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Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
Xiu-Jie Wang, José L Reyes, Nam-Hai Chua, Terry Gaasterland
Genome Biol. 2004; 5(9): R65. Published online 2004 August 31. doi: 10.1186/gb-2004-5-9-r65
PMCID:
PMC522872
Abstract Full Text PDF–886K Supplementary Material

Is Cited by the Following 69 Articles in this Archive:

Identification and Characterization of Small RNAs in the Hyperthermophilic Archaeon Sulfolobus solfataricus
Ning Xu, Yan Li, Ying-Tao Zhao, Li Guo, Yuan-Yuan Fang, Jian-Hua Zhao, Xiu-Jie Wang, Li Huang, Hui-Shan Guo
PLoS One. 2012; 7(4): e35306. Published online 2012 April 13. doi: 10.1371/journal.pone.0035306
PMCID:
PMC3325985
Abstract Full Text PDF–641K Supplementary Material
Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing
Pablo Peláez, Minerva S Trejo, Luis P Iñiguez, Georgina Estrada-Navarrete, Alejandra A Covarrubias, José L Reyes, Federico Sanchez
BMC Genomics. 2012; 13: 83. Published online 2012 March 6. doi: 10.1186/1471-2164-13-83
PMCID:
PMC3359237
Abstract Full Text PDF–1.5M Supplementary Material
Employing machine learning for reliable miRNA target identification in plants
Ashwani Jha, Ravi Shankar
BMC Genomics. 2011; 12: 636. Published online 2011 December 29. doi: 10.1186/1471-2164-12-636
PMCID:
PMC3293931
Abstract Full Text PDF–1.1M Supplementary Material
SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants
Yun Zheng, Yong-Fang Li, Ramanjulu Sunkar, Weixiong Zhang
Nucleic Acids Res. 2012 February; 40(4): e28. Published online 2011 December 2. doi: 10.1093/nar/gkr1092
PMCID:
PMC3287166
Abstract Full Text PDF–15M Supplementary Material
Functions of noncoding RNAs in neural development and neurological diseases
Shan Bian, Tao Sun
Mol Neurobiol. Author manuscript; available in PMC 2011 December 27.
Published in final edited form as: Mol Neurobiol. 2011 December; 44(3): 359–373. Published online 2011 October 4. doi: 10.1007/s12035-011-8211-3
PMCID:
PMC3246283
Abstract Full Text PDF–1.4M
Discovery of barley miRNAs through deep sequencing of short reads
Andreas W Schreiber, Bu-Jun Shi, Chun-Yuan Huang, Peter Langridge, Ute Baumann
BMC Genomics. 2011; 12: 129. Published online 2011 February 25. doi: 10.1186/1471-2164-12-129
PMCID:
PMC3060140
Abstract Full Text PDF–873K Supplementary Material
Onconase Mediated NFKβ Down-Regulation in Malignant Pleural Mesothelioma
Chandra M. Goparaju, Justin D. Blasberg, Stefano Volinia, Jeff Palatini, Sergey Ivanov, Jessica S. Donington, Carlo Croce, Michele Carbone, Haining Yang, Harvey I. Pass
Oncogene. Author manuscript; available in PMC 2011 December 16.
Published in final edited form as: Oncogene. 2011 June 16; 30(24): 2767–2777. Published online 2011 February 14. doi: 10.1038/onc.2010.643
PMCID:
PMC3118086
Abstract Full Text PDF–1.4M Supplementary Material
MicroRNA hsa-miR-613 Targets the Human LXRα Gene and Mediates a Feedback Loop of LXRα Autoregulation
Zhimin Ou, Taira Wada, Roberto Gramignoli, Song Li, Stephen C. Strom, Min Huang, Wen Xie
Mol Endocrinol. 2011 April; 25(4): 584–596. Published online 2011 February 10. doi: 10.1210/me.2010-0360
PMCID:
PMC3063084
Abstract Full Text
Prediction of miRNA targets, affected proteins and their homologs in Glycine max
Pramod Katara, Budhayash Gautam, Himani Kuntal, Vinay Sharma
Bioinformation. 2010; 5(4): 162–165. Published online 2010 September 20.
PMCID:
PMC3040477
Abstract Full Text PDF–88K Supplementary Material
Polymorphisms in Predicted miRNA Binding Sites and Osteoporosis
Shu-Feng Lei, Christopher J Papasian, Hong-Wen Deng
J Bone Miner Res. 2011 January; 26(1): 72–78. Published online 2010 July 16. doi: 10.1002/jbmr.186
PMCID:
PMC3179316
Abstract Full Text PDF–109K
Analysis of Antisense Expression by Whole Genome Tiling Microarrays and siRNAs Suggests Mis-Annotation of Arabidopsis Orphan Protein-Coding Genes
Casey R. Richardson, Qing-Jun Luo, Viktoria Gontcharova, Ying-Wen Jiang, Manoj Samanta, Eunseog Youn, Christopher D. Rock
PLoS One. 2010; 5(5): e10710. Published online 2010 May 26. doi: 10.1371/journal.pone.0010710
PMCID:
PMC2877095
Abstract Full Text PDF–359K Supplementary Material
Identification of miRNA from Porphyra yezoensis by High-Throughput Sequencing and Bioinformatics Analysis
Chengwei Liang, Xiaowen Zhang, Jian Zou, Dong Xu, Feng Su, Naihao Ye
PLoS One. 2010; 5(5): e10698. Published online 2010 May 19. doi: 10.1371/journal.pone.0010698
PMCID:
PMC2873431
Abstract Full Text PDF–269K Supplementary Material
Improvement of the design and generation of highly specific plant knockdown lines using primary synthetic microRNAs (pri-smiRNAs)
Sandra Niemeier, Leonardo Alves, Junior, Thomas Merkle
BMC Res Notes. 2010; 3: 59. Published online 2010 March 4. doi: 10.1186/1756-0500-3-59
PMCID:
PMC2845148
Abstract Full Text PDF–793K Supplementary Material
Small RNA Diversity in Plants and its Impact in Development
Christine Lelandais-Brière, Céline Sorin, Marie Declerck, Abdelali Benslimane, Martin Crespi, Caroline Hartmann
Curr Genomics. 2010 March; 11(1): 14–23. doi: 10.2174/138920210790217918
PMCID:
PMC2851111
Abstract Full Text PDF–292K
PMRD: plant microRNA database
Zhenhai Zhang, Jingyin Yu, Daofeng Li, Zuyong Zhang, Fengxia Liu, Xin Zhou, Tao Wang, Yi Ling, Zhen Su
Nucleic Acids Res. 2010 January; 38(Database issue): D806–D813. Published online 2010 January. doi: 10.1093/nar/gkp818
PMCID:
PMC2808885
Abstract Full Text PDF–2.9M
Rice MicroRNA Effector Complexes and Targets
Liang Wu, Qingqing Zhang, Huanyu Zhou, Fangrui Ni, Xueying Wu, Yijun Qi
Plant Cell. 2009 November; 21(11): 3421–3435. doi: 10.1105/tpc.109.070938
PMCID:
PMC2798332
Abstract Full Text PDF–1.6M Supplementary Material
MicroPC (μPC): A comprehensive resource for predicting and comparing plant microRNAs
Wuttichai Mhuantong, Duangdao Wichadakul
BMC Genomics. 2009; 10: 366. Published online 2009 August 7. doi: 10.1186/1471-2164-10-366
PMCID:
PMC2907689
Abstract Full Text PDF–1.4M Supplementary Material
Identification and characterization of 27 conserved microRNAs in citrus
Changnian Song, Jinggui Fang, Xiaoying Li, Hong Liu, C. Thomas Chao
Planta. 2009 September; 230(4): 671–685. Published online 2009 July 8. doi: 10.1007/s00425-009-0971-x
PMCID:
PMC2729984
Abstract Full Text PDF–999K
Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana
Leonardo Alves-Junior, Sandra Niemeier, Arne Hauenschild, Marc Rehmsmeier, Thomas Merkle
Nucleic Acids Res. 2009 July; 37(12): 4010–4021. Published online 2009 July. doi: 10.1093/nar/gkp272
PMCID:
PMC2709567
Abstract Full Text PDF–2.9M Supplementary Material
Current tools for the identification of miRNA genes and their targets
N. D. Mendes, A. T. Freitas, M.-F. Sagot
Nucleic Acids Res. 2009 May; 37(8): 2419–2433. Published online 2009 May. doi: 10.1093/nar/gkp145
PMCID:
PMC2677885
Abstract Full Text PDF–1.9M Supplementary Material
Parallel DNA pyrosequencing unveils new zebrafish microRNAs
Ana R Soares, Patrícia M Pereira, Bruno Santos, Conceição Egas, Ana C Gomes, Joel Arrais, José L Oliveira, Gabriela R Moura, Manuel AS Santos
BMC Genomics. 2009; 10: 195. Published online 2009 April 27. doi: 10.1186/1471-2164-10-195
PMCID:
PMC2684549
Abstract Full Text PDF–1.2M Supplementary Material
Prediction of guide strand of microRNAs from its sequence and secondary structure
Firoz Ahmed, Hifzur Rahman Ansari, Gajendra PS Raghava
BMC Bioinformatics. 2009; 10: 105. Published online 2009 April 9. doi: 10.1186/1471-2105-10-105
PMCID:
PMC2676257
Abstract Full Text PDF–590K Supplementary Material
Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information
Je-Gun Joung, Zhangjun Fei
BMC Bioinformatics. 2009; 10(Suppl 1): S34. Published online 2009 January 30. doi: 10.1186/1471-2105-10-S1-S34
PMCID:
PMC2648752
Abstract Full Text PDF–305K Supplementary Material
Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae
Laura A. Kavanaugh, Fred S. Dietrich
PLoS Genet. 2009 January; 5(1): e1000321. Published online 2009 January 2. doi: 10.1371/journal.pgen.1000321
PMCID:
PMC2603021
Abstract Full Text PDF–359K Supplementary Material
Evolution of Arabidopsis MIR genes generates novel microRNA classes
Franck Vazquez, Todd Blevins, Jérôme Ailhas, Thomas Boller, Frederick Meins, Jr
Nucleic Acids Res. 2008 November; 36(20): 6429–6438. Published online 2008 November. doi: 10.1093/nar/gkn670
PMCID:
PMC2582634
Abstract Full Text PDF–1.5M Supplementary Material
Selection and mutation on microRNA target sequences during rice evolution
Xingyi Guo, Yijie Gui, Yu Wang, Qian-Hao Zhu, Chris Helliwell, Longjiang Fan
BMC Genomics. 2008; 9: 454. Published online 2008 October 2. doi: 10.1186/1471-2164-9-454
PMCID:
PMC2567346
Abstract Full Text PDF–525K Supplementary Material
Two Cap-Binding Proteins CBP20 and CBP80 are Involved in Processing Primary MicroRNAs
Sanghee Kim, Jun-Yi Yang, Jun Xu, In-Cheol Jang, Michael J. Prigge, Nam-Hai Chua
Plant Cell Physiol. 2008 November; 49(11): 1634–1644. Published online 2008 September 30. doi: 10.1093/pcp/pcn146
PMCID:
PMC2722234
Abstract Full Text PDF–588K Supplementary Material
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
Qian-Hao Zhu, Andrew Spriggs, Louisa Matthew, Longjiang Fan, Gavin Kennedy, Frank Gubler, Chris Helliwell
Genome Res. 2008 September; 18(9): 1456–1465. doi: 10.1101/gr.075572.107
PMCID:
PMC2527712
Abstract Full Text PDF–535K
Identification and characteristics of microRNAs from Bombyx mori
Ping-an He, Zuoming Nie, Jianqing Chen, Jian Chen, Zhengbing Lv, Qing Sheng, Songping Zhou, Xiaolian Gao, Lingyin Kong, Xiangfu Wu, Yongfeng Jin, Yaozhou Zhang
BMC Genomics. 2008; 9: 248. Published online 2008 May 28. doi: 10.1186/1471-2164-9-248
PMCID:
PMC2435238
Abstract Full Text PDF–1.7M Supplementary Material
Interspecies Regulation of MicroRNAs and Their Targets
Misook Ha, Mingxiong Pang, Vikram Agarwal, Z. Jeffrey Chen
Biochim Biophys Acta. Author manuscript; available in PMC 2009 November 1.
Published in final edited form as: Biochim Biophys Acta. 2008 November; 1779(11): 735–742. Published online 2008 March 25. doi: 10.1016/j.bbagrm.2008.03.004
PMCID:
PMC2586835
Abstract Full Text PDF–806K Supplementary Material
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