Publications
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“Prediction of disease-related microRNAs by incorporating functional similarity and common association information”, vol. 13, pp. 2009-2019, 2014.
, “Genetic algorithm-based efficient feature selection for classification of pre-miRNAs”, vol. 10, pp. 588-603, 2011.
, Bartel DP (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
doi:10.1016/S0092-8674(04)00045-5
Batuwita R and Palade V (2009). microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics 25: 989-995.
doi:10.1093/bioinformatics/btp107
PMid:19233894
Berezikov E, Guryev V, van de Belt J, Wienholds E, et al. (2005). Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.
doi:10.1016/j.cell.2004.12.031
PMid:15652478
Bushati N and Cohen SM (2007). microRNA functions. Annu. Rev. Cell Dev. Biol. 23: 175-205.
doi:10.1146/annurev.cellbio.23.090506.123406
PMid:17506695
Chang DT, Wang CC and Chen JW (2008). Using a kernel density estimation based classifier to predict species-specific microRNA precursors. BMC Bioinformatics 9 (Suppl 12): S2.
doi:10.1186/1471-2105-9-S12-S2
PMid:19091019 PMCid:2638167
Chatterjee S and Grosshans H (2009). Active turnover modulates mature microRNA activity in Caenorhabditis elegans. Nature 461: 546-549.
doi:10.1038/nature08349
PMid:19734881
Fera D, Kim N, Shiffeldrim N, Zorn J, et al. (2004). RAG: RNA-As-Graphs web resource. BMC Bioinformatics 5: 88.
doi:10.1186/1471-2105-5-88
PMid:15238163 PMCid:471545
Freyhult E, Gardner PP and Moulton V (2005). A comparison of RNA folding measures. BMC Bioinformatics 6: 241.
doi:10.1186/1471-2105-6-241
PMid:16202126 PMCid:1274297
Gan HH, Fera D, Zorn J, Shiffeldrim N, et al. (2004). RAG: RNA-As-Graphs database - concepts, analysis, and features. Bioinformatics 20: 1285-1291.
doi:10.1093/bioinformatics/bth084
PMid:14962931
Griffiths-Jones S, Saini HK, van Dongen S and Enright AJ (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res. 36: D154-D158.
doi:10.1093/nar/gkm952
PMid:17991681 PMCid:2238936
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, et al. (1994). Fast folding and comparison of RNA secondary structures. Monatshefte fur Chemie/Chemical Monthly 125: 167-188.
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.
doi:10.1093/nar/gkm368
PMid:17553836 PMCid:1933124
Moulton V, Zuker M, Steel M, Pointon R, et al. (2000). Metrics on RNA secondary structures. J. Comput. Biol. 7: 277-292.
doi:10.1089/10665270050081522
PMid:10890402
Nam JW, Shin KR, Han J, Lee Y, et al. (2005). Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res. 33: 3570-3581.
doi:10.1093/nar/gki668
PMid:15987789 PMCid:1159118
Ng KL and Mishra SK (2007). De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics 23: 1321-1330.
doi:10.1093/bioinformatics/btm026
PMid:17267435
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doi:10.1007/PL00006536
PMid:10368436
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doi:10.1093/nar/27.7.1578
PMid:10075987 PMCid:148359
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.
doi:10.1186/1471-2105-6-267
PMid:16274478 PMCid:1315341
Xue C, Li F, He T, Liu GP, et al. (2005). Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics 6: 310.
doi: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.
doi:10.1093/bioinformatics/btl094
PMid:16543277
Yousef M, Jung S, Showe LC and Showe MK (2008). Learning from positive examples when the negative class is undetermined - microRNA gene identification. Algorithms Mol. Biol. 3: 2.
doi:10.1186/1748-7188-3-2
PMid:18226233 PMCid:2248178
Zhang BH, Pan XP, Cox SB, Cobb GP, et al. (2006). Evidence that miRNAs are different from other RNAs. Cell Mol. Life Sci. 63: 246-254.
doi:10.1007/s00018-005-5467-7
PMid:16395542