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2024
Protein S-Nitrosylation: A Chemical Modification with Ubiquitous Biological Activities
The Protein Journal
Adam A. Aboalroub, Khaldun M. Al Azzam
2024
The evolution of S-nitrosylation detection methodology and the role of protein S-nitrosylation in various cancers
Cancer Cell International
Feng Liang, Min Wang, Jiannan Li, Jie Guo
2024
Protein acetylation sites with complex-valued polynomial model
Frontiers of Computer Science
Wenzheng Bao, Bin Yang
2024
iDLB-Pred: identification of disordered lipid binding residues in protein sequences using convolutional neural network
Scientific Reports
Sharaf J. Malebary, Nashwan Alromema
2024
PPSNO: A Feature-Rich SNO Sites Predictor by Stacking Ensemble Strategy from Protein Sequence-Derived Information
Interdisciplinary Sciences: Computational Life Sciences
Lun Zhu, Liuyang Wang, Zexi Yang, Piao Xu, Sen Yang
2023
The ROP2 GTPase Participates in Nitric Oxide (NO)-Induced Root Shortening in Arabidopsis
Plants
Erzsébet Kenesi, Zsuzsanna Kolbert, Nikolett Kaszler, Éva Klement, Dalma Ménesi, Árpád Molnár, Ildikó Valkai, Gábor Feigl, Gábor Rigó, Ágnes Cséplő, Christian Lindermayr, Attila Fehér
2022
Mul-SNO: A Novel Prediction Tool for S-Nitrosylation Sites Based on Deep Learning Methods
IEEE Journal of Biomedical and Health Informatics
Qian Zhao, Jiaqi Ma, Yu Wang, Fang Xie, Zhibin Lv, Yaoqun Xu, Hua Shi, Ke Han
2022
Proteomic Analysis of S-Nitrosation Sites During Somatic Embryogenesis in Brazilian Pine, Araucaria angustifolia (Bertol.) Kuntze
Frontiers in Plant Science
Alexandre Junio Borges Araujo, Giovanni Victorio Cerruti, Rafael Zuccarelli, Marta Rodriguez Ruiz, Luciano Freschi, Ratna Singh, Bruno Maria Moerschbacher, Eny Iochevet Segal Floh, André Luis Wendt dos Santos
2022
iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Sheraz Naseer, Waqar Hussain, Yaser Daanial Khan, Nouman Rasool
2022
ILipo-PseAAC: Identification of Lipoylation Sites Using Statistical Moments and General PseAAC
Computers, Materials & Continua
Samar Nour, Sameh A. Salem, Shahira M. Habashy
2022
Redox Chemistry and Biology of Thiols
Stefano M. Marino, Gustavo Salinas, Vadim N. Gladyshev
2022
A sequence-based two-layer predictor for identifying enhancers and their strength through enhanced feature extraction
Journal of Bioinformatics and Computational Biology
Santhosh Amilpur, Raju Bhukya
2022
The role of nitric oxide (NO) in plant responses to disturbed zinc homeostasis
Plant Stress
Selahattin KONDAK, Árpád MOLNÁR, Dóra OLÁH, Zsuzsanna KOLBERT
2022
Mini-review: Recent advances in post-translational modification site prediction based on deep learning
Computational and Structural Biotechnology Journal
Lingkuan Meng, Wai-Sum Chan, Lei Huang, Linjing Liu, Xingjian Chen, Weitong Zhang, Fuzhou Wang, Ke Cheng, Hongyan Sun, Ka-Chun Wong
2022
A machine learning technique for identifying DNA enhancer regions utilizing CIS-regulatory element patterns
Scientific Reports
Ahmad Hassan Butt, Tamim Alkhalifah, Fahad Alturise, Yaser Daanial Khan
2022
S-Nitrosation of E3 Ubiquitin Ligase Complex Components Regulates Hormonal Signalings in Arabidopsis
Frontiers in Plant Science
Maria Cecilia Terrile, Nuria Malena Tebez, Silvana Lorena Colman, Julieta Lisa Mateos, Esperanza Morato-López, Nuria Sánchez-López, Alicia Izquierdo-Álvarez, Anabel Marina, Luz Irina A. Calderón Villalobos, Mark Estelle, Antonio Martínez-Ruiz, Diego Fernando Fiol, Claudia Anahí Casalongué, María José Iglesias
2022
A Deep Ensemble Predictor for Identifying Anti-Hypertensive Peptides Using Pretrained Protein Embedding
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Yuanying Zhuang, Xiangrong Liu, Yue Zhong, Longxin Wu
2021
Recent Advances in Predicting Protein S‐Nitrosylation Sites
BioMed Research International
Qian Zhao, Jiaqi Ma, Fang Xie, Yu Wang, Yu Zhang, Hui Li, Yuan Sun, Liqi Wang, Mian Guo, Ke Han
2021
iEnhancer-DHF: Identification of Enhancers and Their Strengths Using Optimize Deep Neural Network With Multiple Features Extraction Methods
IEEE Access
Nagina Inayat, Mukhtaj Khan, Nadeem Iqbal, Salman Khan, Mushtaq Raza, Dost Muhammad Khan, Abbas Khan, Dong Qing Wei
2021
iPhosD-PseAAC: Identification of phosphoaspartate sites in proteins using statistical moments and PseAAC
BIOCELL
ALAA OMRAN ALMAGRABI, YASER DAANIAL KHAN, SHER AFZAL KHAN
2021
PA-PseU: An incremental passive-aggressive based method for identifying RNA pseudouridine sites via Chou’s 5-steps rule
Chemometrics and Intelligent Laboratory Systems
Jiesheng Wang, Shengli Zhang
2021
Optimization of serine phosphorylation prediction in proteins by comparing human engineered features and deep representations
Analytical Biochemistry
Sheraz Naseer, Waqar Hussain, Yaser Daanial Khan, Nouman Rasool
2021
Biological Mechanisms of S-Nitrosothiol Formation and Degradation: How Is Specificity of S-Nitrosylation Achieved?
Antioxidants
Christopher M. Massa, Ziping Liu, Sheryse Taylor, Ashley P. Pettit, Marena N. Stakheyeva, Elena Korotkova, Valentina Popova, Elena N. Atochina-Vasserman, Andrew J. Gow
2021
Using CHOU'S 5-Steps Rule to Predict O-Linked Serine Glycosylation Sites by Blending Position Relative Features and Statistical Moment
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Muhammad Aizaz Akmal, Waqar Hussain, Nouman Rasool, Yaser Daanial Khan, Sher Afzal Khan, Kuo-Chen Chou
2021
Computational prediction of NO-dependent posttranslational modifications in plants: Current status and perspectives
Plant Physiology and Biochemistry
Zsuzsanna Kolbert, Christian Lindermayr
2021
iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC
PeerJ
Yaser Daanial Khan, Nabeel Sabir Khan, Sheraz Naseer, Ahmad Hassan Butt
2021
Comparison and Analysis of Computational Methods for Identifying N6-Methyladenosine Sites in Saccharomyces cerevisiae
Current Pharmaceutical Design
Pengmian Feng, Lijing Feng, Chaohui Tang
2021
iEnhancer-KL: A Novel Two-Layer Predictor for Identifying Enhancers by Position Specific of Nucleotide Composition
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Yinuo Lyu, Zhen Zhang, Jiawei Li, Wenying He, Yijie Ding, Fei Guo
2021
Prediction and Analysis of Protein Ubiquitin Sites in the Model Plant A. thaliana
Scientific Programming
Shujun Shan, Yue Qi, Jihong Jiang, Song Guo
2021
Yin and Yang in Post-Translational Modifications of Human D-Amino Acid Oxidase
Frontiers in Molecular Biosciences
Silvia Sacchi, Valentina Rabattoni, Matteo Miceli, Loredano Pollegioni
2021
iTAGPred: A Two-Level Prediction Model for Identification of Angiogenesis and Tumor Angiogenesis Biomarkers
Applied Bionics and Biomechanics
Khalid Allehaibi, Yaser Daanial Khan, Sher Afzal Khan
2021
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 Transactions on Computational Biology and Bioinformatics
Muhammad Awais, Waqar Hussain, Yaser Daanial Khan, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou
2020
Computational Method for Identifying Malonylation Sites by Using Random Forest Algorithm
Combinatorial Chemistry & High Throughput Screening
ShaoPeng Wang, JiaRui Li, Xijun Sun, Yu-Hang Zhang, Tao Huang, Yudong Cai
2020
Locate-R: Subcellular localization of long non-coding RNAs using nucleotide compositions
Genomics
Ahsan Ahmad, Hao Lin, Swakkhar Shatabda
2020
Evolutionary insights into the active-site structures of the metallo-β-lactamase superfamily from a classification study with support vector machine
JBIC Journal of Biological Inorganic Chemistry
Lili Wang, Ling Yang, Yu-lan Feng, Hao Zhang
2020
Glioma stages prediction based on machine learning algorithm combined with protein-protein interaction networks
Genomics
Bing Niu, Chaofeng Liang, Yi Lu, Manman Zhao, Qin Chen, Yuhui Zhang, Linfeng Zheng, Kuo-Chen Chou
2020
Prediction of membrane protein types by fusing protein-protein interaction and protein sequence information
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Xiaolin Zhang, Lei Chen
2020
A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy
Scientific Reports
Mukesh Kumar, Elena Papaleo
2020
An Insightful 10-year Recollection Since the Emergence of the 5-steps Rule
Current Pharmaceutical Design
Kuo-Chen Chou
2020
Plant Life Under Changing Environment
Mounira Chaki, Juan C. Begara-Morales, Raquel Valderrama, Capilla Mata-Pérez, María N. Padilla-Serrano, Juan B. Barroso
2020
Progresses in Predicting Post-translational Modification
International Journal of Peptide Research and Therapeutics
Kuo-Chen Chou
2020
iProtease-PseAAC(2L): A two-layer predictor for identifying proteases and their types using Chou's 5-step-rule and general PseAAC
Analytical Biochemistry
Yaser Daanial Khan, Najm Amin, Waqar Hussain, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou
2020
Mechanistic Insights of Chemicals and Drugs as Risk Factors for Systemic Lupus Erythematosus
Current Medicinal Chemistry
Qingjun Pan, Yun Guo, Linjie Guo, Shuzhen Liao, Chunfei Zhao, Sijie Wang, Hua-Feng Liu
2020
Prediction of lysine formylation sites using the composition of k-spaced amino acid pairs via Chou's 5-steps rule and general pseudo components
Genomics
Zhe Ju, Shi-Yun Wang
2020
iNR-2L: A two-level sequence-based predictor developed via Chou's 5-steps rule and general PseAAC for identifying nuclear receptors and their families
Genomics
Muhammad Kabir, Saeed Ahmad, Muhammad Iqbal, Maqsood Hayat
2020
Identification of prokaryotic promoters and their strength by integrating heterogeneous features
Genomics
Hilal Tayara, Muhammad Tahir, Kil To Chong
2020
Prediction of S-Sulfenylation Sites Using Statistical Moments Based Features via CHOU’S 5-Step Rule
International Journal of Peptide Research and Therapeutics
Ahmad Hassan Butt, Yaser Daanial Khan
2020
cACP: Classifying anticancer peptides using discriminative intelligent model via Chou’s 5-step rules and general pseudo components
Chemometrics and Intelligent Laboratory Systems
Shahid Akbar, Ateeq Ur Rahman, Maqsood Hayat, Mohammad Sohail
2020
Characterization and Identification of Protein S-Nitrosylation Sites Based on Tertiary Structures
International Journal of Bioscience, Biochemistry and Bioinformatics
Tzong-Yi Lee, Justin Bo-Kai Hsu, Tzu-Hao Chang
2020
A Sequence-Based Predictor of Zika Virus Proteins Developed by Integration of PseAAC and Statistical Moments
Combinatorial Chemistry & High Throughput Screening
Waqar Hussain, Nouman Rasool, Yaser D. Khan
2020
iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters
Bioinformatics
Ruhul Amin, Chowdhury Rafeed Rahman, Sajid Ahmed, Md Habibur Rahman Sifat, Md Nazmul Khan Liton, Md Moshiur Rahman, Md Zahid Hossain Khan, Swakkhar Shatabda
2020
Identification of Lysine Carboxylation Sites in Proteins by Integrating Statistical Moments and Position Relative Features via General PseAAC
Current Bioinformatics
Saba Amanat, Adeel Ashraf, Waqar Hussain, Nouman Rasool, Yaser D. Khan
2020
Proposing Pseudo Amino Acid Components is an Important Milestone for Proteome and Genome Analyses
International Journal of Peptide Research and Therapeutics
Kuo-Chen Chou
2020
CanLect-Pred: A Cancer Therapeutics Tool for Prediction of Target Cancerlectins Using Experiential Annotated Proteomic Sequences
IEEE Access
Ahmad Hassan Butt, Yaser Daanial Khan
2020
Prediction of Recombination Spots Using Novel Hybrid Feature Extraction Method via Deep Learning Approach
Frontiers in Genetics
Fatima Khan, Mukhtaj Khan, Nadeem Iqbal, Salman Khan, Dost Muhammad Khan, Abbas Khan, Dong-Qing Wei
2019
Biotechnology
Mahir M. Sharif, Alaa Tharwat, Aboul Ella Hassanien, Hesham A. Hefny
2019
Prediction and functional analysis of prokaryote lysine acetylation site by incorporating six types of features into Chou's general PseAAC
Journal of Theoretical Biology
Guodong Chen, Man Cao, Jialin Yu, Xinyun Guo, Shaoping Shi
2019
pLoc_bal-mGpos: Predict subcellular localization of Gram-positive bacterial proteins by quasi-balancing training dataset and PseAAC
Genomics
Xuan Xiao, Xiang Cheng, Genqiang Chen, Qi Mao, Kuo-Chen Chou
2019
Relationship Between DNA Methylation in Key Region and the Differential Expressions of Genes in Human Breast Tumor Tissue
DNA and Cell Biology
Wen Jin, Qian-Zhong Li, Yong-Chun Zuo, Yan-Ni Cao, Lu-Qiang Zhang, Rui Hou, Wen-Xia Su
2019
iN6-methylat (5-step): identifying DNA N6-methyladenine sites in rice genome using continuous bag of nucleobases via Chou’s 5-step rule
Molecular Genetics and Genomics
Nguyen Quoc Khanh Le
2019
Identifying N6-methyladenosine sites using extreme gradient boosting system optimized by particle swarm optimizer
Journal of Theoretical Biology
Xiaowei Zhao, Ye Zhang, Qiao Ning, Hongrui Zhang, Jinchao Ji, Minghao Yin
2019
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites
Briefings in Bioinformatics
Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D Rawlings, Geoffrey I Webb, Kuo-Chen Chou
2019
UbiSitePred: A novel method for improving the accuracy of ubiquitination sites prediction by using LASSO to select the optimal Chou's pseudo components
Chemometrics and Intelligent Laboratory Systems
Xiaowen Cui, Zhaomin Yu, Bin Yu, Minghui Wang, Baoguang Tian, Qin Ma
2019
SNARE-CNN: a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data
PeerJ Computer Science
Nguyen Quoc Khanh Le, Van-Nui Nguyen
2019
pDHS-DSET: Prediction of DNase I hypersensitive sites in plant genome using DS evidence theory
Analytical Biochemistry
Shanxin Zhang, Jinhe Lin, Lei Su, Zhiping Zhou
2019
iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC
Genomics
Pengmian Feng, Hui Yang, Hui Ding, Hao Lin, Wei Chen, Kuo-Chen Chou
2019
Identification of S-nitrosylation sites based on multiple features combination
Scientific Reports
Taoying Li, Runyu Song, Qian Yin, Mingyue Gao, Yan Chen
2019
A Review on the Recent Developments of Sequence-based Protein Feature Extraction Methods
Current Bioinformatics
Jun Zhang, Bin Liu
2019
iN6-Methyl (5-step): Identifying RNA N6-methyladenosine sites using deep learning mode via Chou's 5-step rules and Chou's general PseKNC
Chemometrics and Intelligent Laboratory Systems
Iman Nazari, Muhammad Tahir, Hilal Tayara, Kil To Chong
2019
Quantitative Structure-activity Relationship of Acetylcholinesterase Inhibitors based on mRMR Combined with Support Vector Regression
Letters in Organic Chemistry
Jiaxiang Wu, Guozhao Mai, Bowen Deng, Jeong Younseo, Dongsu Du, Fuxue Chen, Qiaorong Ma
2019
The Cradle of Gordon Life Science Institute and Its Development and Driving Force
International Journal of Biology and Genetics
2019
19F-NMR in Target-based Drug Discovery
Current Medicinal Chemistry
CongBao Kang
2019
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC
Bioinformatics
Xiang Cheng, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou
2019
Identification of Phage Virion Proteins by Using the g-gap Tripeptide Composition
Letters in Organic Chemistry
Liangwei Yang, Hui Gao, Zhen Liu, Lixia Tang
2019
Prediction of Nitrosocysteine Sites Using Position and Composition Variant Features
Letters in Organic Chemistry
Yaser Daanial Khan, Aroosa Batool, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou
2019
iEnhancer-5Step: Identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding
Analytical Biochemistry
Nguyen Quoc Khanh Le, Edward Kien Yee Yapp, Quang-Thai Ho, N. Nagasundaram, Yu-Yen Ou, Hui-Yuan Yeh
2019
pSSbond-PseAAC: Prediction of disulfide bonding sites by integration of PseAAC and statistical moments
Journal of Theoretical Biology
Yaser Daanial Khan, Mehreen Jamil, Waqar Hussain, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou
2019
Impacts of Pseudo Amino Acid Components and 5-steps Rule to Proteomics and Proteome Analysis
Current Topics in Medicinal Chemistry
Kuo-Chen Chou
2019
A Linear Regression Predictor for Identifying N6-Methyladenosine Sites Using Frequent Gapped K-mer Pattern
Molecular Therapy Nucleic Acids
Y.Y. Zhuang, H.J. Liu, X. Song, Y. Ju, H. Peng
2019
iNuc-ext-PseTNC: an efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou’s PseAAC to pseudo-tri-nucleotide composition
Molecular Genetics and Genomics
Muhammad Tahir, Maqsood Hayat, Sher Afzal Khan
2019
MsDBP: Exploring DNA-Binding Proteins by Integrating Multiscale Sequence Information via Chou’s Five-Step Rule
Journal of Proteome Research
Xiuquan Du, Yanyu Diao, Heng Liu, Shuo Li
2019
iHyd-PseAAC (EPSV): Identifying Hydroxylation Sites in Proteins by Extracting Enhanced Position and Sequence Variant Feature via Chou's 5- Step Rule and General Pseudo Amino Acid Composition
Current Genomics
Asma Ehsan, Muhammad K. Mahmood, Yaser D. Khan, Omar M. Barukab, Sher A. Khan, Kuo-Chen Chou
2019
Predicting protein–protein interactions by fusing various Chou's pseudo components and using wavelet denoising approach
Journal of Theoretical Biology
Baoguang Tian, Xue Wu, Cheng Chen, Wenying Qiu, Qin Ma, Bin Yu
2019
SPrenylC-PseAAC: A sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-prenylation sites in proteins
Journal of Theoretical Biology
Waqar Hussain, Yaser Daanial Khan, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou
2019
dForml(KNN)-PseAAC: Detecting formylation sites from protein sequences using K-nearest neighbor algorithm via Chou's 5-step rule and pseudo components
Journal of Theoretical Biology
Qiao Ning, Zhiqiang Ma, Xiaowei Zhao
2019
IMKPse: Identification of Protein Malonylation Sites by the Key Features Into General PseAAC
IEEE Access
Wenzheng Bao, Bin Yang, De-Shuang Huang, Dong Wang, Qi Liu, Yue-Hui Chen, Rong Bao
2019
pLoc_bal-mHum: Predict subcellular localization of human proteins by PseAAC and quasi-balancing training dataset
Genomics
Kuo-Chen Chou, Xiang Cheng, Xuan Xiao
2019
An Epidemic Avian Influenza Prediction Model Based on Google Trends
Letters in Organic Chemistry
Yi Lu, Shuo Wang, Jianying Wang, Guangya Zhou, Qiang Zhang, Xiang Zhou, Bing Niu, Qin Chen, Kuo-Chen Chou
2019
iPPI-PseAAC(CGR): Identify protein-protein interactions by incorporating chaos game representation into PseAAC
Journal of Theoretical Biology
Jianhua Jia, Xiaoyan Li, Wangren Qiu, Xuan Xiao, Kuo-Chen Chou
2019
iPSW(2L)-PseKNC: A two-layer predictor for identifying promoters and their strength by hybrid features via pseudo K-tuple nucleotide composition
Genomics
Xuan Xiao, Zhao-Chun Xu, Wang-Ren Qiu, Peng Wang, Hui-Ting Ge, Kuo-Chen Chou
2019
Identifying residues that determine palmitoylation using association rule mining
Bioinformatics
Bandana Kumari, Ravindra Kumar, Manish Kumar
2019
iRNA-PseKNC(2methyl): Identify RNA 2'-O-methylation sites by convolution neural network and Chou's pseudo components
Journal of Theoretical Biology
Muhammad Tahir, Hilal Tayara, Kil To Chong
2019
iDNA6mA (5-step rule): Identification of DNA N6-methyladenine sites in the rice genome by intelligent computational model via Chou's 5-step rule
Chemometrics and Intelligent Laboratory Systems
Muhammad Tahir, Hilal Tayara, Kil To Chong
2019
Biological Production of (S)-acetoin: A State-of-the-Art Review
Current Topics in Medicinal Chemistry
Neng-Zhong Xie, Jian-Xiu Li, Ri-Bo Huang
2019
Identifying Cancer Targets Based on Machine Learning Methods via Chou’s 5-steps Rule and General Pseudo Components
Current Topics in Medicinal Chemistry
Ruirui Liang, Jiayang Xie, Chi Zhang, Mengying Zhang, Hai Huang, Haizhong Huo, Xin Cao, Bing Niu
2019
iMethylK-PseAAC: Improving Accuracy of Lysine Methylation Sites Identification by Incorporating Statistical Moments and Position Relative Features into General PseAAC via Chou’s 5-steps Rule
Current Genomics
Sarah Ilyas, Waqar Hussain, Adeel Ashraf, Yaser Daanial Khan, Sher Afzal Khan, Kuo- Chen Chou
2019
Recent Advances in Computational Methods for Identifying Anticancer Peptides
Current Drug Targets
Pengmian Feng, Zhenyi Wang
2019
SPalmitoylC-PseAAC: A sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-palmitoylation sites in proteins
Analytical Biochemistry
Waqar Hussain, Yaser Daanial Khan, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou
2019
iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments via Chou’s 5-steps Rule and Pseudo Components
Current Genomics
Omar Barukab, Yaser Daanial Khan, Sher Afzal Khan, Kuo-Chen Chou
2019
Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications
Briefings in Bioinformatics
Shaoping Shi, Lina Wang, Man Cao, Guodong Chen, Jialin Yu
2019
The Impact of Statin Therapy on the Survival of Patients with Gastrointestinal Cancer
Current Drug Targets
Meysam Gachpazan, Hoda Kashani, Majid Khazaei, Seyed Mahdi Hassanian, Majid Rezayi, Fereshteh Asgharzadeh, Majid Ghayour-Mobarhan, Gordon A. Ferns, Amir Avan
2019
iRSpot-PDI: Identification of recombination spots by incorporating dinucleotide property diversity information into Chou's pseudo components
Genomics
Lichao Zhang, Liang Kong
2019
Advances in Predicting Subcellular Localization of Multi-label Proteins and its Implication for Developing Multi-target Drugs
Current Medicinal Chemistry
Kuo-Chen Chou
2019
Established and In-trial GPCR Families in Clinical Trials: A Review for Target Selection
Current Drug Targets
Surovi Saikia, Manobjyoti Bordoloi, Rajeev Sarmah
2018
PseUI: Pseudouridine sites identification based on RNA sequence information
BMC Bioinformatics
Jingjing He, Ting Fang, Zizheng Zhang, Bei Huang, Xiaolei Zhu, Yi Xiong
2018
RBSURFpred: Modeling protein accessible surface area in real and binary space using regularized and optimized regression
Journal of Theoretical Biology
Sumit Tarafder, Md. Toukir Ahmed, Sumaiya Iqbal, Md Tamjidul Hoque, M. Sohel Rahman
2018
Efficient computational model for classification of protein localization images using Extended Threshold Adjacency Statistics and Support Vector Machines
Computer Methods and Programs in Biomedicine
Muhammad Tahir, Bismillah Jan, Maqsood Hayat, Shakir Ullah Shah, Muhammad Amin
2018
Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate
International Journal of Molecular Sciences
Chun Yu, Xiao Li, Hong Yang, Ying Li, Wei Xue, Yu Chen, Lin Tao, Feng Zhu
2018
Methods in Molecular Biology
Rosario Carmona, M. Claros, Juan de Alché
2018
Computational Structural Biology of S-nitrosylation of Cancer Targets
Frontiers in Oncology
Emmanuelle Bignon, Maria Francesca Allega, Marta Lucchetta, Matteo Tiberti, Elena Papaleo
2018
Detecting Succinylation sites from protein sequences using ensemble support vector machine
BMC Bioinformatics
Qiao Ning, Xiaosa Zhao, Lingling Bao, Zhiqiang Ma, Xiaowei Zhao
2018
BlaPred: Predicting and classifying β-lactamase using a 3-tier prediction system via Chou's general PseAAC
Journal of Theoretical Biology
Abhishikha Srivastava, Ravindra Kumar, Manish Kumar
2018
pLoc_bal-mGneg: Predict subcellular localization of Gram-negative bacterial proteins by quasi-balancing training dataset and general PseAAC
Journal of Theoretical Biology
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
2018
pLoc-mGneg: Predict subcellular localization of Gram-negative bacterial proteins by deep gene ontology learning via general PseAAC
Genomics
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
2018
Identify Gram-negative bacterial secreted protein types by incorporating different modes of PSSM into Chou’s general PseAAC via Kullback–Leibler divergence
Journal of Theoretical Biology
Yunyun Liang, Shengli Zhang
2018
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC
Bioinformatics
Bin Liu, Fan Weng, De-Shuang Huang, Kuo-Chen Chou
2018
70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features
BMC Systems Biology
Wenying He, Cangzhi Jia, Yucong Duan, Quan Zou
2018
pLoc-mEuk: Predict subcellular localization of multi-label eukaryotic proteins by extracting the key GO information into general PseAAC
Genomics
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
2018
LAIPT: Lysine Acetylation Site Identification with Polynomial Tree
International Journal of Molecular Sciences
Wenzheng Bao, Bin Yang, Zhengwei Li, Yong Zhou
2018
Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams
PLOS ONE
Abdollah Dehzangi, Yosvany López, Sunil Pranit Lal, Ghazaleh Taherzadeh, Abdul Sattar, Tatsuhiko Tsunoda, Alok Sharma
2018
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC
Bioinformatics
Bin Liu, Fan Yang, De-Shuang Huang, Kuo-Chen Chou
2018
Analysis and prediction of ion channel inhibitors by using feature selection and Chou's general pseudo amino acid composition
Journal of Theoretical Biology
Juan Mei, Yi Fu, Ji Zhao
2018
EvoStruct-Sub: An accurate Gram-positive protein subcellular localization predictor using evolutionary and structural features
Journal of Theoretical Biology
Md. Raihan Uddin, Alok Sharma, Dewan Md Farid, Md. Mahmudur Rahman, Abdollah Dehzangi, Swakkhar Shatabda
2018
iRNA(m6A)-PseDNC: Identifying N6-methyladenosine sites using pseudo dinucleotide composition
Analytical Biochemistry
Wei Chen, Hui Ding, Xu Zhou, Hao Lin, Kuo-Chen Chou
2018
iKcr-PseEns: Identify lysine crotonylation sites in histone proteins with pseudo components and ensemble classifier
Genomics
Wang-Ren Qiu, Bi-Qian Sun, Xuan Xiao, Zhao-Chun Xu, Jian-Hua Jia, Kuo-Chen Chou
2018
iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites
Molecular Therapy - Nucleic Acids
Wei Chen, Pengmian Feng, Hui Yang, Hui Ding, Hao Lin, Kuo-Chen Chou
2018
iGlu-Lys: A Predictor for Lysine Glutarylation Through Amino Acid Pair Order Features
IEEE Transactions on NanoBioscience
Yan Xu, Yingxi Yang, Jun Ding, Chunhui Li
2018
iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach
Bioinformatics
Bin Liu, Kai Li, De-Shuang Huang, Kuo-Chen Chou
2018
Analysis and prediction of presynaptic and postsynaptic neurotoxins by Chou's general pseudo amino acid composition and motif features
Journal of Theoretical Biology
Juan Mei, Ji Zhao
2018
Prediction of S-sulfenylation sites using mRMR feature selection and fuzzy support vector machine algorithm
Journal of Theoretical Biology
Zhe Ju, Shi-Yun Wang
2018
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome
Bioinformatics
Fuyi Li, Chen Li, Tatiana T Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W Purcell, A Ian Smith, Trevor Lithgow, Roger J Daly, Jiangning Song, Kuo-Chen Chou
2018
DPP-PseAAC: A DNA-binding protein prediction model using Chou’s general PseAAC
Journal of Theoretical Biology
M. Saifur Rahman, Swakkhar Shatabda, Sanjay Saha, M. Kaykobad, M. Sohel Rahman
2018
Human serine racemase is nitrosylated at multiple sites
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Francesco Marchesani, Stefano Bruno, Gianluca Paredi, Samanta Raboni, Barbara Campanini, Andrea Mozzarelli
2018
O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique
Bioinformatics
Cangzhi Jia, Yun Zuo, Quan Zou
2018
Prediction of DNase I hypersensitive sites in plant genome using multiple modes of pseudo components
Analytical Biochemistry
Shanxin Zhang, Weichao Zhuang, Zhenghong Xu
2018
iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC
Bioinformatics
Zhen-Dong Su, Yan Huang, Zhao-Yue Zhang, Ya-Wei Zhao, Dong Wang, Wei Chen, Kuo-Chen Chou, Hao Lin
2018
pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information
Bioinformatics
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
2018
Predicting lysine lipoylation sites using bi-profile bayes feature extraction and fuzzy support vector machine algorithm
Analytical Biochemistry
Zhe Ju, Shi-Yun Wang
2018
iPhosY-PseAAC: identify phosphotyrosine sites by incorporating sequence statistical moments into PseAAC
Molecular Biology Reports
Yaser Daanial Khan, Nouman Rasool, Waqar Hussain, Sher Afzal Khan, Kuo-Chen Chou
2018
NucPosPred: Predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC
Journal of Theoretical Biology
Cangzhi Jia, Qing Yang, Quan Zou
2017
2L-PCA: a two-level principal component analyzer for quantitative drug design and its applications
Oncotarget
Qi-Shi Du, Shu-Qing Wang, Neng-Zhong Xie, Qing-Yan Wang, Ri-Bo Huang, Kuo-Chen Chou
2017
Prediction of interface residue based on the features of residue interaction network
Journal of Theoretical Biology
Xiong Jiao, Shoba Ranganathan
2017
iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC
Molecular Therapy - Nucleic Acids
Pengmian Feng, Hui Ding, Hui Yang, Wei Chen, Hao Lin, Kuo-Chen Chou
2017
pLoc-mGpos: Incorporate Key Gene Ontology Information into General PseAAC for Predicting Subcellular Localization of Gram-Positive Bacterial Proteins
Natural Science
Xuan Xiao, Xiang Cheng, Shengchao Su, Qi Mao, Kuo-Chen Chou
2017
Genome-Wide Prediction of DNA Methylation Using DNA Composition and Sequence Complexity in Human
International Journal of Molecular Sciences
Chengchao Wu, Shixin Yao, Xinghao Li, Chujia Chen, Xuehai Hu
2017
Highly accurate prediction of protein self-interactions by incorporating the average block and PSSM information into the general PseAAC
Journal of Theoretical Biology
Jing-Xuan Zhai, Tian-Jie Cao, Ji-Yong An, Yong-Tao Bian
2017
A novel feature ranking method for prediction of cancer stages using proteomics data
PLOS ONE
Ehsan Saghapour, Saeed Kermani, Mohammadreza Sehhati
2017
Prediction of protein N-formylation using the composition of k-spaced amino acid pairs
Analytical Biochemistry
Zhe Ju, Jun-Zhe Cao
2017
iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences
Oncotarget
Wei Chen, Pengmian Feng, Hui Yang, Hui Ding, Hao Lin, Kuo-Chen Chou
2017
Small molecular floribundiquinone B derived from medicinal plants inhibits acetylcholinesterase activity
Oncotarget
Bing Niu, Mengying Zhang, Pu Du, Li Jiang, Rui Qin, Qiang Su, Fuxue Chen, Dongshu Du, Yilai Shu, Kuo-Chen Chou
2017
Transmembrane region prediction by using sequence-derived features and machine learning methods
RSC Advances
Renxiang Yan, Xiaofeng Wang, Lanqing Huang, Yarong Tian, Weiwen Cai
2017
pDHS-SVM: A prediction method for plant DNase I hypersensitive sites based on support vector machine
Journal of Theoretical Biology
Shanxin Zhang, Zhiping Zhou, Xinmeng Chen, Yong Hu, Lindong Yang
2017
iATC-mHyb: a hybrid multi-label classifier for predicting the classification of anatomical therapeutic chemicals
Oncotarget
Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou
2017
S-SulfPred: A sensitive predictor to capture S-sulfenylation sites based on a resampling one-sided selection undersampling-synthetic minority oversampling technique
Journal of Theoretical Biology
Cangzhi Jia, Yun Zuo
2017
Pse-Analysis: a python package for DNA/RNA and protein/peptide sequence analysis based on pseudo components and kernel methods
Oncotarget
Bin Liu, Hao Wu, Deyuan Zhang, Xiaolong Wang, Kuo-Chen Chou
2017
Multi‐iPPseEvo: A Multi‐label Classifier for Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into Chou′s General PseAAC via Grey System Theory
Molecular Informatics
Wang‐Ren Qiu, Quan‐Shu Zheng, Bi‐Qian Sun, Xuan Xiao
2017
Extracting features from protein sequences to improve deep extreme learning machine for protein fold recognition
Journal of Theoretical Biology
Wisam Ibrahim, Mohammad Saniee Abadeh
2017
Advances in Computational Intelligence and Robotics
Mahir M. Sharif, Alaa Tharwat, Aboul Ella Hassanien, Hesham A. Hefny
2017
pLoc-mPlant: predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into general PseAAC
Molecular BioSystems
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
2017
pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC
Gene
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
2017
Prediction of lysine propionylation sites using biased SVM and incorporating four different sequence features into Chou’s PseAAC
Journal of Molecular Graphics and Modelling
Zhe Ju, Jian-Jun He
2017
2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function
Molecular Therapy - Nucleic Acids
Bin Liu, Fan Yang, Kuo-Chen Chou
2017
iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition
Oncotarget
Wang-Ren Qiu, Shi-Yu Jiang, Zhao-Chun Xu, Xuan Xiao, Kuo-Chen Chou
2017
Prediction of lysine crotonylation sites by incorporating the composition of k-spaced amino acid pairs into Chou’s general PseAAC
Journal of Molecular Graphics and Modelling
Zhe Ju, Jian-Jun He
2017
iACP-GAEnsC: Evolutionary genetic algorithm based ensemble classification of anticancer peptides by utilizing hybrid feature space
Artificial Intelligence in Medicine
Shahid Akbar, Maqsood Hayat, Muhammad Iqbal, Mian Ahmad Jan
2017
EnhancerPred2.0: predicting enhancers and their strength based on position-specific trinucleotide propensity and electron–ion interaction potential feature selection
Molecular BioSystems
Wenying He, Cangzhi Jia
2017
Predicting protein amidation sites by orchestrating amino acid sequence features
Journal of Physics: Conference Series
Shuqiu Zhao, Hua Yu, Xiujun Gong
2017
S -nitroso- and nitro- proteomes in the olive ( Olea europaea L.) pollen. Predictive versus experimental data by nano-LC-MS
Data in Brief
Rosario Carmona, María José Jimenez-Quesada, Elena Lima-Cabello, José Ángel Traverso, Antonio Jesús Castro, M. Gonzalo Claros, Juan de Dios Alché
2017
Generation of nitric oxide by olive (Olea europaea L.) pollen during in vitro germination and assessment of the S-nitroso- and nitro-proteomes by computational predictive methods
Nitric Oxide
María José Jimenez-Quesada, Rosario Carmona, Elena Lima-Cabello, José Ángel Traverso, Antonio Jesús Castro, M. Gonzalo Claros, Juan de Dios Alché
2017
Protein–protein interaction site predictions with minimum covariance determinant and Mahalanobis distance
Journal of Theoretical Biology
Zhijun Qiu, Bo Zhou, Jiangfeng Yuan
2016
iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition
Oncotarget
Chang-Jian Zhang, Hua Tang, Wen-Chao Li, Hao Lin, Wei Chen, Kuo-Chen Chou
2016
Identification of protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition
Journal of Biomolecular Structure and Dynamics
Jianhua Jia, Zi Liu, Xuan Xiao, Bingxiang Liu, Kuo-Chen Chou
2016
iSuc-PseOpt: Identifying lysine succinylation sites in proteins by incorporating sequence-coupling effects into pseudo components and optimizing imbalanced training dataset
Analytical Biochemistry
Jianhua Jia, Zi Liu, Xuan Xiao, Bingxiang Liu, Kuo-Chen Chou
2016
iNuc-STNC: a sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept of SAAC and Chou's PseAAC
Molecular BioSystems
Muhammad Tahir, Maqsood Hayat
2016
Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks
Scientific Reports
Yiheng Wang, Tong Liu, Dong Xu, Huidong Shi, Chaoyang Zhang, Yin-Yuan Mo, Zheng Wang
2016
iROS-gPseKNC: Predicting replication origin sites in DNA by incorporating dinucleotide position-specific propensity into general pseudo nucleotide composition
Oncotarget
Xuan Xiao, Han-Xiao Ye, Zi Liu, Jian-Hua Jia, Kuo-Chen Chou
2016
Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition
Journal of Theoretical Biology
Xiaowei Zhao, Qiao Ning, Meiyue Ai, Haiting Chai, Guifu Yang
2016
iPhos-PseEn: Identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier
Oncotarget
Wang-Ren Qiu, Xuan Xiao, Zhao-Chun Xu, Kuo-Chen Chou
2016
Predicting Golgi-resident protein types using pseudo amino acid compositions: Approaches with positional specific physicochemical properties
Journal of Theoretical Biology
Ya-Sen Jiao, Pu-Feng Du
2016
iPTM-mLys: identifying multiple lysine PTM sites and their different types
Bioinformatics
Wang-Ren Qiu, Bi-Qian Sun, Xuan Xiao, Zhao-Chun Xu, Kuo-Chen Chou
2016
“iSS-Hyb-mRMR”: Identification of splicing sites using hybrid space of pseudo trinucleotide and pseudo tetranucleotide composition
Computer Methods and Programs in Biomedicine
Muhammad Iqbal, Maqsood Hayat
2016
Predicting lysine phosphoglycerylation with fuzzy SVM by incorporating k-spaced amino acid pairs into Chou׳s general PseAAC
Journal of Theoretical Biology
Zhe Ju, Jun-Zhe Cao, Hong Gu
2016
iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach
Journal of Biomolecular Structure and Dynamics
Bin Liu, Longyun Fang, Fule Liu, Xiaolong Wang, Kuo-Chen Chou
2016
iAFP-Ense: An Ensemble Classifier for Identifying Antifreeze Protein by Incorporating Grey Model and PSSM into PseAAC
The Journal of Membrane Biology
Xuan Xiao, Mengjuan Hui, Zi Liu
2016
iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets
Molecules
Jianhua Jia, Zi Liu, Xuan Xiao, Bingxiang Liu, Kuo-Chen Chou
2016
iACP: a sequence-based tool for identifying anticancer peptides
Oncotarget
Wei Chen, Hui Ding, Pengmian Feng, Hao Lin, Kuo-Chen Chou
2016
An estimator for local analysis of genome based on the minimal absent word
Journal of Theoretical Biology
Lianping Yang, Xiangde Zhang, Haoyue Fu, Chenhui Yang
2016
iRSpot-GAEnsC: identifing recombination spots via ensemble classifier and extending the concept of Chou’s PseAAC to formulate DNA samples
Molecular Genetics and Genomics
Muhammad Kabir, Maqsood Hayat
2016
iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition
Bioinformatics
Bin Liu, Longyun Fang, Ren Long, Xun Lan, Kuo-Chen Chou
2016
iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sampling and incorporating sequence coupled effects into general PseAAC
Oncotarget
Jianhua Jia, Zi Liu, Xuan Xiao, Bingxiang Liu, Kuo-Chen Chou
2015
3D model for Cancerous Inhibitor of Protein Phosphatase 2A armadillo domain unveils highly conserved protein–protein interaction characteristics
Journal of Theoretical Biology
Käthe M. Dahlström, Tiina A. Salminen
2015
Probabilistic expression of spatially varied amino acid dimers into general form of Chou׳s pseudo amino acid composition for protein fold recognition
Journal of Theoretical Biology
Harsh Saini, Gaurav Raicar, Alok Sharma, Sunil Lal, Abdollah Dehzangi, James Lyons, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano
2015
iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach
Journal of Biomolecular Structure and Dynamics
Xuan Xiao, Jian-Liang Min, Wei-Zhong Lin, Zi Liu, Xiang Cheng, Kuo-Chen Chou
2015
Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences
Molecular BioSystems
Wei Chen, Hao Lin, Kuo-Chen Chou
2015
Role of structural flexibility in the evolution of emerin
Journal of Theoretical Biology
Jia Yuan, Bin Xue
2015
PseDNA‐Pro: DNA‐Binding Protein Identification by Combining Chou’s PseAAC and Physicochemical Distance Transformation
Molecular Informatics
Bin Liu, Jinghao Xu, Shixi Fan, Ruifeng Xu, Jiyun Zhou, Xiaolong Wang
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
Jianhua Jia, Zi Liu, Xuan Xiao, Bingxiang Liu, Kuo-Chen Chou
2015
Gram-positive and Gram-negative protein subcellular localization by incorporating evolutionary-based descriptors into Chou׳s general PseAAC
Journal of Theoretical Biology
Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, James Lyons, Kuldip Paliwal, Abdul Sattar
2015
iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition
Analytical Biochemistry
Wei Chen, Pengmian Feng, Hui Ding, Hao Lin, Kuo-Chen Chou
2015
iLM-2L: A two-level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating K-gap amino acid pairs into Chou׳s general PseAAC
Journal of Theoretical Biology
Zhe Ju, Jun-Zhe Cao, Hong Gu
2015
iUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model
Journal of Biomolecular Structure and Dynamics
Wang-Ren Qiu, Xuan Xiao, Wei-Zhong Lin, Kuo-Chen Chou
2015
miRNA-dis: microRNA precursor identification based on distance structure status pairs
Molecular BioSystems
Bin Liu, Longyun Fang, Junjie Chen, Fule Liu, Xiaolong Wang
2015
TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition
The Journal of Membrane Biology
Xue He, Ke Han, Jun Hu, Hui Yan, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
2015
Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation
BMC Systems Biology
Ruifeng Xu, Jiyun Zhou, Hongpeng Wang, Yulan He, Xiaolong Wang, Bin Liu
2015
PGlcS: Prediction of protein O-GlcNAcylation sites with multiple features and analysis
Journal of Theoretical Biology
Xiaowei Zhao, Qiao Ning, Haiting Chai, Meiyue Ai, Zhiqiang Ma
2015
Discrimination of membrane transporter protein types using K-nearest neighbor method derived from the similarity distance of total diversity measure
Molecular BioSystems
Yong-Chun Zuo, Wen-Xia Su, Shi-Hua Zhang, Shan-Shan Wang, Cheng-Yan Wu, Lei Yang, Guang-Peng Li
2015
iTIS-PseKNC: Identification of Translation Initiation Site in human genes using pseudo k-tuple nucleotides composition
Computers in Biology and Medicine
Muhammad Kabir, Muhammad Iqbal, Saeed Ahmad, Maqsood Hayat
2015
Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy
Journal of Theoretical Biology
Bin Liu, Longyun Fang, Shanyi Wang, Xiaolong Wang, Hongtao Li, Kuo-Chen Chou
2014
Multi-Label Learning With Fuzzy Hypergraph Regularization for Protein Subcellular Location Prediction
IEEE Transactions on NanoBioscience
Jing Chen, Yuan Yan Tang, C. L. Philip Chen, Bin Fang, Yuewei Lin, Zhaowei Shang
2014
GPCRserver: an accurate and novel G protein-coupled receptor predictor
Mol. BioSyst.
Renxiang Yan, Xiaofeng Wang, Lanqing Huang, Jun Lin, Weiwen Cai, Ziding Zhang
2014
iNitro-Tyr: Prediction of Nitrotyrosine Sites in Proteins with General Pseudo Amino Acid Composition
PLoS ONE
Yan Xu, Xin Wen, Li-Shu Wen, Ling-Yun Wu, Nai-Yang Deng, Kuo-Chen Chou
2014
A protein structural classes prediction method based on PSI-BLAST profile
Journal of Theoretical Biology
Shuyan Ding, Shoujiang Yan, Shuhua Qi, Yan Li, Yuhua Yao
2014
Computational Prediction of Candidate Proteins for S-Nitrosylation in Arabidopsis thaliana
PLoS ONE
Mounira Chaki, Izabella Kovacs, Manuel Spannagl, Christian Lindermayr
2014
Prediction of Protein S-Nitrosylation Sites Based on Adapted Normal Distribution Bi-Profile Bayes and Chou’s Pseudo Amino Acid Composition
International Journal of Molecular Sciences
Cangzhi Jia, Xin Lin, Zhiping Wang
2014
Prediction of Protein–Protein Interaction with Pairwise Kernel Support Vector Machine
International Journal of Molecular Sciences
Shao-Wu Zhang, Li-Yang Hao, Ting-He Zhang
2014
Prediction of posttranslational modification sites from amino acid sequences with kernel methods
Journal of Theoretical Biology
Yan Xu, Xiaobo Wang, Yongcui Wang, Yingjie Tian, Xiaojian Shao, Ling-Yun Wu, Naiyang Deng
2014
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection
Bioinformatics
Bin Liu, Deyuan Zhang, Ruifeng Xu, Jinghao Xu, Xiaolong Wang, Qingcai Chen, Qiwen Dong, Kuo-Chen Chou
2014
An effective haplotype assembly algorithm based on hypergraph partitioning
Journal of Theoretical Biology
Xiao Chen, Qinke Peng, Libin Han, Tao Zhong, Tao Xu
2014
iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition
Analytical Biochemistry
Wei Chen, Peng-Mian Feng, En-Ze Deng, Hao Lin, Kuo-Chen Chou
2014
iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition
International Journal of Molecular Sciences
Yan Xu, Xin Wen, Xiao-Jian Shao, Nai-Yang Deng, Kuo-Chen Chou
2014
Identifying ion channel genes related to cardiomyopathy using a novel decision forest strategy
Molecular BioSystems
Jie Zhang, Guanghua Wang, Jian Feng, LiJuan Zhang, Jue Li
2014
iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking
International Journal of Molecular Sciences
Yue-Nong Fan, Xuan Xiao, Jian-Liang Min, Kuo-Chen Chou
2014
Prediction of bacterial protein subcellular localization by incorporating various features into Chou's PseAAC and a backward feature selection approach
Biochimie
Liqi Li, Sanjiu Yu, Weidong Xiao, Yongsheng Li, Maolin Li, Lan Huang, Xiaoqi Zheng, Shiwen Zhou, Hua Yang
2014
iCTX-Type: A Sequence-Based Predictor for Identifying the Types of Conotoxins in Targeting Ion Channels
BioMed Research International
Hui Ding, En-Ze Deng, Lu-Feng Yuan, Li Liu, Hao Lin, Wei Chen, Kuo-Chen Chou
2014
Transmission of intra-cellular genetic information: A system proposal
Journal of Theoretical Biology
L.C.B. Faria, A.S.L. Rocha, R. Palazzo
2014
Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping
Journal of Theoretical Biology
James Lyons, Neela Biswas, Alok Sharma, Abdollah Dehzangi, Kuldip K. Paliwal
2014
Prediction of protein structure classes by incorporating different protein descriptors into general Chou’s pseudo amino acid composition
Journal of Theoretical Biology
Loris Nanni, Sheryl Brahnam, Alessandra Lumini
2014
iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components
International Journal of Molecular Sciences
Wang-Ren Qiu, Xuan Xiao, Kuo-Chen Chou
2014
PSNO: Predicting Cysteine S-Nitrosylation Sites by Incorporating Various Sequence-Derived Features into the General Form of Chou’s PseAAC
International Journal of Molecular Sciences
Jian Zhang, Xiaowei Zhao, Pingping Sun, Zhiqiang Ma
2014
R3P-Loc: A compact multi-label predictor using ridge regression and random projection for protein subcellular localization
Journal of Theoretical Biology
Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung
2014
Constructing a linear QSAR for some metabolizable drugs by human or pig flavin-containing monooxygenases using some molecular features selected by a genetic algorithm trained SVM
Journal of Theoretical Biology
Thy-Hou Lin, Tsung-Lin Tsai
2014
iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition
PLoS ONE
Bin Liu, Jinghao Xu, Xun Lan, Ruifeng Xu, Jiyun Zhou, Xiaolong Wang, Kuo-Chen Chou
2014
Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome
Chromosome Research
Yongchun Zuo, Pengfei Zhang, Li Liu, Tao Li, Yong Peng, Guangpeng Li, Qianzhong Li
2014
iSS-PseDNC: Identifying Splicing Sites Using Pseudo Dinucleotide Composition
BioMed Research International
Wei Chen, Peng-Mian Feng, Hao Lin, Kuo-Chen Chou
2014
TIBS: A web database to browse gene expression in irritable bowel syndrome
Journal of Theoretical Biology
Jing Yan, Yan Xu, Brian Hu, Sammy Alnajm, Lina Liu, Yin Lu, Zhiguang Sun, Feng Cheng
2014
PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition
Analytical Biochemistry
Wei Chen, Tian-Yu Lei, Dian-Chuan Jin, Hao Lin, Kuo-Chen Chou
2014
iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach
BioMed Research International
Wang-Ren Qiu, Xuan Xiao, Wei-Zhong Lin, Kuo-Chen Chou
2014
iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition
Nucleic Acids Research
Hao Lin, En-Ze Deng, Hui Ding, Wei Chen, Kuo-Chen Chou
2014
Prediction of the determinants of thermal stability by linear discriminant analysis: The case of the glutamate dehydrogenase protein family
Journal of Theoretical Biology
Angelo Pavesi
2014
A set of descriptors for identifying the protein–drug interaction in cellular networking
Journal of Theoretical Biology
Loris Nanni, Alessandra Lumini, Sheryl Brahnam
2014
Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology
Journal of Theoretical Biology
Mohammad Reza Bakhtiarizadeh, Mohammad Moradi-Shahrbabak, Mansour Ebrahimi, Esmaeil Ebrahimie
2014
Human proteins characterization with subcellular localizations
Journal of Theoretical Biology
Lei Yang, Yingli Lv, Tao Li, Yongchun Zuo, Wei Jiang
2013
PFP-RFSM: Protein fold prediction by using random forests and sequence motifs
Journal of Biomedical Science and Engineering
Junfei Li, Jigang Wu, Ke Chen
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