-
1
-
-
58249088751
-
MicroRNAs: Target recognition and regulatory functions
-
Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
-
(2009)
Cell
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
2
-
-
84876939170
-
The long and short of microRNA
-
Yates, L.A., Norbury, C.J. and Gilbert, R.J. (2013) The long and short of microRNA. Cell, 153, 516-519.
-
(2013)
Cell
, vol.153
, pp. 516-519
-
-
Yates, L.A.1
Norbury, C.J.2
Gilbert, R.J.3
-
3
-
-
84922391559
-
Posttranscriptional regulation of gene expression by Piwi proteins and piRNAs
-
Watanabe, T. and Lin, H. (2014) Posttranscriptional regulation of gene expression by Piwi proteins and piRNAs. Mol. Cell, 56, 18-27.
-
(2014)
Mol. Cell
, vol.56
, pp. 18-27
-
-
Watanabe, T.1
Lin, H.2
-
4
-
-
50149095122
-
Endogenous small interfering RNAs in animals
-
Okamura, K. and Lai, E.C. (2008) Endogenous small interfering RNAs in animals. Nat. Rev. Mol. Cell Biol., 9, 673-678.
-
(2008)
Nat. Rev. Mol. Cell Biol.
, vol.9
, pp. 673-678
-
-
Okamura, K.1
Lai, E.C.2
-
5
-
-
0035984059
-
Endogenous and silencing-associated small RNAs in plants
-
Llave, C., Kasschau, K.D., Rector, M.A. and Carrington, J.C. (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell, 14, 1605-1619.
-
(2002)
Plant Cell
, vol.14
, pp. 1605-1619
-
-
Llave, C.1
Kasschau, K.D.2
Rector, M.A.3
Carrington, J.C.4
-
6
-
-
84908125804
-
MicroRNAome genome: A treasure for cancer diagnosis and therapy
-
Berindan-Neagoe, I., Monroig, P.D., Pasculli, B. and Calin, G.A. (2014) MicroRNAome genome: a treasure for cancer diagnosis and therapy. CA Cancer J. Clin, 64, 311-336.
-
(2014)
CA Cancer J. Clin
, vol.64
, pp. 311-336
-
-
Berindan-Neagoe, I.1
Monroig, P.D.2
Pasculli, B.3
Calin, G.A.4
-
7
-
-
2142654329
-
MicroRNA-directed cleavage of HOXB8 mRNA
-
Yekta, S., Shih, I.H. and Bartel, D.P. (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304, 594-596.
-
(2004)
Science
, vol.304
, pp. 594-596
-
-
Yekta, S.1
Shih, I.H.2
Bartel, D.P.3
-
8
-
-
77955492563
-
Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases
-
Karginov, F.V., Cheloufi, S., Chong, M.M., Stark, A., Smith, A.D. and Hannon, G.J. (2010) Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol. Cell, 38, 781-788.
-
(2010)
Mol. Cell
, vol.38
, pp. 781-788
-
-
Karginov, F.V.1
Cheloufi, S.2
Chong, M.M.3
Stark, A.4
Smith, A.D.5
Hannon, G.J.6
-
9
-
-
77955475953
-
Expanding the microRNA targeting code: Functional sites with centered pairing
-
Shin, C., Nam, J.W., Farh, K.K., Chiang, H.R., Shkumatava, A. and Bartel, D.P. (2010) Expanding the microRNA targeting code: functional sites with centered pairing. Mol. Cell, 38, 789-802.
-
(2010)
Mol. Cell
, vol.38
, pp. 789-802
-
-
Shin, C.1
Nam, J.W.2
Farh, K.K.3
Chiang, H.R.4
Shkumatava, A.5
Bartel, D.P.6
-
10
-
-
84898725704
-
Cnidarian microRNAs frequently regulate targets by cleavage
-
Moran, Y., Fredman, D., Praher, D., Li, X.Z., Wee, L.M., Rentzsch, F., Zamore, P.D., Technau, U. and Seitz, H. (2014) Cnidarian microRNAs frequently regulate targets by cleavage. Genome Res., 24, 651-663.
-
(2014)
Genome Res.
, vol.24
, pp. 651-663
-
-
Moran, Y.1
Fredman, D.2
Praher, D.3
Li, X.Z.4
Wee, L.M.5
Rentzsch, F.6
Zamore, P.D.7
Technau, U.8
Seitz, H.9
-
11
-
-
80455143733
-
MiRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA
-
Hansen, T.B., Wiklund, E.D., Bramsen, J.B., Villadsen, S.B., Statham, A.L., Clark, S.J. and Kjems, J. (2011) miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J., 30, 4414-4422.
-
(2011)
EMBO J.
, vol.30
, pp. 4414-4422
-
-
Hansen, T.B.1
Wiklund, E.D.2
Bramsen, J.B.3
Villadsen, S.B.4
Statham, A.L.5
Clark, S.J.6
Kjems, J.7
-
12
-
-
84923879619
-
Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline
-
Watanabe, T., Cheng, E.C., Zhong, M. and Lin, H. (2014) Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline. Genome Res, 25, 368-380.
-
(2014)
Genome Res
, vol.25
, pp. 368-380
-
-
Watanabe, T.1
Cheng, E.C.2
Zhong, M.3
Lin, H.4
-
13
-
-
84922153415
-
MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes
-
Zhang, P., Kang, J.Y., Gou, L.T., Wang, J., Xue, Y., Skogerboe, G., Dai, P., Huang, D.W., Chen, R., Fu, X.D. et al. (2015) MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes. Cell Res., 25, 193-207.
-
(2015)
Cell Res.
, vol.25
, pp. 193-207
-
-
Zhang, P.1
Kang, J.Y.2
Gou, L.T.3
Wang, J.4
Xue, Y.5
Skogerboe, G.6
Dai, P.7
Huang, D.W.8
Chen, R.9
Fu, X.D.10
-
14
-
-
49449118943
-
Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
-
German, M.A., Pillay, M., Jeong, D.H., Hetawal, A., Luo, S., Janardhanan, P., Kannan, V., Rymarquis, L.A., Nobuta, K., German, R. et al. (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol., 26, 941-946.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 941-946
-
-
German, M.A.1
Pillay, M.2
Jeong, D.H.3
Hetawal, A.4
Luo, S.5
Janardhanan, P.6
Kannan, V.7
Rymarquis, L.A.8
Nobuta, K.9
German, R.10
-
15
-
-
63849207321
-
Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome
-
German, M.A., Luo, S., Schroth, G., Meyers, B.C. and Green, P.J. (2009) Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat. Protoc., 4, 356-362.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 356-362
-
-
German, M.A.1
Luo, S.2
Schroth, G.3
Meyers, B.C.4
Green, P.J.5
-
16
-
-
44449142226
-
A link between RNA metabolism and silencing affecting Arabidopsis development
-
Gregory, B.D., O'Malley, R.C., Lister, R., Urich, M.A., Tonti-Filippini, J., Chen, H., Millar, A.H. and Ecker, J.R. (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Dev. Cell, 14, 854-866.
-
(2008)
Dev. Cell
, vol.14
, pp. 854-866
-
-
Gregory, B.D.1
O'Malley, R.C.2
Lister, R.3
Urich, M.A.4
Tonti-Filippini, J.5
Chen, H.6
Millar, A.H.7
Ecker, J.R.8
-
17
-
-
84883212289
-
Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis
-
Karlova, R., van Haarst, J.C., Maliepaard, C., de Geest, H., Bovy, A.G., Lammers, M., Angenent, G.C. and de Maagd, R.A. (2013) Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J. Exp. Bot., 64, 1863-1878.
-
(2013)
J. Exp. Bot.
, vol.64
, pp. 1863-1878
-
-
Karlova, R.1
Van Haarst, J.C.2
Maliepaard, C.3
De Geest, H.4
Bovy, A.G.5
Lammers, M.6
Angenent, G.C.7
De-Maagd, R.A.8
-
18
-
-
84893176226
-
Identification of miRNAs and their target genes in peach (Prunus persica L.) using high-throughput sequencing and degradome analysis
-
Luo, X.Y., Gao, Z.H., Shi, T., Cheng, Z.M., Zhang, Z. and Ni, Z.J. (2013) Identification of miRNAs and their target genes in peach (Prunus persica L.) using high-throughput sequencing and degradome analysis. PloS One, 8, e79090.
-
(2013)
PloS One
, vol.8
, pp. e79090
-
-
Luo, X.Y.1
Gao, Z.H.2
Shi, T.3
Cheng, Z.M.4
Zhang, Z.5
Ni, Z.J.6
-
19
-
-
78651307694
-
StarBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
-
Yang, J.H., Li, J.H., Shao, P., Zhou, H., Chen, Y.Q. and Qu, L.H. (2011) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res., 39, D202-D209.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D202-D209
-
-
Yang, J.H.1
Li, J.H.2
Shao, P.3
Zhou, H.4
Chen, Y.Q.5
Qu, L.H.6
-
20
-
-
58049220318
-
CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets
-
Addo-Quaye, C., Miller, W. and Axtell, M.J. (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics, 25, 130-131.
-
(2009)
Bioinformatics
, vol.25
, pp. 130-131
-
-
Addo-Quaye, C.1
Miller, W.2
Axtell, M.J.3
-
21
-
-
84863238628
-
SeqTar: An effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants
-
Zheng, Y., Li, Y.F., Sunkar, R. and Zhang, W.X. (2012) SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants. Nucleic Acids Res., 40, e28.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e28
-
-
Zheng, Y.1
Li, Y.F.2
Sunkar, R.3
Zhang, W.X.4
-
22
-
-
84922394706
-
SPARTA: A parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software
-
Kakrana, A., Hammond, R., Patel, P., Nakano, M. and Meyers, B.C. (2014) sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software. Nucleic Acids Res., 42, e139.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. e139
-
-
Kakrana, A.1
Hammond, R.2
Patel, P.3
Nakano, M.4
Meyers, B.C.5
-
23
-
-
84864459173
-
PAREsnip: A tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing
-
Folkes, L., Moxon, S., Woolfenden, H.C., Stocks, M.B., Szittya, G., Dalmay, T. and Moulton, V. (2012) PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Res., 40, e103.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e103
-
-
Folkes, L.1
Moxon, S.2
Woolfenden, H.C.3
Stocks, M.B.4
Szittya, G.5
Dalmay, T.6
Moulton, V.7
-
24
-
-
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., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
-
(2013)
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
-
25
-
-
58149185123
-
Ensembl 2009
-
Hubbard, T.J., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D690-D697
-
-
Hubbard, T.J.1
Aken, B.L.2
Ayling, S.3
Ballester, B.4
Beal, K.5
Bragin, E.6
Brent, S.7
Chen, Y.8
Clapham, P.9
Clarke, L.10
-
26
-
-
84875404794
-
The UCSC Genome Browser database: Extensions and updates 2013
-
Meyer, L.R., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Kuhn, R.M., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., Rhead, B. et al. (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res., 41, D64-D69.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D64-D69
-
-
Meyer, L.R.1
Zweig, A.S.2
Hinrichs, A.S.3
Karolchik, D.4
Kuhn, R.M.5
Wong, M.6
Sloan, C.A.7
Rosenbloom, K.R.8
Roe, G.9
Rhead, B.10
-
27
-
-
84865760395
-
GENCODE: The reference human genome annotation for the ENCODE Project
-
Harrow, J., Frankish, A., Gonzalez, J.M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B.L., Barrell, D., Zadissa, A., Searle, S. et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res., 22, 1760-1774.
-
(2012)
Genome Res.
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
Aken, B.L.7
Barrell, D.8
Zadissa, A.9
Searle, S.10
-
28
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
29
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
30
-
-
43449091567
-
Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
-
Addo-Quaye, C., Eshoo, T.W., Bartel, D.P. and Axtell, M.J. (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol., 18, 758-762.
-
(2008)
Curr. Biol.
, vol.18
, pp. 758-762
-
-
Addo-Quaye, C.1
Eshoo, T.W.2
Bartel, D.P.3
Axtell, M.J.4
-
31
-
-
2342626647
-
The RNA-induced silencing complex is a Mg2+-dependent endonuclease
-
Schwarz, D.S., Tomari, Y. and Zamore, P.D. (2004) The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr. Biol., 14, 787-791.
-
(2004)
Curr. Biol.
, vol.14
, pp. 787-791
-
-
Schwarz, D.S.1
Tomari, Y.2
Zamore, P.D.3
-
33
-
-
84984686092
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B (Methodological), 57, 289-300.
-
(1995)
J. R. Stat. Soc. B (Methodological)
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
34
-
-
84899865836
-
A non-canonical plant microRNA target site
-
Brousse, C., Liu, Q.K., Beauclair, L., Deremetz, A., Axtell, M.J. and Bouche, N. (2014) A non-canonical plant microRNA target site. Nucleic Acids Res., 42, 5270-5279.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 5270-5279
-
-
Brousse, C.1
Liu, Q.K.2
Beauclair, L.3
Deremetz, A.4
Axtell, M.J.5
Bouche, N.6
-
35
-
-
77954184918
-
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics
-
Bonnet, E., He, Y., Billiau, K. and Van de Peer, Y. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics, 26, 1566-1568.
-
(2010)
Bioinformatics
, vol.26
, pp. 1566-1568
-
-
Bonnet, E.1
He, Y.2
Billiau, K.3
Van-De-Peer, Y.4
-
36
-
-
84891796290
-
MiRTarBase update 2014: An information resource for experimentally validated miRNA-target interactions
-
Hsu, S.D., Tseng, Y.T., Shrestha, S., Lin, Y.L., Khaleel, A., Chou, C.H., Chu, C.F., Huang, H.Y., Lin, C.M., Ho, S.Y. et al. (2014) miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res., 42, D78-D85.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D78-D85
-
-
Hsu, S.D.1
Tseng, Y.T.2
Shrestha, S.3
Lin, Y.L.4
Khaleel, A.5
Chou, C.H.6
Chu, C.F.7
Huang, H.Y.8
Lin, C.M.9
Ho, S.Y.10
-
37
-
-
0037320231
-
P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function
-
Kasschau, K.D., Xie, Z., Allen, E., Llave, C., Chapman, E.J., Krizan, K.A. and Carrington, J.C. (2003) P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev. Cell, 4, 205-217.
-
(2003)
Dev. Cell
, vol.4
, pp. 205-217
-
-
Kasschau, K.D.1
Xie, Z.2
Allen, E.3
Llave, C.4
Chapman, E.J.5
Krizan, K.A.6
Carrington, J.C.7
|