Found 3 results
Filters: Author is L.L. Hu  [Clear All Filters]
L. L. Hu, Huang, Y., Wang, Q. C., Zou, Q., and Jiang, Y., 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. 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. PMid:15965474   Borchert GM, Lanier W and Davidson BL (2006). RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 13: 1097-1101. 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.   Carrington JC and Ambros V (2003). Role of microRNAs in plant and animal development. Science 301: 336-338. 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. 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. PMid:19433510 PMCid:2703919   Hofacker IL (2003). Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429-3431. 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. 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. 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. 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. 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. 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. 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. PMid:14508493   Li PW, Lu XY, Li CZ, Fang J, et al. (2007). Advances in the study of plant microRNAs. Yi Chuan 29: 283-288. PMid:17369147   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, et al. (2003). The microRNAs of Caenorhabditis elegans. Genes Dev.   Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, et al. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906. PMid:10706289   Ruby JG, Jan C, Player C, Axtell MJ, et al. (2006). Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127: 1193-1207. PMid:17174894   Sankoff D, Kruskal JB, Mainville S and Cedergren RJ (1983). Fast Algorithms to Determine RNA Secondary Structures Containing Multiple Loops. In: Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison (Sankoff D and Kruskal JB, eds.). Chapter 3. Addison-Wesley, Reading, 93-120.   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. 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. 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   L.L. Hu et al. 4538 coding regions in genome scale sequences. BMC Bioinformatics 12: 107.   Xue C, Li F, He T, Liu GP, et al. (2005). Classification of real and pseudo microRNA precursors using local structuresequence features and support vector machine. BMC Bioinformatics 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. 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. 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. PMid:19215914   Zou Q, Lin C, Liu XY, Han YP, et al. (2011). Novel representation of RNA secondary structure used to improve prediction algorithms. Genet. Mol. Res. 10: 1986-1998. PMid:21948761   Zuker M (1989a). Computer prediction of RNA structure. Methods Enzymol. 180: 262-288.   Zuker M (1989b). On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52. PMid:2468181   Zuker M (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415. PMid:12824337 PMCid:169194   Zuker M and Stiegler P (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9: 133-148. PMid:6163133 PMCid:326673