To support the psRNATarget, please cite: Xinbin Dai and Patrick X. Zhao, psRNATarget: A Plant Small RNA Target Analysis Server, Nucleic Acids Research, 2011, W155-9. doi: 10.1093/nar/gkr319.
The Zhao Bioinformatics Laboratory
psRNATarget: A Plant Small RNA Target Analysis Server   
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To Reference psRNATarget, Please Cite:
Xinbin Dai and Patrick X. Zhao, psRNATarget: A Plant Small RNA Target Analysis Server, Nucleic Acids Research, 2011, doi: 10.1093/nar/GKR319. (Link).

List of Papers Citing the psRNATarget Server(as of Feburary 2011 per Google Scholar):

  1. Ruan,M., Zhao,Y., Meng,Z., Wang,X., Yang,W. (2009) Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics, 94:263-268.
  2. Naqvi,A.R., Choudhury,N.R., Mukherjee,S.K., Haq,Q.M. (2011) In silico analysis reveals that several tomato microRNA/microRNA* sequences exhibit propensity to bind to tomato leaf curl virus (ToLCV) associated genomes and most of their encoded open reading frames (ORFs). Plant Physiol Biochem, 49:13-17.
  3. Zhang,Z., Yu,J., Li,D., Zhang,Z., Liu,F., Zhou,X., Wang,T., Ling,Y., Su,Z. (2010) PMRD: plant microRNA database. Nucleic Acids Res., 38:806-813.
  4. Trap-Gentil MV, Hébrard C, Lafon-Placette C, Delaunay A, Hagège D, Joseph C, Brignolas F, Lefebvre M, Barnes S, Maury S. (2011) Time course and amplitude of DNA methylation in the shoot apical meristem are critical points for bolting induction in sugar beet and bolting tolerance between genotypes. J Exp Bot, 62, 2011 Jan 12. doi: 10.1093/jxb/erq433 [Epub ahead of print]
  5. Chen,M., Meng,Y., Mao,C., Chen,D., Wu,P. (2010) Methodological framework for functional characterization of plant microRNAs. J Exp Bot, 61:2271-2280.
  6. Kantar,M., Lucas,S.J., Budak,H. (2010) miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta. DOI: 10.1007/s00425-010-1309-4
  7. Zhang,X., Zou,Z., Zhang,J., Zhang,Y., Han,Q., Hu,T., Xu,X., Liu,H., Li,H., Ye,Z. (2011) Over-expression of sly-miR156a in tomato results in multiple vegetative and reproductive trait alterations and partial phenocopy of the sft mutant. FEBS Lett, 585:435-439.
  8. Lv,D., Bai,X., Li,Y., Ding,X., Ge,Y., Cai,H., Ji,W., Wu,N., Zhu,Y. (2011) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene, 459:39-47.
  9. Lang,Q., Jin,C., Lai,L., Feng,J., Chen,S., Chen,J. (2011) Tobacco microRNAs prediction and their expression infected with Cucumber mosaic virus and Potato virus X. Mol Biol Rep., 38:1523-1531.
  10. Meng,Y., Shao,C., Chen,M. (2011) Toward microRNA-mediated gene regulatory networks in plants. Brief Bioinform., doi: 10.1093/bib/bbq091
  11. Klevebring,D., Street,N.R., Fahlgren,N., Kasschau,K.D., Carrington,J.C., Lundeberg,J., Jansson,S. (2009) Genome-wide profiling of populus small RNAs. BMC Genomics. 10:620.
  12. Lang,Q., Zhou,X., Zhang,X., Drabek,R., Zuo,Z., Ren,Y., Li,T., Chen,J., Gao,X. (2011) Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection. J Zhejiang Univ Sci B., 12:116-125.
  13. Valdés-López O, Yang SS, Aparicio-Fabre R, Graham PH, Reyes JL, Vance CP, Hernández G. (2010) MicroRNA expression profile in common bean (Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity. New Phytol., 187:805-818.
  14. Gao,P., Bai,X., Yang,L., Lv,D., Pan,X., Li,Y., Cai,H., Ji,W., Chen,Q., Zhu,Y. (2011) osa-MIR393: a salinity- and alkaline stress-related microRNA gene. Mol Biol Rep., 38:237-242.
  15. Gao,P., Bai,X., Yang,L., Lv,D., Li,Y., Cai,H., Ji,W., Guo,D., Zhu,Y. (2010) Over-expression of osa-MIR396c decreases salt and alkali stress tolerance. Planta, 231:991-1001.
  16. Zhao,C., Xia,H., Frazier,T., Yao,Y., Bi,Y., Li,A., Li,M., Li,C., Zhang,B., Wang,X. (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol., 10:3.
  17. Bonnet,E., He,Y., Billiau,K. et al. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics. 26:1566-1568.
  18. Schwach,F., Moxon,S., Moulton,V., Dalmay,T. (2009) Deciphering the diversity of small RNAs in plants: the long and short of it. Brief Funct Genomic Proteomic., 8:472-481.
  19. Xu,Q., Liu,Y., Zhu,A., Wu,X., Ye,J., Yu,K., Guo,W., Deng,X. (2010) Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type. BMC Genomics, 11:246.
  20. Misra,P., Pandey,A., Tiwari,M., Chandrashekar,K., Sidhu,O.P., Asif,M.H., Chakrabarty,D., Singh,P.K., Trivedi,P.K., Nath,P., Tuli,R. (2010) Modulation of transcriptome and metabolome of tobacco by Arabidopsis transcription factor, AtMYB12, leads to insect resistance. Plant Physiol., 152:2258-2268.
  21. Buhtz,A., Pieritz,J., Springer,F., Kehr,J. (2010) Phloem small RNAs, nutrient stress responses, and systemic mobility. BMC Plant Biol., 10:64.
  22. Manila,T.M., Riju,A., Lakshmi,K. et al. (2009) In silico microRNA identification from paprika (Capsicum annuum) ESTs. http://precedings.nature.com/documents/3737/version/1
  23. Trindade,I., Capitao,C., Dalmay,T., Fevereiro,M.P., Santos,D.M. (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta, 231:705-16.
  24. Zhang,X., Zou,Z., Gong,P., Zhang,J., Ziaf,K., Li,H., Xiao,F., Ye,Z. (2011) Over-expression of microRNA169 confers enhanced drought tolerance to tomato. Biotechnol Lett., 33:403-409.
  25. Zeng,H., Zhu,Y., Huang,S., Yang,Z. (2010) Analysis of phosphorus-deficient responsive miRNAs and cis-elements from soybean (Glycine max L.). J Plant Physiol., 167:1289-1297.
  26. Xu,C., Yang,R., Li,W., Fu,F. (2010) Identification of 21 microRNAs in maize and their differential expression under drought stress. African Journal of Biotechnology. 9:4741-4753.
  27. Zhou,J., Zhuo,R., Liu,M. et al. (2010) Identification and Characterization of Novel MicroRNAs from Populus cathayana Rehd. Plant Mol Biol Rep., DOI 10.1007/s11105-010-0225-x
  28. Lundmark,M., K?rner,C.J., Nielsen,T.H. (2010) Global analysis of microRNA in Arabidopsis in response to phosphate starvation as studied by locked nucleic acid-based microarrays. Physiol Plant., 140:57-68.
  29. Zhang,X., Li,H., Zhang,J., Zhang,C., Gong,P., Ziaf,K., Xiao,F., Ye,Z. (2010) Expression of artificial microRNAs in tomato confers efficient and stable virus resistance in a cell-autonomous manner. Transgenic Res, DOI 10.1007/s11248-010-9440-3.
  30. Bhardwaj,J., Mohammad,H., Yadav,S.K. (2010) Computational identification of microRNAs and their targets from the expressed sequence tags of horsegram (Macrotyloma uniflorum (Lam.) Verdc.). J Struct Funct Genomics., 11:233-240.

 

Table 1 Part of citation statistics on miRNAs and their target genes predicted by psRNATarget between 2009 and 2010.

# of miRNA# of target genes predicted by psRNATargetReference
3234(Ruan et al., 2009)
87(Bhardwaj et al., 2010)
5727(Zeng et al., 2010)
2030(Zhao et al., 2010)
8548(Xu et al., 2010b)
28(Zhang et al., 2010a)
1512(Klevebring et al., 2009)
79(Lundmark et al., 2010)
47(Zhou et al., 2010)
1421(Xu et al., 2010a)
813(Naqvi et al., 2011)
85135(Manila et al., 2009)
23(Chen et al., 2010)
22(Allen et al., 2010)
1113(Valdés-López et al., 2010)
32(Trindade et al., 2010)
14(Zhang et al., 2010b)

  


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