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2020 – today
- 2021
[j62]Muhammad Awais
, Waqar Hussain, Yaser Daanial Khan, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou:
iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition. IEEE ACM Trans. Comput. Biol. Bioinform. 18(2): 596-610 (2021)- [j61]Muhammad Aizaz Akmal, Waqar Hussain, Nouman Rasool, Yaser Daanial Khan, Sher Afzal Khan, Kuo-Chen Chou:
Using CHOU'S 5-Steps Rule to Predict O-Linked Serine Glycosylation Sites by Blending Position Relative Features and Statistical Moment. IEEE ACM Trans. Comput. Biol. Bioinform. 18(5): 2045-2056 (2021) - 2020
- [j60]Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song:
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Briefings Bioinform. 21(3): 1047-1057 (2020)
2010 – 2019
- 2019
- [j59]Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou:
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. Briefings Bioinform. 20(2): 638-658 (2019) - [j58]Fuyi Li, Yanan Wang, Chen Li, Tatiana T. Marquez-Lago, André Leier, Neil D. Rawlings, Gholamreza Haffari, Jerico Nico De Leon Revote, Tatsuya Akutsu, Kuo-Chen Chou, Anthony W. Purcell, Robert N. Pike, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song:
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. Briefings Bioinform. 20(6): 2150-2166 (2019) - [j57]Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song:
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. Briefings Bioinform. 20(6): 2185-2199 (2019) - [j56]Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li, Kuo-Chen Chou, Jiangning Song:
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Briefings Bioinform. 20(6): 2267-2290 (2019) - [j55]Xiang Cheng, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou:
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC. Bioinform. 35(3): 398-406 (2019) - [j54]Jiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow:
Bastion3: a two-layer ensemble predictor of type III secreted effectors. Bioinform. 35(12): 2017-2028 (2019) - [j53]Meng Zhang, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Cunshuo Fan, Chee Keong Kwoh, Kuo-Chen Chou, Jiangning Song, Cangzhi Jia:
MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters. Bioinform. 35(17): 2957-2965 (2019) - [j52]Fuyi Li, Yang Zhang, Anthony W. Purcell, Geoffrey I. Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li, Jiangning Song:
Positive-unlabelled learning of glycosylation sites in the human proteome. BMC Bioinform. 20(1): 112:1-112:17 (2019) - 2018
- [j51]Bin Liu, Fan Yang, De-Shuang Huang, Kuo-Chen Chou:
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC. Bioinform. 34(1): 33-40 (2018) - [j50]Jiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike:
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinform. 34(4): 684-687 (2018) - [j49]Xiang Cheng, Xuan Xiao, Kuo-Chen Chou:
pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information. Bioinform. 34(9): 1448-1456 (2018) - [j48]Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Yanan Wang, Geoffrey I. Webb, Alexander Ian Smith, Roger J. Daly, Kuo-Chen Chou, Jiangning Song:
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. Bioinform. 34(14): 2499-2502 (2018) - [j47]Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T. Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu, Kuo-Chen Chou, Richard A. Strugnell, Jiangning Song, Trevor Lithgow:
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinform. 34(15): 2546-2555 (2018) - [j46]Bin Liu, Fan Weng, De-Shuang Huang, Kuo-Chen Chou:
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC. Bioinform. 34(18): 3086-3093 (2018) - [j45]Bin Liu, Kai Li, De-Shuang Huang, Kuo-Chen Chou:
iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach. Bioinform. 34(22): 3835-3842 (2018) - [j44]Zhen-Dong Su, Yan Huang, Zhao-Yue Zhang, Ya-Wei Zhao, Dong Wang, Wei Chen, Kuo-Chen Chou, Hao Lin:
iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC. Bioinform. 34(24): 4196-4204 (2018) - [j43]Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W. Purcell, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, Jiangning Song, Kuo-Chen Chou:
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. Bioinform. 34(24): 4223-4231 (2018) - 2017
- [j42]Bin Liu, Shanyi Wang, Ren Long, Kuo-Chen Chou:
iRSpot-EL: identify recombination spots with an ensemble learning approach. Bioinform. 33(1): 35-41 (2017) - [j41]Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou:
iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals. Bioinform. 33(3): 341-346 (2017) - [j40]Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou:
iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals. Bioinform. 33(16): 2610 (2017) - [j39]Jiawei Wang, Bingjiao Yang, Jerico Nico De Leon Revote, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Jiangning Song, Kuo-Chen Chou, Trevor Lithgow:
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles. Bioinform. 33(17): 2756-2758 (2017) - [j38]Xiang Cheng, Shu-Guang Zhao, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou:
pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites. Bioinform. 33(22): 3524-3531 (2017) - 2016
- [j37]Bin Liu, Longyun Fang, Ren Long, Xun Lan, Kuo-Chen Chou:
iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition. Bioinform. 32(3): 362-369 (2016) - [j36]Bin Liu, Ren Long, Kuo-Chen Chou:
iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework. Bioinform. 32(16): 2411-2418 (2016) - [j35]Wangren Qiu, Bi-Qian Sun, Xuan Xiao, Zhao-Chun Xu, Kuo-Chen Chou:
iPTM-mLys: identifying multiple lysine PTM sites and their different types. Bioinform. 32(20): 3116-3123 (2016) - [j34]Jianhua Jia, Liuxia Zhang, Zi Liu, Xuan Xiao, Kuo-Chen Chou:
pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC. Bioinform. 32(20): 3133-3141 (2016) - 2015
- [j33]Wei Chen, Xitong Zhang, Jordan Brooker, Hao Lin, Liqing Zhang, Kuo-Chen Chou:
PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions. Bioinform. 31(1): 119-120 (2015) - [j32]Bin Liu, Fule Liu, Longyun Fang, Xiaolong Wang, Kuo-Chen Chou:
repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects. Bioinform. 31(8): 1307-1309 (2015) - [j31]Bin Liu, Fule Liu, Xiaolong Wang, Junjie Chen, Longyun Fang, Kuo-Chen Chou:
Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences. Nucleic Acids Res. 43(Webserver-Issue): W65-W71 (2015) - 2014
- [j30]Bin Liu, Deyuan Zhang, Ruifeng Xu, Jinghao Xu, Xiaolong Wang, Qingcai Chen, Qiwen Dong, Kuo-Chen Chou:
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. Bioinform. 30(4): 472-479 (2014) - [j29]Shou-Hui Guo, En-Ze Deng, Liqin Xu, Hui Ding, Hao Lin, Wei Chen, Kuo-Chen Chou:
iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Bioinform. 30(11): 1522-1529 (2014) - 2011
- [c1]Hui Liu, Xiang Liu, Kuo-Chen Chou:
Minimal and optimal subsites set of HIV-1 protease cleavage site based on rough set. iCAST 2011: 265-269 - 2010
- [j28]Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou, Hai-Peng Li:
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC Bioinform. 11: 293 (2010) - [j27]Zhiyuan Xie, Tao Zhang, Jing-Fang Wang, Kuo-Chen Chou, Dongqing Wei:
The computational model to predict accurately inhibitory activity for inhibitors towardsCYP3A4. Comput. Biol. Medicine 40(11-12): 845-852 (2010) - [j26]Lin Zhu, Jie Yang, Jiangning Song, Kuo-Chen Chou, Hong-Bin Shen:
Improving the accuracy of predicting disulfide connectivity by feature selection. J. Comput. Chem. 31(7): 1478-1485 (2010)
2000 – 2009
- 2009
- [j25]Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Zong-Wen Pang, Li-Qin Du, Kuo-Chen Chou:
Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design. J. Comput. Chem. 30(2): 295-304 (2009) - [j24]Xuan Xiao, Pu Wang, Kuo-Chen Chou:
GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes. J. Comput. Chem. 30(9): 1414-1423 (2009) - 2008
- [j23]Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Li-Qin Du, Kuo-Chen Chou:
Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR). J. Comput. Chem. 29(2): 211-219 (2008) - [j22]Xuan Xiao, Wei-Zhong Lin, Kuo-Chen Chou:
Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes. J. Comput. Chem. 29(12): 2018-2024 (2008) - [j21]Guillermín Agüero-Chapín, Agostinho Antunes, Florencio M. Ubeira, Kuo-Chen Chou, Humberto González Díaz:
Comparative Study of Topological Indices of Macro/Supramolecular RNA Complex Networks. J. Chem. Inf. Model. 48(11): 2265-2277 (2008) - 2007
- [j20]Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Cheng-Hua Wang, Kuo-Chen Chou:
Peptide reagent design based on physical and chemical properties of amino acid residues. J. Comput. Chem. 28(12): 2043-2050 (2007) - 2006
- [j19]Hong-Bin Shen, Kuo-Chen Chou:
Ensemble classifier for protein fold pattern recognition. Bioinform. 22(14): 1717-1722 (2006) - [j18]Tongliang Zhang, Yongsheng Ding, Kuo-Chen Chou:
Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence. Comput. Biol. Chem. 30(5): 367-371 (2006) - [j17]Xuan Xiao, Shihuang Shao, Zheng-De Huang, Kuo-Chen Chou:
Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor. J. Comput. Chem. 27(4): 478-482 (2006) - [j16]Qishi Du, Dapeng Li, Wen-Zhang He, Kuo-Chen Chou:
Heuristic molecular lipophilicity potential (HMLP): Lipophilicity and hydrophilicity of amino acid side chains. J. Comput. Chem. 27(6): 685-692 (2006) - 2005
- [j15]Kuo-Chen Chou:
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinform. 21(1): 10-19 (2005) - [j14]Kuo-Chen Chou, Yu-Dong Cai:
Predicting protein localization in budding Yeast. Bioinform. 21(7): 944-950 (2005) - [j13]Suzanne W. Sirois, George E. Hatzakis, Dongqing Wei, Qishi Du, Kuo-Chen Chou:
Assessment of chemical libraries for their druggability. Comput. Biol. Chem. 29(1): 55-67 (2005) - [j12]Qishi Du, Paul G. Mezey, Kuo-Chen Chou:
Heuristic molecular lipophilicity potential (HMLP): A 2D-QSAR study to LADH of molecular family pyrazole and derivatives. J. Comput. Chem. 26(5): 461-470 (2005) - [j11]Kuo-Chen Chou, Yu-Dong Cai:
Prediction of Membrane Protein Types by Incorporating Amphipathic Effects. J. Chem. Inf. Model. 45(2): 407-413 (2005) - 2004
- [j10]Zheng Rong Yang, Kuo-Chen Chou:
Bio-support vector machines for computational proteomics. Bioinform. 20(5): 735-741 (2004) - [j9]Zheng Rong Yang, Kuo-Chen Chou:
Predicting the linkage sites in glycoproteins using bio-basis function neural network. Bioinform. 20(6): 903-908 (2004) - [j8]Yu-Dong Cai, Kuo-Chen Chou:
Predicting subcellular localization of proteins in a hybridization space. Bioinform. 20(7): 1151-1156 (2004) - [j7]Suzanne W. Sirois, Dongqing Wei, Qishi Du, Kuo-Chen Chou:
Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points. J. Chem. Inf. Model. 44(3): 1111-1122 (2004) - 2003
- [j6]Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou:
Prediction of protein secondary structure content by artificial neural network. J. Comput. Chem. 24(6): 727-731 (2003) - [j5]Zheng Rong Yang, Kuo-Chen Chou:
Mining Biological Data Using Self-Organizing Map. J. Chem. Inf. Comput. Sci. 43(6): 1748-1753 (2003) - 2002
- [j4]Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou:
Artificial Neural Network Model for Predicting Protein Subcellular Location. Comput. Chem. 26(2): 179-182 (2002) - [j3]Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu, Kuo-Chen Chou:
Prediction of Protein Structural Classes by Support Vector Machines. Comput. Chem. 26(3): 293-296 (2002) - [j2]Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu, Kuo-Chen Chou:
Artificial Neural Network Method for Predicting Protein Secondary Structure Content. Comput. Chem. 26(4): 347-350 (2002) - [j1]Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu, Kuo-Chen Chou:
Support vector machines for predicting HIV protease cleavage sites in protein. J. Comput. Chem. 23(2): 267-274 (2002)
Coauthor Index
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