-
1
-
-
60149088848
-
Origins and Mechaisms of miRNAs and siRNAs
-
10.1016/j.cell.2009.01.035, 2675692, 19239886
-
Carthew RW, Sontheimer EJ. Origins and Mechaisms of miRNAs and siRNAs. Cell 2009, 136(4):642-655. 10.1016/j.cell.2009.01.035, 2675692, 19239886.
-
(2009)
Cell
, vol.136
, Issue.4
, pp. 642-655
-
-
Carthew, R.W.1
Sontheimer, E.J.2
-
2
-
-
33645525893
-
MicroRNAS and their regulatory roles in plants
-
10.1146/annurev.arplant.57.032905.105218, 16669754
-
Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 2006, 57:19-53. 10.1146/annurev.arplant.57.032905.105218, 16669754.
-
(2006)
Annu Rev Plant Biol
, vol.57
, pp. 19-53
-
-
Jones-Rhoades, M.W.1
Bartel, D.P.2
Bartel, B.3
-
3
-
-
0035955374
-
Identification of novel genes coding for small expressed RNAs
-
10.1126/science.1064921, 11679670
-
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001, 294:853-858. 10.1126/science.1064921, 11679670.
-
(2001)
Science
, vol.294
, pp. 853-858
-
-
Lagos-Quintana, M.1
Rauhut, R.2
Lendeckel, W.3
Tuschl, T.4
-
4
-
-
0035955361
-
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
-
10.1126/science.1065062, 11679671
-
Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001, 294:858-862. 10.1126/science.1065062, 11679671.
-
(2001)
Science
, vol.294
, pp. 858-862
-
-
Lau, N.C.1
Lim, L.P.2
Weinstein, E.G.3
Bartel, D.P.4
-
5
-
-
0034597777
-
Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
-
10.1038/35040556, 11081512
-
Pasquinell AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000, 408:86-89. 10.1038/35040556, 11081512.
-
(2000)
Nature
, vol.408
, pp. 86-89
-
-
Pasquinell, A.E.1
Reinhart, B.J.2
Slack, F.3
Martindale, M.Q.4
Kuroda, M.I.5
-
6
-
-
52949088691
-
A toolkit for analysing large-scale plant small RNA datasets
-
10.1093/bioinformatics/btn428, 18713789
-
Moxon S, Schwach F, Dalmay T, Maclean D, Studholme DJ, Moulton V. A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 2008, 24(19):2252-2253. 10.1093/bioinformatics/btn428, 18713789.
-
(2008)
Bioinformatics
, vol.24
, Issue.19
, pp. 2252-2253
-
-
Moxon, S.1
Schwach, F.2
Dalmay, T.3
Maclean, D.4
Studholme, D.J.5
Moulton, V.6
-
7
-
-
67849114241
-
MiRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments
-
10.1093/nar/gkp347, 2703919, 19433510
-
Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, Aransay AM. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 2009, (37 Web Server):W68-76. 10.1093/nar/gkp347, 2703919, 19433510.
-
(2009)
Nucleic Acids Res
, Issue.37
-
-
Hackenberg, M.1
Sturm, M.2
Langenberger, D.3
Falcón-Pérez, J.M.4
Aransay, A.M.5
-
8
-
-
77954330416
-
MirTools: microRNA profiling and discovery based on high-throughput sequencing
-
10.1093/nar/gkq393, 2896132, 20478827
-
Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res 2010, 38(Suppl):W392-7. 10.1093/nar/gkq393, 2896132, 20478827.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.SUPPL
-
-
Zhu, E.1
Zhao, F.2
Xu, G.3
Hou, H.4
Zhou, L.5
Li, X.6
Sun, Z.7
Wu, J.8
-
9
-
-
41849084855
-
Discovering microRNAs from deep sequencing data using miRDeep
-
Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008, 26(4):407-415.
-
(2008)
Nat Biotechnol
, vol.26
, Issue.4
, 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
-
10
-
-
70449639806
-
MiRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression
-
10.1186/1471-2105-10-328, 2767369, 19821977
-
Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS. miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics 2009, 10(1):328. 10.1186/1471-2105-10-328, 2767369, 19821977.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.1
, pp. 328
-
-
Wang, W.C.1
Lin, F.M.2
Chang, W.C.3
Lin, K.Y.4
Huang, H.D.5
Lin, N.S.6
-
11
-
-
79952448266
-
MiroPipeline
-
MiroPipeline. , http://seq.crg.es/main/bin/view/Home/MiroPipeline
-
-
-
-
12
-
-
33845688601
-
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
-
10.1101/gad.1476406, 1698448, 17182867
-
Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20(24):3407-3425. 10.1101/gad.1476406, 1698448, 17182867.
-
(2006)
Genes Dev
, vol.20
, Issue.24
, pp. 3407-3425
-
-
Rajagopalan, R.1
Vaucheret, H.2
Trejo, J.3
Bartel, D.P.4
-
13
-
-
42149157716
-
Identification of novel and candidate miRNAs in rice by high throughput sequencing
-
10.1186/1471-2229-8-25, 2292181, 18312648
-
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 2008, 8:25. 10.1186/1471-2229-8-25, 2292181, 18312648.
-
(2008)
BMC Plant Biol
, vol.8
, pp. 25
-
-
Sunkar, R.1
Zhou, X.2
Zheng, Y.3
Zhang, W.4
Zhu, J.K.5
-
14
-
-
73649133268
-
A genome-wide characterization of microRNA genes in maize
-
10.1371/journal.pgen.1000716, 2773440, 19936050
-
Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D. A genome-wide characterization of microRNA genes in maize. PLoS Genet 2009, 5(11):e1000716. 10.1371/journal.pgen.1000716, 2773440, 19936050.
-
(2009)
PLoS Genet
, vol.5
, Issue.11
-
-
Zhang, L.1
Chia, J.M.2
Kumari, S.3
Stein, J.C.4
Liu, Z.5
Narechania, A.6
Maher, C.A.7
Guill, K.8
McMullen, M.D.9
Ware, D.10
-
16
-
-
10244243802
-
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
-
10.1093/bioinformatics/bth374, 15217813
-
Bonnet E, Wuyts J, Rouzé P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 2004, 20:2911-2917. 10.1093/bioinformatics/bth374, 15217813.
-
(2004)
Bioinformatics
, vol.20
, pp. 2911-2917
-
-
Bonnet, E.1
Wuyts, J.2
Rouzé, P.3
Van de Peer, Y.4
-
17
-
-
0025731211
-
A Comparison of Optimal and Suboptimal RNA Secondary Structures Predicted by Free Energy Minimization with Structures Determined by Phylogenetic Comparison
-
10.1093/nar/19.10.2707, 328190, 1710343
-
Zuker M, Jaeger JA, Turner DH. A Comparison of Optimal and Suboptimal RNA Secondary Structures Predicted by Free Energy Minimization with Structures Determined by Phylogenetic Comparison. Nucleic Acids Res 1991, 19:2707-2714. 10.1093/nar/19.10.2707, 328190, 1710343.
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 2707-2714
-
-
Zuker, M.1
Jaeger, J.A.2
Turner, D.H.3
-
18
-
-
34249772381
-
Fast Folding and Comparison of RNA Secondary Structures
-
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P. Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 1994, 125:167-188.
-
(1994)
Monatshefte f. Chemie
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, S.4
Tacker, M.5
Schuster, P.6
-
19
-
-
38549150275
-
MiRBase: tools for microRNA genomics
-
2238936, 17991681
-
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, (36 Database):D154-D158. 2238936, 17991681.
-
(2008)
Nucleic Acids Res
, Issue.36
-
-
Griffiths-Jones, S.1
Saini, H.K.2
van Dongen, S.3
Enright, A.J.4
-
20
-
-
0023984725
-
A program for predicting significant RNA secondary structures
-
Le SV, Chen JH, Currey KM, Maizel JV. A program for predicting significant RNA secondary structures. Comput Appl Biosci 1988, 4:153-159.
-
(1988)
Comput Appl Biosci
, vol.4
, pp. 153-159
-
-
Le, S.V.1
Chen, J.H.2
Currey, K.M.3
Maizel, J.V.4
-
21
-
-
0024345473
-
Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses
-
10.1093/nar/17.15.6143, 318267, 2549508
-
Le SY, Chen JH, Maizel JV. Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses. Nucleic Acids Res 1989, 17:6143-6152. 10.1093/nar/17.15.6143, 318267, 2549508.
-
(1989)
Nucleic Acids Res
, vol.17
, pp. 6143-6152
-
-
Le, S.Y.1
Chen, J.H.2
Maizel, J.V.3
-
22
-
-
0027751663
-
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
-
10.1016/0092-8674(93)90529-Y, 8252621
-
Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854. 10.1016/0092-8674(93)90529-Y, 8252621.
-
(1993)
Cell
, vol.75
, pp. 843-854
-
-
Lee, R.C.1
Feinbaum, R.L.2
Ambros, V.3
-
23
-
-
0037144457
-
Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
-
10.1126/science.1076311, 12242443
-
Llave C, Xie Z, Kasschau KD, Carrington JC. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297:2053-2056. 10.1126/science.1076311, 12242443.
-
(2002)
Science
, vol.297
, pp. 2053-2056
-
-
Llave, C.1
Xie, Z.2
Kasschau, K.D.3
Carrington, J.C.4
-
24
-
-
0036645146
-
MicroRNAs in plants
-
10.1101/gad.1004402, 186362, 12101121
-
Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev 2002, 16:1616-1626. 10.1101/gad.1004402, 186362, 12101121.
-
(2002)
Genes Dev
, vol.16
, pp. 1616-1626
-
-
Reinhart, B.J.1
Weinstein, E.G.2
Rhoades, M.W.3
Bartel, B.4
Bartel, D.P.5
-
25
-
-
12744261466
-
Computational prediction of miRNAs in Arabidopsis thaliana
-
10.1101/gr.2908205, 540280, 15632092
-
Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 2005, 15:78-91. 10.1101/gr.2908205, 540280, 15632092.
-
(2005)
Genome Res
, vol.15
, pp. 78-91
-
-
Adai, A.1
Johnson, C.2
Mlotshwa, S.3
Archer-Evans, S.4
Manocha, V.5
Vance, V.6
Sundaresan, V.7
-
26
-
-
58249088751
-
MicroRNAs: target recognition and regulatory functions
-
Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009, 36(2):215-233.
-
(2009)
Cell
, vol.36
, Issue.2
, pp. 215-233
-
-
Bartel, D.P.1
-
27
-
-
0346094457
-
Prediction of mammalian microRNA targets
-
10.1016/S0092-8674(03)01018-3, 14697198
-
Lewis N, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
-
(2003)
Cell
, vol.115
, pp. 787-798
-
-
Lewis, N.1
Shih, I.H.2
Jones-Rhoades, M.W.3
Bartel, D.P.4
Burge, C.B.5
-
28
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
10.1016/j.cell.2004.12.035, 15652477
-
Lewis N, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20. 10.1016/j.cell.2004.12.035, 15652477.
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, N.1
Burge, C.B.2
Bartel, D.P.3
-
29
-
-
20944450160
-
Combinatorial microRNA target predictions
-
10.1038/ng1536, 15806104
-
Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions. Nat. Genet 2005, 37:495-500. 10.1038/ng1536, 15806104.
-
(2005)
Nat. Genet
, vol.37
, pp. 495-500
-
-
Krek, A.1
Grün, D.2
Poy, M.N.3
Wolf, R.4
Rosenberg, L.5
Epstein, E.J.6
MacMenamin, P.7
da Piedade, I.8
Gunsalus, K.C.9
Stoffel, M.10
Rajewsky, N.11
-
30
-
-
2942672580
-
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
-
10.1016/j.molcel.2004.05.027, 15200956
-
Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004, 14(6):787-799. 10.1016/j.molcel.2004.05.027, 15200956.
-
(2004)
Mol Cell
, vol.14
, Issue.6
, pp. 787-799
-
-
Jones-Rhoades, M.W.1
Bartel, D.P.2
-
31
-
-
60149090481
-
Criteria for annotation of plant MicroRNAs
-
10.1105/tpc.108.064311, 2630443, 19074682
-
Meyers BC, Axtell MJ, Bartel B, et al. Criteria for annotation of plant MicroRNAs. Plant Cell 2008, 20(12):3186-3190. 10.1105/tpc.108.064311, 2630443, 19074682.
-
(2008)
Plant Cell
, vol.20
, Issue.12
, pp. 3186-3190
-
-
Meyers, B.C.1
Axtell, M.J.2
Bartel, B.3
-
32
-
-
56649102410
-
Evolution of Arabidopsis MIR genes generates novel microRNA classes
-
10.1093/nar/gkn670, 2582634, 18842626
-
Vazquez F, Blevins T, Ailhas J, Boller T, Meins F. Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res 2008, 36(20):6429-6438. 10.1093/nar/gkn670, 2582634, 18842626.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.20
, pp. 6429-6438
-
-
Vazquez, F.1
Blevins, T.2
Ailhas, J.3
Boller, T.4
Meins, F.5
-
33
-
-
75549083571
-
PMRD: plant microRNA database
-
10.1093/nar/gkp818, 2808885, 19808935
-
Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z. PMRD: plant microRNA database. Nucleic Acids Res 2010, (38 Database):D806-D813. 10.1093/nar/gkp818, 2808885, 19808935.
-
(2010)
Nucleic Acids Res
, Issue.38
-
-
Zhang, Z.1
Yu, J.2
Li, D.3
Zhang, Z.4
Liu, F.5
Zhou, X.6
Wang, T.7
Ling, Y.8
Su, Z.9
-
34
-
-
79952444595
-
Maize genome cDNA sequences
-
Maize genome cDNA sequences. , http://ftp.maizesequence.org/release-4a.53/filtered-set/ZmB73_4a.53_filtered_cdna.fasta.gz
-
-
-
-
35
-
-
79952455853
-
Phytozome-v6.0
-
Phytozome-v6.0. , http://www.phytozome.net/
-
-
-
-
36
-
-
79952452336
-
MiRCheck
-
miRCheck. , http://web.wi.mit.edu/bartel/pub/softwareDocs/miRcheck.tar
-
-
-
-
37
-
-
79951780811
-
R: A language and environment for statistical computing
-
R: A language and environment for statistical computing. , http://www.R-project.org
-
-
-
-
38
-
-
84872041337
-
MathWorld--A Wolfram Web Resource
-
MathWorld--A Wolfram Web Resource. , http://mathworld.wolfram.com/SigmoidFunction.html
-
-
-
-
39
-
-
0031574072
-
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
-
10.1093/nar/25.24.4876, 147148, 9396791
-
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882. 10.1093/nar/25.24.4876, 147148, 9396791.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
40
-
-
79952440174
-
Small RNA sequences from maize seedlings
-
Small RNA sequences from maize seedlings. , http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM448856
-
-
-
-
41
-
-
0034053725
-
A greedy algorithm for aligning DNA sequences
-
10.1089/10665270050081478, 10890397
-
Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7(1-2):203-14. 10.1089/10665270050081478, 10890397.
-
(2000)
J Comput Biol
, vol.7
, Issue.1-2
, pp. 203-214
-
-
Zhang, Z.1
Schwartz, S.2
Wagner, L.3
Miller, W.4
-
42
-
-
67650711615
-
SOAP2: an improved ultrafast tool for short read alignment
-
10.1093/bioinformatics/btp336, 19497933
-
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25(15):1966-1967. 10.1093/bioinformatics/btp336, 19497933.
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
Lam, T.W.4
Yiu, S.M.5
Kristiansen, K.6
Wang, J.7
-
43
-
-
79952453014
-
Unmasked maize genome sequence
-
Unmasked maize genome sequence. , http://ftp.maizesequence.org/release-4a.53/assembly/ZmB73_AGPv1_genome.fasta.gz
-
-
-
-
44
-
-
79952453323
-
Maize genome annotation in GFF format
-
Maize genome annotation in GFF format. , http://ftp.maizesequence.org/release-4a.53/filtered-set/ZmB73_4a.53_FGS.gff.gz
-
-
-
-
45
-
-
79952454251
-
Non-coding RNA sequence databse
-
Non-coding RNA sequence databse. , http://www.ncrna.org/frnadb
-
-
-
|