Publications

Found 3 results
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2011
P. Xuan, Guo, M. Z., Wang, J., Wang, C. Y., Liu, X. Y., and Liu, Y., 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 Quinlan JR (1993). C4.5: Programs for Machine Learning. Morgan Kaufmann Publishers, San Mateo. Schultes EA, Hraber PT and LaBean TH (1999). Estimating the contributions of selection and self-organization in RNA secondary structure. J. Mol. Evol. 49: 76-83. doi:10.1007/PL00006536 PMid:10368436 Seffens W and Digby D (1999). mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res. 27: 1578-1584. 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
2010
J. Wang, Zou, Q., and Guo, M. Z., Mining SNPs from EST sequences using filters and ensemble classifiers, vol. 9, pp. 820-834, 2010.
Altschul SF, Madden TL, Schaffer AA, Zhang J, et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. http://dx.doi.org/10.1093/nar/25.17.3389 PMid:9254694 PMCid:146917   Barker G, Batley J, O' Sullivan H, Edwards KJ, et al. (2003). Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19: 421-422. http://dx.doi.org/10.1093/bioinformatics/btf881 PMid:12584131   Batley J, Barker G, O'Sullivan H, Edwards KJ, et al. (2003). Mining for single nucleotide polymorphisms and insertions/ deletions in maize expressed sequence tag data. Plant Physiol. 132: 84-91. http://dx.doi.org/10.1104/pp.102.019422 PMid:12746514 PMCid:166954   Clifford R, Edmonson M, Hu Y, Nguyen C, et al. (2000). Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project. Genome Res. 10: 1259-1265. http://dx.doi.org/10.1101/gr.10.8.1259 PMid:10958644 PMCid:310932   Deutsch S, Iseli C, Bucher P, Antonarakis SE, et al. (2001). A cSNP map and database for human chromosome 21. Genome Res. 11: 300-307. PMid:11157793 PMCid:311032   Frank E and Witten IH (2005). Data Mining: Practical machine learning tools and techniques. 2nd edn. Morgan Kaufmann, San Francisco.   Frank E, Hall M, Trigg L, Holmes G, et al. (2004). Data mining in bioinformatics using Weka. Bioinformatics 20: 2479-2481. http://dx.doi.org/10.1093/bioinformatics/bth261 PMid:15073010   Holliday R and Grigg GW (1993). DNA methylation and mutation. Mutat. Res. 285: 61-67. http://dx.doi.org/10.1016/0027-5107(93)90052-H   Huang X and Madan A (1999). CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877. http://dx.doi.org/10.1101/gr.9.9.868 PMid:10508846 PMCid:310812   Huntley D, Baldo A, Johri S and Sergot M (2006). SEAN: SNP prediction and display program utilizing EST sequence clusters. Bioinformatics 22: 495-496. http://dx.doi.org/10.1093/bioinformatics/btk006 PMid:16357032   Irizarry K, Kustanovich V, Li C, Brown N, et al. (2000). Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. Nat. Genet. 26: 233-236. http://dx.doi.org/10.1038/79981 PMid:11017085   Krogh A and Vedelsby J (1995). Advances in Neural Information Processing Systems 7. In: Neural Network Ensembles, Cross Validation, and Active Learning (Krogh A and Vedelsby J, eds.). MIT Press, Cambridge, 231-238.   Marth GT, Korf I, Yandell MD, Yeh RT, et al. (1999). A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23: 452-456. http://dx.doi.org/10.1038/70570 PMid:10581034   Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, et al. (2000). An SNP map of human chromosome 22. Nature 407: 516-520. http://dx.doi.org/10.1038/35035089 PMid:11029003   Ning Z, Caccamo M and Mullikin JC (2005). ssahaSNP-A polymorphism detection tool by genomic alignment. Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05), Stanford, 251-254.   Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, et al. (1999). Mining SNPs from EST databases. Genome Res. 9: 167-174. PMid:10022981 PMCid:310719   Savage D, Batley J, Erwin T, Logan E, et al. (2005). SNPServer: a real-time SNP discovery tool. Nucleic Acids Res. 33: W493-W495. http://dx.doi.org/10.1093/nar/gki462 PMid:15980519 PMCid:1160223   Sherry ST, Ward MH, Kholodov M, Baker J, et al. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29: 308-311. http://dx.doi.org/10.1093/nar/29.1.308 PMid:11125122 PMCid:29783   Taillon-Miller P, Gu Z, Li Q, Hillier LD, et al. (1998). Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res. 748: 754.   Zhang J, Wheeler DA, Yakub I, Wei S, et al. (2005). SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS. Comput. Biol. 1: e53. http://dx.doi.org/10.1371/journal.pcbi.0010053 PMid:16261194 PMCid:1274293