A framework for improving microRNA prediction in non-human genomes
作者： Robert J. Peace , Kyle K. Biggar , Kenneth B. Storey , James R. Green
DOI: 10.1093/NAR/GKV698
关键词: False positive paradox 、 Computational biology 、 Genomics 、 Genome 、 Biology 、 Random forest 、 Support vector machine 、 Genetics 、 Feature (machine learning) 、 Human genome 、 Sequence
摘要: … The four pre-trained microPred-like and HeteroMirPred-like species-specific miRNA prediction systems evaluated in this study are available as SMIRP, at http://bioinf.sce.carleton.ca/…
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oxfordjournals.org参考文章(61)
David P Bartel, MicroRNAs: Genomics, Biogenesis, Mechanism, and Function Cell. ,vol. 116, pp. 281- 297 ,(2004) , 10.1016/S0092-8674(04)00045-5
I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, P. Schuster, Fast folding and comparison of RNA secondary structures Monatshefte Fur Chemie. ,vol. 125, pp. 167- 188 ,(1994) , 10.1007/BF00818163
Alain Sewer, Nicodème Paul, Pablo Landgraf, Alexei Aravin, Sébastien Pfeffer, Michael J Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan, Identification of clustered microRNAs using an ab initio prediction method BMC Bioinformatics. ,vol. 6, pp. 267- 267 ,(2005) , 10.1186/1471-2105-6-267
Chenghai Xue, Fei Li, Tao He, Guo-Ping Liu, Yanda Li, Xuegong Zhang, Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine BMC Bioinformatics. ,vol. 6, pp. 310- 310 ,(2005) , 10.1186/1471-2105-6-310
Kyle K. Biggar, Samantha F. Kornfeld, Yulia Maistrovski, Kenneth B. Storey, MicroRNA Regulation in Extreme Environments: Differential Expression of MicroRNAs in the Intertidal Snail Littorina littorea During Extended Periods of Freezing and Anoxia Genomics, Proteomics & Bioinformatics. ,vol. 10, pp. 302- 309 ,(2012) , 10.1016/J.GPB.2012.09.002
Cindy Körner, Ioanna Keklikoglou, Christian Bender, Angelika Wörner, Ewald Münstermann, Stefan Wiemann, MicroRNA-31 Sensitizes Human Breast Cells to Apoptosis by Direct Targeting of Protein Kinase C ϵ (PKCϵ) Journal of Biological Chemistry. ,vol. 288, pp. 8750- 8761 ,(2013) , 10.1074/JBC.M112.414128
A. La Torre, S. Georgi, T. A. Reh, Conserved microRNA pathway regulates developmental timing of retinal neurogenesis Proceedings of the National Academy of Sciences of the United States of America. ,vol. 110, pp. 201301837- ,(2013) , 10.1073/PNAS.1301837110
Ivani de ON Lopes, Alexander Schliep, André CP de LF de Carvalho, None, The discriminant power of RNA features for pre-miRNA recognition. BMC Bioinformatics. ,vol. 15, pp. 124- 124 ,(2014) , 10.1186/1471-2105-15-124
Leyi Wei, Minghong Liao, Yue Gao, Rongrong Ji, Zengyou He, Quan Zou, Improved and promising identification of human MicroRNAs by incorporating a high-quality negative set IEEE/ACM Transactions on Computational Biology and Bioinformatics. ,vol. 11, pp. 192- 201 ,(2014) , 10.1109/TCBB.2013.146
Sheng-Da Hsu, Yu-Ting Tseng, Sirjana Shrestha, Yu-Ling Lin, Anas Khaleel, Chih-Hung Chou, Chao-Fang Chu, Hsi-Yuan Huang, Ching-Min Lin, Shu-Yi Ho, Ting-Yan Jian, Feng-Mao Lin, Tzu-Hao Chang, Shun-Long Weng, Kuang-Wen Liao, I-En Liao, Chun-Chi Liu, Hsien-Da Huang, miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions Nucleic Acids Research. ,vol. 42, pp. 78- 85 ,(2014) , 10.1093/NAR/GKT1266