Kuo-Chen Chou

Publication Activity (10 Years)

Years Active: 2002-2021
Publications (10 Years): 29

Top Topics

Subcellular Localization

Training Dataset

Informative Features

Top Venues

Briefings Bioinform.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

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) (2021)
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) (2021)
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) (2020)
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) (2019)
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) (2019)
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) (2019)
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) (2019)
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) (2019)
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) (2019)
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) (2019)
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) (2019)
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) (2018)
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) (2018)
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) (2018)
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) (2018)
Bin Liu, Fan Weng, De-Shuang Huang, Kuo-Chen Chou
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC. Bioinform. 34 (18) (2018)
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) (2018)
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) (2018)
Bin Liu, Kai Li, De-Shuang Huang, Kuo-Chen Chou
iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach. Bioinform. 34 (22) (2018)
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) (2018)
Bin Liu, Shanyi Wang, Ren Long, Kuo-Chen Chou
iRSpot-EL: identify recombination spots with an ensemble learning approach. Bioinform. 33 (1) (2017)
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) (2017)
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) (2017)
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) (2017)
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) (2017)
Bin Liu, Longyun Fang, Ren Long, Xun Lan, Kuo-Chen Chou
-tuple nucleotide composition. Bioinform. 32 (3) (2016)
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) (2016)
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) (2016)
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) (2016)
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) (2015)
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) (2015)
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) (2015)
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) (2014)
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) (2014)
Hui Liu, Xiang Liu, Kuo-Chen Chou
Minimal and optimal subsites set of HIV-1 protease cleavage site based on rough set. iCAST (2011)
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) (2010)
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 (2010)
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) (2010)
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) (2009)
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) (2009)
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) (2008)
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) (2008)
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) (2008)
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) (2007)
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) (2006)
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) (2006)
Tongliang Zhang, Yongsheng Ding, Kuo-Chen Chou
Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence. Comput. Biol. Chem. 30 (5) (2006)
Hong-Bin Shen, Kuo-Chen Chou
Ensemble classifier for protein fold pattern recognition. Bioinform. 22 (14) (2006)
Kuo-Chen Chou, Yu-Dong Cai
Prediction of Membrane Protein Types by Incorporating Amphipathic Effects. J. Chem. Inf. Model. 45 (2) (2005)
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) (2005)
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) (2005)
Kuo-Chen Chou
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinform. 21 (1) (2005)
Kuo-Chen Chou, Yu-Dong Cai
Predicting protein localization in budding Yeast. Bioinform. 21 (7) (2005)
Zheng Rong Yang, Kuo-Chen Chou
Bio-support vector machines for computational proteomics. Bioinform. 20 (5) (2004)
Zheng Rong Yang, Kuo-Chen Chou
Predicting the linkage sites in glycoproteins using bio-basis function neural network. Bioinform. 20 (6) (2004)
Yu-Dong Cai, Kuo-Chen Chou
Predicting subcellular localization of proteins in a hybridization space. Bioinform. 20 (7) (2004)
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) (2004)
Zheng Rong Yang, Kuo-Chen Chou
Mining Biological Data Using Self-Organizing Map. J. Chem. Inf. Comput. Sci. 43 (6) (2003)
Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou
Prediction of protein secondary structure content by artificial neural network. J. Comput. Chem. 24 (6) (2003)
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) (2002)
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) (2002)
Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou
Artificial Neural Network Model for Predicting Protein Subcellular Location. Comput. Chem. 26 (2) (2002)
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) (2002)