Kuo-Chen Chou

63 papers Journal 62Unranked 1
YearRankTypeTitle / Venue / Authors
2021 J jnl
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.
Muhammad Aizaz Akmal, Waqar Hussain, Nouman Rasool, Yaser Daanial Khan, Sher Afzal Khan, Kuo-Chen Chou
2021 J jnl
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.
Muhammad Awais, Waqar Hussain, Yaser Daanial Khan, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou
2020 J jnl
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.
Briefings Bioinform.
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
2019 J jnl
Bastion3: a two-layer ensemble predictor of type III secreted effectors.
Bioinform.
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
2019 J jnl
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.
Briefings Bioinform.
Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song
2019 J jnl
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.
Briefings Bioinform.
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
2019 J jnl
MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters.
Bioinform.
Meng Zhang, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Cunshuo Fan, Chee Keong Kwoh, Kuo-Chen Chou, Jiangning Song, Cangzhi Jia
2019 J jnl
Positive-unlabelled learning of glycosylation sites in the human proteome.
BMC Bioinform.
Fuyi Li, Yang Zhang, Anthony W. Purcell, Geoffrey I. Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li, Jiangning Song
2019 J jnl
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.
Briefings Bioinform.
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
2019 J jnl
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.
Briefings Bioinform.
Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou
2019 J jnl
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC.
Bioinform.
Xiang Cheng, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou
2018 J jnl
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.
Bioinform.
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
2018 J jnl
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.
Bioinform.
Jiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike
2018 J jnl
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
Bioinform.
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
2018 J jnl
iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach.
Bioinform.
Bin Liu, Kai Li, De-Shuang Huang, Kuo-Chen Chou
2018 J jnl
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences.
Bioinform.
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
2018 J jnl
iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC.
Bioinform.
Zhen-Dong Su, Yan Huang, Zhao-Yue Zhang, Ya-Wei Zhao, Dong Wang, Wei Chen, Kuo-Chen Chou, Hao Lin
2018 J jnl
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC.
Bioinform.
Bin Liu, Fan Yang, De-Shuang Huang, Kuo-Chen Chou
2018 J jnl
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC.
Bioinform.
Bin Liu, Fan Weng, De-Shuang Huang, Kuo-Chen Chou
2018 J jnl
pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information.
Bioinform.
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
2017 J jnl
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.
Bioinform.
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
2017 J jnl
iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals.
Bioinform.
Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou
2017 J jnl
iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals.
Bioinform.
Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou
2017 J jnl
iRSpot-EL: identify recombination spots with an ensemble learning approach.
Bioinform.
Bin Liu, Shanyi Wang, Ren Long, Kuo-Chen Chou
2017 J jnl
pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites.
Bioinform.
Xiang Cheng, Shu-Guang Zhao, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou
2016 J jnl
iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.
Bioinform.
Bin Liu, Ren Long, Kuo-Chen Chou
2016 J jnl
iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo
Bioinform.
Bin Liu, Longyun Fang, Ren Long, Xun Lan, Kuo-Chen Chou
2016 J jnl
iPTM-mLys: identifying multiple lysine PTM sites and their different types.
Bioinform.
Wangren Qiu, Bi-Qian Sun, Xuan Xiao, Zhao-Chun Xu, Kuo-Chen Chou
2016 J jnl
pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC.
Bioinform.
Jianhua Jia, Liuxia Zhang, Zi Liu, Xuan Xiao, Kuo-Chen Chou
2015 J jnl
Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
Nucleic Acids Res.
Bin Liu, Fule Liu, Xiaolong Wang, Junjie Chen, Longyun Fang, Kuo-Chen Chou
2015 J jnl
PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions.
Bioinform.
Wei Chen, Xitong Zhang, Jordan Brooker, Hao Lin, Liqing Zhang, Kuo-Chen Chou
2015 J jnl
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.
Bin Liu, Fule Liu, Longyun Fang, Xiaolong Wang, Kuo-Chen Chou
2014 J jnl
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection.
Bioinform.
Bin Liu, Deyuan Zhang, Ruifeng Xu, Jinghao Xu, Xiaolong Wang, Qingcai Chen, Qiwen Dong, Kuo-Chen Chou
2014 J jnl
iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition.
Bioinform.
Shou-Hui Guo, En-Ze Deng, Liqin Xu, Hui Ding, Hao Lin, Wei Chen, Kuo-Chen Chou
2011 — conf
Minimal and optimal subsites set of HIV-1 protease cleavage site based on rough set.
iCAST
Hui Liu, Xiang Liu, Kuo-Chen Chou
2010 J jnl
Improving the accuracy of predicting disulfide connectivity by feature selection.
J. Comput. Chem.
Lin Zhu, Jie Yang, Jiangning Song, Kuo-Chen Chou, Hong-Bin Shen
2010 J jnl
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition.
BMC Bioinform.
Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou, Hai-Peng Li
2010 J jnl
The computational model to predict accurately inhibitory activity for inhibitors towardsCYP3A4.
Comput. Biol. Medicine
Zhiyuan Xie, Tao Zhang, Jing-Fang Wang, Kuo-Chen Chou, Dongqing Wei
2009 J jnl
Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design.
J. Comput. Chem.
Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Zong-Wen Pang, Li-Qin Du, Kuo-Chen Chou
2009 J jnl
GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes.
J. Comput. Chem.
Xuan Xiao, Pu Wang, Kuo-Chen Chou
2008 J jnl
Comparative Study of Topological Indices of Macro/Supramolecular RNA Complex Networks.
J. Chem. Inf. Model.
Guillermín Agüero-Chapín, Agostinho Antunes, Florencio M. Ubeira, Kuo-Chen Chou, Humberto González Díaz
2008 J jnl
Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR).
J. Comput. Chem.
Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Li-Qin Du, Kuo-Chen Chou
2008 J jnl
Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes.
J. Comput. Chem.
Xuan Xiao, Wei-Zhong Lin, Kuo-Chen Chou
2007 J jnl
Peptide reagent design based on physical and chemical properties of amino acid residues.
J. Comput. Chem.
Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Cheng-Hua Wang, Kuo-Chen Chou
2006 J jnl
Ensemble classifier for protein fold pattern recognition.
Bioinform.
Hong-Bin Shen, Kuo-Chen Chou
2006 J jnl
Heuristic molecular lipophilicity potential (HMLP): Lipophilicity and hydrophilicity of amino acid side chains.
J. Comput. Chem.
Qishi Du, Dapeng Li, Wen-Zhang He, Kuo-Chen Chou
2006 J jnl
Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence.
Comput. Biol. Chem.
Tongliang Zhang, Yongsheng Ding, Kuo-Chen Chou
2006 J jnl
Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor.
J. Comput. Chem.
Xuan Xiao, Shihuang Shao, Zheng-De Huang, Kuo-Chen Chou
2005 J jnl
Assessment of chemical libraries for their druggability.
Comput. Biol. Chem.
Suzanne W. Sirois, George E. Hatzakis, Dongqing Wei, Qishi Du, Kuo-Chen Chou
2005 J jnl
Heuristic molecular lipophilicity potential (HMLP): A 2D-QSAR study to LADH of molecular family pyrazole and derivatives.
J. Comput. Chem.
Qishi Du, Paul G. Mezey, Kuo-Chen Chou
2005 J jnl
Predicting protein localization in budding Yeast.
Bioinform.
Kuo-Chen Chou, Yu-Dong Cai
2005 J jnl
Prediction of Membrane Protein Types by Incorporating Amphipathic Effects.
J. Chem. Inf. Model.
Kuo-Chen Chou, Yu-Dong Cai
2005 J jnl
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes.
Bioinform.
Kuo-Chen Chou
2004 J jnl
Bio-support vector machines for computational proteomics.
Bioinform.
Zheng Rong Yang, Kuo-Chen Chou
2004 J jnl
Predicting subcellular localization of proteins in a hybridization space.
Bioinform.
Yu-Dong Cai, Kuo-Chen Chou
2004 J jnl
Predicting the linkage sites in glycoproteins using bio-basis function neural network.
Bioinform.
Zheng Rong Yang, Kuo-Chen Chou
2004 J jnl
Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points.
J. Chem. Inf. Model.
Suzanne W. Sirois, Dongqing Wei, Qishi Du, Kuo-Chen Chou
2003 J jnl
Mining Biological Data Using Self-Organizing Map.
J. Chem. Inf. Comput. Sci.
Zheng Rong Yang, Kuo-Chen Chou
2003 J jnl
Prediction of protein secondary structure content by artificial neural network.
J. Comput. Chem.
Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou
2002 J jnl
Artificial Neural Network Method for Predicting Protein Secondary Structure Content.
Comput. Chem.
Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu, Kuo-Chen Chou
2002 J jnl
Artificial Neural Network Model for Predicting Protein Subcellular Location.
Comput. Chem.
Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou
2002 J jnl
Prediction of Protein Structural Classes by Support Vector Machines.
Comput. Chem.
Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu, Kuo-Chen Chou
2002 J jnl
Support vector machines for predicting HIV protease cleavage sites in protein.
J. Comput. Chem.
Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu, Kuo-Chen Chou