Publications
Found 11 results
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“Decreased TIM-3 mRNA expression in peripheral blood mononuclear cells from nephropathy patients”, vol. 14, pp. 6543-6548, 2015.
, “Development and characterization of polymorphic microsatellite markers for Castanopsis hystrix (Fagaceae)”, vol. 14, pp. 2436-2439, 2015.
, “A discriminative method for protein remote homology detection based on N-Gram”, vol. 14, pp. 69-78, 2015.
, , “Wnt/β-catenin aids in regulating the proliferation of hepG2 cells mediated by thy-1”, vol. 13, pp. 5115-5127, 2014.
, ,
“Benchmark comparison of ab initio microRNA identification methods and software”, vol. 11, pp. 4525-4538, 2012.
, Batuwita R and Palade V (2009). microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics 25: 989-995.
http://dx.doi.org/10.1093/bioinformatics/btp107
PMid:19233894
Bentwich I, Avniel A, Karov Y, Aharonov R, et al. (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37: 766-770.
http://dx.doi.org/10.1038/ng1590
PMid:15965474
Borchert GM, Lanier W and Davidson BL (2006). RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 13: 1097-1101.
http://dx.doi.org/10.1038/nsmb1167
PMid:17099701
Brennecke J, Hipfner DR, Stark A, Russell RB, et al. (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113: 25-36.
http://dx.doi.org/10.1016/S0092-8674(03)00231-9
Carrington JC and Ambros V (2003). Role of microRNAs in plant and animal development. Science 301: 336-338.
http://dx.doi.org/10.1126/science.1085242
PMid:12869753
Friedlander MR, Chen W, Adamidi C, Maaskola J, et al. (2008). Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol. 26: 407-415.
http://dx.doi.org/10.1038/nbt1394
PMid:18392026
Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, et al. (2009). miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 37: W68-W76.
http://dx.doi.org/10.1093/nar/gkp347
PMid:19433510 PMCid:2703919
Hofacker IL (2003). Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429-3431.
http://dx.doi.org/10.1093/nar/gkg599
PMid:12824340 PMCid:169005
Huang JC, Babak T, Corson TW, Chua G, et al. (2007). Using expression profiling data to identify human microRNA targets. Nat. Methods 4: 1045-1049.
http://dx.doi.org/10.1038/nmeth1130
PMid:18026111
Huang Y, Zou Q, Tang SM, Wang LG, et al. (2010). Computational identification and characteristics of novel microRNAs from the silkworm (Bombyx mori L.). Mol. Biol. Rep. 37: 3171-3176.
http://dx.doi.org/10.1007/s11033-009-9897-4
PMid:19823945
Huang Y, Shen XJ, Zou Q, Wang SP, et al. (2011a). Biological functions of microRNAs: a review. J. Physiol. Biochem. 67: 129-139.
http://dx.doi.org/10.1007/s13105-010-0050-6
PMid:20981514
Huang Y, Zou Q, Wang SP, Tang SM, et al. (2011b). The discovery approaches and detection methods of microRNAs. Mol. Biol. Rep. 38: 4125-4135.
http://dx.doi.org/10.1007/s11033-010-0532-1
PMid:21107708
Jiang P, Wu H, Wang W, Ma W, et al. (2007). MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 35: W339-W344.
http://dx.doi.org/10.1093/nar/gkm368
PMid:17553836 PMCid:1933124
Kumar S, Ansari FA and Scaria V (2009). Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features. Virol. J. 6: 129.
http://dx.doi.org/10.1186/1743-422X-6-129
PMid:19691855 PMCid:2743665
Lee Y, Ahn C, Han J, Choi H, et al. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419.
http://dx.doi.org/10.1038/nature01957
PMid:14508493
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http://dx.doi.org/10.1360/yc-007-0283
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http://dx.doi.org/10.1016/j.cell.2006.10.040
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Sewer A, Paul N, Landgraf P, Aravin A, et al. (2005). Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6: 267.
http://dx.doi.org/10.1186/1471-2105-6-267
PMid:16274478 PMCid:1315341
Wang X, Zhang J, Li F, Gu J, et al. (2005). MicroRNA identification based on sequence and structure alignment. Bioinformatics 21: 3610-3614.
http://dx.doi.org/10.1093/bioinformatics/bti562
PMid:15994192
Wu Y, Wei B, Liu H, Li T, et al. (2011). MiRPara: a SVM-based software tool for prediction of most probable microRNA
Genetics and Molecular Research 11 (4): 4525-4538 (2012) ©FUNPEC-RP www.funpecrp.com.br
L.L. Hu et al. 4538 coding regions in genome scale sequences. BMC Bioinformatics 12: 107.
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http://dx.doi.org/10.1186/1471-2105-6-310
PMid:16381612 PMCid:1360673
Yousef M, Nebozhyn M, Shatkay H, Kanterakis S, et al. (2006). Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier. Bioinformatics 22: 1325-1334.
http://dx.doi.org/10.1093/bioinformatics/btl094
PMid:16543277
Zeng Y, Yi R and Cullen BR (2005). Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J. 24: 138-148.
http://dx.doi.org/10.1038/sj.emboj.7600491
PMid:15565168 PMCid:544904
Zou Q, Zhao T, Liu Y and Guo M (2009). Predicting RNA secondary structure based on the class information and Hopfield network. Comput. Biol. Med. 39: 206-214.
http://dx.doi.org/10.1016/j.compbiomed.2008.12.010
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http://dx.doi.org/10.1126/science.2468181
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http://dx.doi.org/10.1093/nar/gkg595
PMid:12824337 PMCid:169194
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http://dx.doi.org/10.1093/nar/9.1.133
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“Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures”, vol. 11, pp. 987-1001, 2012.
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http://dx.doi.org/10.1016/S0300-9084(00)00610-6
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http://dx.doi.org/10.1105/tpc.109.071472
PMid:19934379 PMCid:2798323
Häder DP and Sinha RP (2005). Solar ultraviolet radiation-induced DNA damage in aquatic organisms: potential environmental impact. Mutat. Res. 571: 221-233.
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Inada M, Sasaki T, Yukawa M, Tsudzuki T, et al. (2004). A systematic search for RNA editing sites in pea chloroplasts: an editing event causes diversification from the evolutionarily conserved amino acid sequence. Plant Cell Physiol. 45: 1615-1622.
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Jiang Y, Yu J, Yao Y, Song M, et al. (2010). Research progress of cotton chloroplast genome. Cotton Sci. 22: 495-500.
Kahlau S, Aspinall S, Gray JC and Bock R (2006). Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J. Mol. Evol. 63: 194-207.
http://dx.doi.org/10.1007/s00239-005-0254-5
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Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, et al. (2003). RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res. 31: 2417-2423.
http://dx.doi.org/10.1093/nar/gkg327
PMid:12711687 PMCid:154213
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Lutz KA and Maliga P (2001). Lack of conservation of editing sites in mRNAs that encode subunits of the NAD(P)H dehydrogenase complex in plastids and mitochondria of Arabidopsis thaliana. Curr. Genet. 40: 214-219.
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Miyata Y and Sugita M (2004). Tissue- and stage-specific RNA editing of rps 14 transcripts in moss (Physcomitrella patens) chloroplasts. J. Plant Physiol. 161: 113-115.
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Okuda K, Chateigner-Boutin AL, Nakamura T, Delannoy E, et al. (2009). Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts. Plant Cell 21: 146-156.
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Okuda K, Hammani K, Tanz SK, Peng L, et al. (2010). The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. Plant J. 61: 339-349.
http://dx.doi.org/10.1111/j.1365-313X.2009.04059.x
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Robbins JC, Heller WP and Hanson MR (2009). A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript. RNA 15: 1142-1153.
http://dx.doi.org/10.1261/rna.1533909
PMid:19395655 PMCid:2685521
Sasaki T, Yukawa Y, Miyamoto T, Obokata J, et al. (2003). Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): comparative analysis shows the involvement of distinct trans-factors for ndhB editing. Mol. Biol. Evol. 20: 1028-1035.
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Sasaki Y and Nagano Y (2004). Plant acetyl-CoA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding. Biosci. Biotechnol. Biochem. 68: 1175-1184.
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