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Thompson, T.B., Chou, K.C. and Zheng, C. (1995) Neural Network Prediction of the HIV-1 Protease Cleavage Sites. Journal of Theoretical Biology, 177, 369-379. https://doi.org/10.1006/jtbi.1995.0254
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Feng, P.M., Chen, W., Lin, H. and Chou, K.C. (2013) iHSP-PseRAAAC: Identifying the Heat Shock Protein Families Using Pseudo Reduced Amino Acid Alphabet Composition. Analytical Biochemistry, 442, 118-125. https://doi.org/10.1016/j.ab.2013.05.024
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Chen, W., Feng, P.M., Lin, H. and Chou, K.C. (2013) iRSpot-PseDNC: Identify Recombination Spots with Pseudo Dinucleotide Composition. Nucleic Acids Research, 41, e68. https://doi.org/10.1093/nar/gks1450
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Xiao, X., Wang, P. and Chou, K.C. (2012) iNR-PhysChem: A Sequence-Based Predictor for Identifying Nuclear Receptors and Their Subfamilies via Physical-Chemical Property Matrix. PLoS ONE, 7, e30869. https://doi.org/10.1371/journal.pone.0030869
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Chen, J., Long, R., Wang, X.L., Liu, B., Chou, K.C. (2016) dRHP-PseRA: Detecting Remote Homology Proteins Using Profile-Based Pseudo Protein Sequence and Rank Aggregation. Scientific Reports, 6, 32333. https://doi.org/10.1038/srep32333
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Liu, B., Zhang, D., Xu, R., Xu, J., Wang, X., Chen, Q., Dong, Q. and Chou, K.C. (2014) Combining evolutionary Information Extracted from Frequency Profiles with Sequence-Based Kernels for Protein Remote Homology Detection. Bioinformatics, 30, 472-479. https://doi.org/10.1093/bioinformatics/btt709
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Liu, B., Fang, L., Wang, S., Wang, X., Li, H. and Chou, K.C. (2015) Identification of microRNA Precursor with the Degenerate K-Tuple or Kmer Strategy. Journal of Theoretical Biology, 385, 153-159. https://doi.org/10.1016/j.jtbi.2015.08.025
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Liu, B., Fang, L., Liu, F., Wang, X. and Chou, K.C. (2016) iMiRNA-PseDPC: microRNA Precursor Identification with a Pseudo Distance-Pair Composition Approach. Journal of Biomolecular Structure and Dynamics (JBSD), 34, 223-235. https://doi.org/10.1080/07391102.2015.1014422
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Liu, B., Fang, L., Long, R., Lan, X. and Chou, K.C. (2016) iEnhancer-2L: A Two-Layer Predictor for Identifying Enhancers and Their Strength by Pseudo k-Tuple Nucleotide Composition. Bioinformatics, 32, 362-369. https://doi.org/10.1093/bioinformatics/btv604
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Chou, K.C. and Cai, Y.D. (2006) Prediction of Protease Types in a Hybridization Space. Biochem Biophys Res Comm (BBRC), 339, 1015-1020.
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Lin, W.Z., Fang, J.A., Xiao, X. and Chou, K.C. (2011) iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model. PLoS ONE, 6, e24756.
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Kandaswamy, K.K., Chou, K.C., Martinetz, T., Moller, S., Suganthan, P.N., Sridharan, S. and Pugalenthi, G. (2011) AFP-Pred: A Random Forest Approach for Predicting Antifreeze Proteins from Sequence-Derived Properties. Journal of Theoretical Biology, 270, 56-62. https://doi.org/10.1016/j.jtbi.2010.10.037
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Jia, J., Liu, Z., Xiao, X. and Chou, K.C. (2015) iPPI-Esml: An Ensemble Classifier for Identifying the Interactions of Proteins by Incorporating Their Physicochemical Properties and Wavelet Transforms into PseAAC. Journal of Theoretical Biology, 377, 47-56. https://doi.org/10.1016/j.jtbi.2015.04.011
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Jia, J., Liu, Z., Xiao, X., Liu, B. and Chou, K.C. (2016) iSuc-PseOpt: Identifying Lysine Succinylation Sites in Proteins by Incorporating Sequence-Coupling Effects into Pseudo Components and Optimizing Imbalanced Training Dataset. Analytical Biochemistry, 497, 48-56. https://doi.org/10.1016/j.ab.2015.12.009
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Jia, J., Liu, Z., Xiao, X., Liu, B. and Chou, K.C. (2016) pSuc-Lys: Predict Lysine Succinylation Sites in Proteins with PseAAC and Ensemble Random Forest Approach. Journal of Theoretical Biology, 394, 223-230. https://doi.org/10.1016/j.jtbi.2016.01.020
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Jia, J., Liu, Z., Xiao, X., Liu, B. and Chou, K.C. (2016) iCar-PseCp: Identify Carbonylation Sites in Proteins by Monto Carlo Sampling and Incorporating Sequence Coupled Effects into General PseAAC. Oncotarget, 7, 34558-34570.
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Qiu, W.R., Sun, B.Q., Xiao, X., Xu, D. and Chou, K.C. (2016) iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory. Molecular Informatics. https://doi.org/10.1002/minf.201600010
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Lin, H., Ding, H., Guo, F.-B., Zhang, A.Y. and Huang, J. (2008) Predicting Subcellular Localization of Mycobacterial Proteins by Using Chou’s Pseudo Amino Acid Composition. Protein & Peptide Letters, 15, 739-744. https://doi.org/10.2174/092986608785133681
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