-
1
-
-
14044251458
-
Human MicroRNA targets
-
John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C. and Marks, D.S. (2004) Human MicroRNA targets. PLoS Biol., 2, e363.
-
(2004)
PLoS Biol.
, vol.2
, pp. e363
-
-
John, B.1
Enright, A.J.2
Aravin, A.3
Tuschl, T.4
Sander, C.5
Marks, D.S.6
-
2
-
-
3042767202
-
MicroRNAs: Small RNAs with a big role in gene regulation
-
He, L. and Hannon, G.J. (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet., 5, 522-531.
-
(2004)
Nat. Rev. Genet
, vol.5
, pp. 522-531
-
-
He, L.1
Hannon, G.J.2
-
3
-
-
84877677064
-
Classification and comparison of small RNAs from plants
-
Axtell, M.J. (2013) Classification and comparison of small RNAs from plants. Annu. Rev. Plant Biol., 64, 137-159.
-
(2013)
Annu. Rev. Plant Biol.
, vol.64
, pp. 137-159
-
-
Axtell, M.J.1
-
4
-
-
84926409098
-
Role of microRNAs in plant drought tolerance
-
Ferdous, J., Hussain, S.S. and Shi, B.-J. (2015) Role of microRNAs in plant drought tolerance. Plant Biotechnol. J., 13, 293-305.
-
(2015)
Plant Biotechnol. J.
, vol.13
, pp. 293-305
-
-
Ferdous, J.1
Hussain, S.S.2
Shi, B.-J.3
-
5
-
-
84879176878
-
A comprehensive expression profile of microRNAs and other classes of non-coding small RNAs in barley under phosphorous-deficient and -sufficient conditions
-
Hackenberg, M., Huang, P.-J., Huang, C.-Y., Shi, B.-J., Gustafson, P. and Langridge, P. (2013) A comprehensive expression profile of microRNAs and other classes of non-coding small RNAs in barley under phosphorous-deficient and -sufficient conditions. DNA Res., 20, 109-125.
-
(2013)
DNA Res.
, vol.20
, pp. 109-125
-
-
Hackenberg, M.1
Huang, P.-J.2
Huang, C.-Y.3
Shi, B.-J.4
Gustafson, P.5
Langridge, P.6
-
7
-
-
80051713296
-
Angiogenin-induced tRNA fragments inhibit translation initiation
-
Ivanov, P., Emara, M.M., Villen, J., Gygi, S.P. and Anderson, P. (2011) Angiogenin-induced tRNA fragments inhibit translation initiation. Mol. Cell, 43, 613-623.
-
(2011)
Mol. Cell
, vol.43
, pp. 613-623
-
-
Ivanov, P.1
Emara, M.M.2
Villen, J.3
Gygi, S.P.4
Anderson, P.5
-
8
-
-
81755161195
-
Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines
-
Gottwein, E., Corcoran, D.L., Mukherjee, N., Skalsky, R.L., Hafner, M., Nusbaum, J.D., Shamulailatpam, P., Love, C.L., Dave, S.S., Tuschl, T. et al. (2011) Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe, 10, 515-526.
-
(2011)
Cell Host Microbe
, vol.10
, pp. 515-526
-
-
Gottwein, E.1
Corcoran, D.L.2
Mukherjee, N.3
Skalsky, R.L.4
Hafner, M.5
Nusbaum, J.D.6
Shamulailatpam, P.7
Love, C.L.8
Dave, S.S.9
Tuschl, T.10
-
9
-
-
77957938117
-
Viruses, microRNAs, and host interactions
-
Skalsky, R.L. and Cullen, B.R. (2010) Viruses, microRNAs, and host interactions. Annu. Rev. Microbiol., 64, 123-141.
-
(2010)
Annu. Rev. Microbiol.
, vol.64
, pp. 123-141
-
-
Skalsky, R.L.1
Cullen, B.R.2
-
10
-
-
84888363237
-
Small RNA-mediated regulation of host-pathogen interactions
-
Harris, J.F., Micheva-Viteva, S., Li, N. and Hong-Geller, E. (2013) Small RNA-mediated regulation of host-pathogen interactions. Virulence, 4, 785-795.
-
(2013)
Virulence
, vol.4
, pp. 785-795
-
-
Harris, J.F.1
Micheva-Viteva, S.2
Li, N.3
Hong-Geller, E.4
-
11
-
-
20444460289
-
MicroRNA expression profiles classify human cancers
-
Lu, J., Getz, G., Miska, E.A., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebert, B.L., Mak, R.H., Ferrando, A.A. et al. (2005) MicroRNA expression profiles classify human cancers. Nature, 435, 834-838.
-
(2005)
Nature
, vol.435
, pp. 834-838
-
-
Lu, J.1
Getz, G.2
Miska, E.A.3
Alvarez-Saavedra, E.4
Lamb, J.5
Peck, D.6
Sweet-Cordero, A.7
Ebert, B.L.8
Mak, R.H.9
Ferrando, A.A.10
-
12
-
-
84867546396
-
Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions
-
Nolte-'t Hoen, E.N.M., Buermans, H.P.J., Waasdorp, M., Stoorvogel, W., Wauben, M.H.M. and 't Hoen, P.A.C. (2012) Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res., 40, 9272-9285.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 9272-9285
-
-
Nolte'T Hoen, E.N.M.1
Buermans, H.P.J.2
Waasdorp, M.3
Stoorvogel, W.4
Wauben, M.H.M.5
'T Hoen, P.A.C.6
-
13
-
-
84907415649
-
Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes
-
Koppers-Lalic, D., Hackenberg, M., Bijnsdorp, I.V., van Eijndhoven, M.A.J., Sadek, P., Sie, D., Zini, N., Middeldorp, J.M., Ylstra, B., de Menezes, R.X. et al. (2014) Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes. Cell Rep., 8, 1649-1658.
-
(2014)
Cell Rep.
, vol.8
, pp. 1649-1658
-
-
Koppers-Lalic, D.1
Hackenberg, M.2
Bijnsdorp, I.V.3
Van Eijndhoven, M.A.J.4
Sadek, P.5
Sie, D.6
Zini, N.7
Middeldorp, J.M.8
Ylstra, B.9
De Menezes, R.X.10
-
14
-
-
77957091969
-
Circulating microRNA in body fluid: A new potential biomarker for cancer diagnosis and prognosis
-
Kosaka, N., Iguchi, H. and Ochiya, T. (2010) Circulating microRNA in body fluid: a new potential biomarker for cancer diagnosis and prognosis. Cancer Sci., 101, 2087-2092.
-
(2010)
Cancer Sci.
, vol.101
, pp. 2087-2092
-
-
Kosaka, N.1
Iguchi, H.2
Ochiya, T.3
-
15
-
-
84901833952
-
Surface analysis of Dicrocoelium dendriticum. The molecular characterization of exosomes reveals the presence of miRNAs
-
Bernal, D., Trelis, M., Montaner, S., Cantalapiedra, F., Galiano, A., Hackenberg, M. and Marcilla, A. (2014) Surface analysis of Dicrocoelium dendriticum. The molecular characterization of exosomes reveals the presence of miRNAs. J. Proteomics, 105, 232-241.
-
(2014)
J. Proteomics
, vol.105
, pp. 232-241
-
-
Bernal, D.1
Trelis, M.2
Montaner, S.3
Cantalapiedra, F.4
Galiano, A.5
Hackenberg, M.6
Marcilla, A.7
-
16
-
-
84921530965
-
Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity
-
Buck, A.H., Coakley, G., Simbari, F., McSorley, H.J., Quintana, J.F., Le Bihan, T., Kumar, S., Abreu-Goodger, C., Lear, M., Harcus, Y. et al. (2014) Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nat. Commun., 5, 5488.
-
(2014)
Nat. Commun.
, vol.5
, pp. 5488
-
-
Buck, A.H.1
Coakley, G.2
Simbari, F.3
McSorley, H.J.4
Quintana, J.F.5
Le Bihan, T.6
Kumar, S.7
Abreu-Goodger, C.8
Lear, M.9
Harcus, Y.10
-
17
-
-
52949088691
-
A toolkit for analysing large-scale plant small RNA datasets
-
Moxon, S., Schwach, F., Dalmay, T., Maclean, D., Studholme, D.J. and Moulton, V. (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics, 24, 2252-2253.
-
(2008)
Bioinformatics
, vol.24
, pp. 2252-2253
-
-
Moxon, S.1
Schwach, F.2
Dalmay, T.3
Maclean, D.4
Studholme, D.J.5
Moulton, V.6
-
18
-
-
41849084855
-
Discovering microRNAs from deep sequencing data using miRDeep
-
Friedländer, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S. and Rajewsky, N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 407-415
-
-
Friedländer, M.R.1
Chen, W.2
Adamidi, C.3
Maaskola, J.4
Einspanier, R.5
Knespel, S.6
Rajewsky, N.7
-
19
-
-
67849114241
-
MiRanalyzer: A microRNA detection and analysis tool for next-generation sequencing experiments
-
Hackenberg, M., Sturm, M., Langenberger, D., Falcón-Pérez, J.M. and Aransay, A.M. (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 37, W68-W76.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W68-W76
-
-
Hackenberg, M.1
Sturm, M.2
Langenberger, D.3
Falcón-Pérez, J.M.4
Aransay, A.M.5
-
20
-
-
79959953839
-
MiRanalyzer: An update on the detection and analysis of microRNAs in high-throughput sequencing experiments
-
Hackenberg, M., Rodríguez-Ezpeleta, N. and Aransay, A.M. (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res., 39, W132-W138.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W132-W138
-
-
Hackenberg, M.1
Rodríguez-Ezpeleta, N.2
Aransay, A.M.3
-
21
-
-
77951655424
-
SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells
-
Pantano, L., Estivill, X. and Martí, E. (2010) SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res., 38, e34.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e34
-
-
Pantano, L.1
Estivill, X.2
Martí, E.3
-
22
-
-
79960019676
-
DARIO: A ncRNA detection and analysis tool for next-generation sequencing experiments
-
Fasold, M., Langenberger, D., Binder, H., Stadler, P.F. and Hoffmann, S. (2011) DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 39, W112-W117.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W112-W117
-
-
Fasold, M.1
Langenberger, D.2
Binder, H.3
Stadler, P.F.4
Hoffmann, S.5
-
23
-
-
84865121074
-
The UEA sRNA workbench: A suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets
-
Stocks, M.B., Moxon, S., Mapleson, D., Woolfenden, H.C., Mohorianu, I., Folkes, L., Schwach, F., Dalmay, T. and Moulton, V. (2012) The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics, 28, 2059-2061.
-
(2012)
Bioinformatics
, vol.28
, pp. 2059-2061
-
-
Stocks, M.B.1
Moxon, S.2
Mapleson, D.3
Woolfenden, H.C.4
Mohorianu, I.5
Folkes, L.6
Schwach, F.7
Dalmay, T.8
Moulton, V.9
-
24
-
-
84855293838
-
MiRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
-
Friedländer, M.R., Mackowiak, S.D., Li, N., Chen, W. and Rajewsky, N. (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40, 37-52.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 37-52
-
-
Friedländer, M.R.1
Mackowiak, S.D.2
Li, N.3
Chen, W.4
Rajewsky, N.5
-
25
-
-
84878022987
-
ShortStack: Comprehensive annotation and quantification of small RNA genes
-
Axtell, M.J. (2013) ShortStack: comprehensive annotation and quantification of small RNA genes. RNA, 19, 740-751.
-
(2013)
RNA
, vol.19
, pp. 740-751
-
-
Axtell, M.J.1
-
26
-
-
84880902774
-
MirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing
-
Wu, J., Liu, Q., Wang, X., Zheng, J., Wang, T., You, M., Sheng Sun, Z. and Shi, Q. (2013) mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing. RNA Biol., 10, 1087-1092.
-
(2013)
RNA Biol.
, vol.10
, pp. 1087-1092
-
-
Wu, J.1
Liu, Q.2
Wang, X.3
Zheng, J.4
Wang, T.5
You, M.6
Sheng Sun, Z.7
Shi, Q.8
-
27
-
-
84942924912
-
SRNAbench: Profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments
-
Barturen, G., Rueda, A., Hamberg, M., Alganza, A., Lebron, R., Kotsyfakis, M., Shi, B.-J., Koppers-Lalic, D. and Hackenberg, M. (2014) sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments. Methods Next Gener. Seq., 1, 21-31.
-
(2014)
Methods Next Gener. Seq.
, vol.1
, pp. 21-31
-
-
Barturen, G.1
Rueda, A.2
Hamberg, M.3
Alganza, A.4
Lebron, R.5
Kotsyfakis, M.6
Shi, B.-J.7
Koppers-Lalic, D.8
Hackenberg, M.9
-
28
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
-
(2010)
Genome Biol.
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
29
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M.D., McCarthy, D.J. and Smyth, G.K. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
30
-
-
83055192078
-
Differential expression in RNA-seq: A matter of depth
-
Tarazona, S., Garcia-Alcalde, F., Dopazo, J., Ferrer, A. and Conesa, A. (2011) Differential expression in RNA-seq: a matter of depth. Genome research, 21, 2213-2223.
-
(2011)
Genome Research
, vol.21
, pp. 2213-2223
-
-
Tarazona, S.1
Garcia-Alcalde, F.2
Dopazo, J.3
Ferrer, A.4
Conesa, A.5
-
31
-
-
34748821761
-
The role of site accessibility in microRNA target recognition
-
Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. and Segal, E. (2007) The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278-1284.
-
(2007)
Nat. Genet
, vol.39
, pp. 1278-1284
-
-
Kertesz, M.1
Iovino, N.2
Unnerstall, U.3
Gaul, U.4
Segal, E.5
-
32
-
-
77952671774
-
TargetSpy: A supervised machine learning approach for microRNA target prediction
-
Sturm, M., Hackenberg, M., Langenberger, D. and Frishman, D. (2010) TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics, 11, 292.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 292
-
-
Sturm, M.1
Hackenberg, M.2
Langenberger, D.3
Frishman, D.4
-
33
-
-
84864491712
-
PsRobot: A web-based plant small RNA meta-analysis toolbox
-
Wu, H.-J., Ma, Y.-K., Chen, T., Wang, M. and Wang, X.-J. (2012) PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res., 40, W22-W28.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W22-W28
-
-
Wu, H.-J.1
Ma, Y.-K.2
Chen, T.3
Wang, M.4
Wang, X.-J.5
-
34
-
-
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
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
37
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
-
(2000)
Nat. Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
38
-
-
44349171852
-
Annotation-Modules: A tool for finding significant combinations of multisource annotations for gene lists
-
Hackenberg, M. and Matthiesen, R. (2008) Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists. Bioinformatics, 24, 1386-1393.
-
(2008)
Bioinformatics
, vol.24
, pp. 1386-1393
-
-
Hackenberg, M.1
Matthiesen, R.2
-
39
-
-
84862176128
-
TarBase 6.0: Capturing the exponential growth of miRNA targets with experimental support
-
Vergoulis, T., Vlachos, I.S., Alexiou, P., Georgakilas, G., Maragkakis, M., Reczko, M., Gerangelos, S., Koziris, N., Dalamagas, T. and Hatzigeorgiou, A.G. (2012) TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res., 40, D222-D229.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D222-D229
-
-
Vergoulis, T.1
Vlachos, I.S.2
Alexiou, P.3
Georgakilas, G.4
Maragkakis, M.5
Reczko, M.6
Gerangelos, S.7
Koziris, N.8
Dalamagas, T.9
Hatzigeorgiou, A.G.10
-
40
-
-
79959967431
-
PsRNATarget: A plant small RNA target analysis server
-
Dai, X. and Zhao, P.X. (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res., 39, W155-W159.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W155-W159
-
-
Dai, X.1
Zhao, P.X.2
-
41
-
-
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
-
42
-
-
84879755312
-
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications
-
Röhr, C., Kerick, M., Fischer, A., Kühn, A., Kashofer, K., Timmermann, B., Daskalaki, A., Meinel, T., Drichel, D., Börno, S.T. et al. (2013) High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. PLoS One, 8, e67461.
-
(2013)
PLoS One
, vol.8
, pp. e67461
-
-
Röhr, C.1
Kerick, M.2
Fischer, A.3
Kühn, A.4
Kashofer, K.5
Timmermann, B.6
Daskalaki, A.7
Meinel, T.8
Drichel, D.9
Börno, S.T.10
-
43
-
-
84984676179
-
A Salmonella-encoded microRNA-like RNA facilitates bacterial invasion and intracellular replication via suppressing host cell inducible nitric oxide synthase (MPF3P.809)
-
Gu, H., Zhang, T., Li, D., Liu, F., Zhang, C.-Y. and Zen, K. (2014) A Salmonella-encoded microRNA-like RNA facilitates bacterial invasion and intracellular replication via suppressing host cell inducible nitric oxide synthase (MPF3P.809). J. Immunol., 192, 132.
-
(2014)
J. Immunol.
, vol.192
, pp. 132
-
-
Gu, H.1
Zhang, T.2
Li, D.3
Liu, F.4
Zhang, C.-Y.5
Zen, K.6
|