X.P., Cox,S.B., Cobb,G.P. and Anderson,T.A. (2006) Evidence that miRNAs are different from other RNAs. Cell Mol. Life Sci., 63, 246-254.
-
(2006)
Cell Mol. Life Sci
, vol.63
, pp. 246-254
-
-
Zhang, B.H.1
Pan, X.P.2
Cox, S.B.3
Cobb, G.P.4
Anderson, T.A.5
-
35
-
-
13444252847
-
Rfam: Annotating non-coding RNAs in complete genomes
-
Griffiths-Jones,S., Moxon,S., Marshall,M., Khanna,A., Eddy,S.R. and Bateman,A. (2005) Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Griffiths-Jones, S.1
Moxon, S.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
Bateman, A.6
-
36
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li,W. and Godzik,A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
37
-
-
32544440797
-
RNAshapes: An integrated RNA analysis package based on abstract shapes
-
Steffen,P., Voss,B., Rehmsmeier,M., Reeder,J. and Giegerich,R. (2006) RNAshapes: An integrated RNA analysis package based on abstract shapes. Bioinformatics, 22, 500-503.
-
(2006)
Bioinformatics
, vol.22
, pp. 500-503
-
-
Steffen, P.1
Voss, B.2
Rehmsmeier, M.3
Reeder, J.4
Giegerich, R.5
-
38
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh,K. and Toh,H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform., 9, 286-298.
-
(2008)
Brief Bioinform
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
39
-
-
38549105500
-
OrthoDB: The hierarchical catalog of eukaryotic orthologs
-
Kriventseva,E.V., Rahman,N., Espinosa,O. and Zdobnov,E.M. (2008) OrthoDB: The hierarchical catalog of eukaryotic orthologs. Nucleic Acids Res., 36, D271-D275.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Kriventseva, E.V.1
Rahman, N.2
Espinosa, O.3
Zdobnov, E.M.4
-
40
-
-
23144452802
-
PARALIGN: Rapid and sensitive sequence similarity searches powered by parallel computing technology
-
Saebo,P.E., Andersen,S.M., Myrseth,J., Laerdahl,J.K. and Rognes,T. (2005) PARALIGN: Rapid and sensitive sequence similarity searches powered by parallel computing technology. Nucleic Acids Res., 33, W535-W539.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Saebo, P.E.1
Andersen, S.M.2
Myrseth, J.3
Laerdahl, J.K.4
Rognes, T.5
-
41
-
-
44349140636
-
R-Coffee: A method for multiple alignment of non-coding RNA
-
Wilm,A., Higgins,D.G. and Notredame,C. (2008) R-Coffee: A method for multiple alignment of non-coding RNA. Nucleic Acids Res., 36 e52.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wilm, A.1
Higgins, D.G.2
Notredame, C.3
-
42
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar,R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
43
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do,C.B., Mahabhashyam,M.S., Brudno,M. and Batzoglou,S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
-
(2005)
Genome Res
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.2
Brudno, M.3
Batzoglou, S.4
-
44
-
-
0036301332
-
Secondary structure prediction for aligned RNA sequences
-
Hofacker,I.L., Fekete,M. and Stadler,P.F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
-
(2002)
J. Mol. Biol
, vol.319
, pp. 1059-1066
-
-
Hofacker, I.L.1
Fekete, M.2
Stadler, P.F.3
|