Yen-Wei Chu Professor
E-MAIL:ywchu@nchu.edu.tw
Lab:Natural Computing & Bioinformatics Core Laboratory
Office:Health Inspection and Quarantine Building, Room 704
Office Tel:(04)22840338 # 7041
Fax:(04)22859329
Lab Location:Health Inspection and Quarantine Building, Room 706
Lab Tel:(04)22840338 # 7061

•   Experience

Position Institution Company Date of Start & End
ProfessorInstitute of Genomics and Bioinformatics,
National Chung Hsing University
2019/08 - present
EditorInternational Journal of Genomics, Proteomics, Metabolomics & Bioinformatics2017/12 - present
EditorInternational Journal of Pharmacology, Phytochemistry and Ethnomedicine2015/11 - present
EditorJournal of Biochemistry and Molecular Biology Research2014/10 - present
EditorJournal of Computation in biosciences and engineering2013/11 - present
CommissionerDepartment of Health, Executive Yuan, R.O.C.2006 - present
Lead Guest EditorJournal of Neuroscience and Neuroengineering2012 - 2013
Associate ProfessorInstitute of Genomics and Bioinformatics,
National Chung Hsing University
2012/08 - 2019/07
Assistant ProfessorInstitute of Genomics and Bioinformatics,
National Chung Hsing University
2008/08 - 2012/07
Assistant ProfessorDepartment of Bioinformatics, Asia University2006/08 - 2008/07
LecturerDepartment of Information Management,
Yuanpei University
2005/08 - 2006/07
LecturerDepartment of information management,
China University of Technology
2003/09 - 2005/07
ConsultantIT Division,Transformer Bobbin Industrial Co.,LTD1998/03 - 2000/03
LecturerAssociation of Electronic Multi-education, R.O.C.1997/03 - 1999/06
Ph.D.Department of Computer Science,
National Chiao Tung University
1998/09 - 2006/07
M. S.Department of Computer Science,
National Chiao Tung University
1996/09 - 1998/07
B. S.Department of Computer Science,
National Chiao Tung University
1992/09 - 1996/07

•   Research Interests

  • Bioinformatics Algorithms
  • Computational Epigenetics
  • Artificial Intelligence
  • Intelligent Systems

•   Selected Papers

Journal (*Corresponding author) :

  • Jone-Han Liu, Chi-Chang Chang, Chi-Wei Chen, Li-Ting Wong and Yen-Wei Chu* (2019) Conservation region finding for influenza A viruses by machine learning methods of N-linked glycosylation sites and B-cell epitopes, Mathematical Biosciences, 315:108217. (SCI)
  • Chi-Chou Liao, Liang-Jwu Chen, Shuen-Fang Lo, Chi-Wei Chen and Yen-Wei Chu* (2019) EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches, PLoS Comput Biol, 15(5):e1006942. (SCI)
  • Kai-Po Chang, Yen-Wei Chu* and John Wang (2019) Analysis of Hormone Receptor Status in Primary and Recurrent Breast Cancer Via Data Mining Pathology Reports, Open Medicine, 20(14): 91-98. (SCI)
  • Jehn-Hwa Kuo, Chi-Chang Chang, Chi-Wei Chen, Heng-Hao Liang, Chih-Yen Chang and Yen-Wei Chu* (2019) Sequence-Based Structural B-cell Epitope Prediction by Using Two Layer SVM Model and Association Rule Features, Current Bioinformatics, DOI: 10.2174/1574893614666181123155831 (SCI)
  • Yu-Ting Chen, Chi-Chang Chang, Chi-Wei Chen, Kuan-Chun Chen and Yen-Wei Chu* (2019) MADS-Box Gene Classification in Angiosperms by Clustering and Machine Learning Approaches, Frontiers in Genetics, 8(9): 707. (SCI)
  • Chi-Wei Chen, Kai-Po Chang, Cheng-Wei Ho, Hsung-Pin Chang and Yen-Wei Chu* (2018) KStable: A Computational Method for Predicting Protein Thermal Stability Changes by K-Star with Regular-mRMR Feature Selection, Entropy, 20(12): 988. (SCI)
  • Chi-Chang Chang,Chi-Hua Tung,Chi-Wei Chen,Chin-Hau Tu and Yen-Wei Chu* (2018) SUMOgo: Prediction of sumoylation sites on lysines by motif screening models and the effects of various post-translational modifications. scientific report, 19;8(1):15512. doi: https://doi.org/10.1038/s41598-018-33951-5 (SCI)
  • Quan Zou, Chi-Wei Chen, Hao-Chen Chang and Yen-Wei Chu* (2018) Identifying Cleavage Sites of Gelatinases A and B by Integrating Feature Computing Models. Journal of Universal Computer Science, Vol. 24, No. 6, pp. 711-724 (SCI)
  • Chi-Chou Huang, Chi-Chang Chang, Chi-Wei Chen, Shao-yu Ho, Hsung-Pin Chang and Yen-Wei Chu* (2018) PClass: Protein Quaternary Structure Classification by Using Bootstrapping Strategy as Model Selection. Genes, Vol. 9, No. 2, pii: E91. doi: 10.3390/genes9020091 (SCI)
  • Chi-Wei Chen, Chi-Chang Chang, Hui-Chih Hung, Hsung-Pin Chang and Yen-Wei Chu* (2018) Constructing Feature Models for Citrullination Sites Prediction. Journal of Quality, Vol. 25, No. 3, doi:10.6220/joq.201806_25(3).0004 (EI)
  • Chi-Hua Tung, Pei-Wei Shueng, Yen-Wei Chu*, Chi-Wei Chen, Chian-Ying Chen (2017) Identifying Post-Translational Modification Crosstalks for Breast Cancer. Journal of Computing Science and Engineering, Vol. 11, No. 4, pp. 111-120 (EI)
  • Chi-Hua Tung, Chi-Wei Chen, Han-Hao Sun, Yen-Wei Chu* (2017) Predicting human protein subcellular localization by heterogeneous and comprehensive approaches, PLoS ONE, 12(6):e0178832. doi: 10.1371/journal.pone.0178832 (SCI)
  • Chi-Hua Tung, Chi-Wei Chen, Ren-Chao Guo, Hui-Fuang Ng, Yen-Wei Chu* (2016) QuaBingo: A Prediction System for Protein Quaternary Structure Attributes Using Block Composition, BioMed Research International, 2016:9480276, doi:10.1155/2016/9480276 (SCI: 2.134)
  • Han-Ju Chien+, Yen-Wei Chu+, Chi-Wei Chen, Yu-Min Juang, Min-Wei Chien, Chih-Wei Liu, Chia-Chang Wu, Jason T.C. Tzen and Chien-Chen Lai* (2016) 2-DE combined with two-layer feature selection accurately establishes the origin of oolong tea, Food Chemistry, 211:392-9, doi:10.1016/j.foodchem.2016.05.043 (SCI: 4.052, Co-first Author)
  • Chi-Wei Chen, Jerome Lin, Yen-Wei Chu* (2013) iStable: Off-the-shelf Predictor Integration for Predicting Protein Stability Changes, BMC Bioinformatics, 14(suppl 2):S5, doi:10.1186/1471-2105-14-S2-S5 (SCI: 2.435, ranking: 17.9%)
  • Wei-Jie Pan, Chi-Wei Chen, Heng-Hao Liang, Yen-Wei Chu* (2012) Selecting High Efficacy siRNAs by Computational Models, Advanced Science Letters, 18: 141-144. (SCI: 1.253, rank: 25%)
  • Chang-Hsien Yang, Yu-Yun Chang, Chi-Wei Chen, Min-Cheng Chan, Yen-Wei Chu* (2012) iMADS: The Class Identification of MADS-box Gene on Angiosperm, Advanced Science Letters, 18: 170-175. (SCI: 1.253, rank: 25%)
  • Po-Chang Chang, Wei-Jie Pan, Chi-Wei Chen,Yu-Ting Chen and Yen-Wei Chu* (2012) DEsi: an design engine of siRNA that integrates SVMs prediction and feature filters, Biocatalysis and Agricultural Biotechnology, doi: 10.1016/j.bcab.2012.01.005
  • Wei-Jie Pan, Chi-Wei Chen and Yen-Wei Chu* (2011)siPRED: Predicting siRNA efficacy using various characteristic methods, PLoS ONE, doi: 10.1371/journal.pone.0027602 (SCI: 3.057)
  • Yu-Yun Chang+,Yen-Wei Chu+, Chi-Wei Chen, Wei-Ming Leu, Hsing-Fun Hsu and Chang-Hsien Yang* (2011) Characterization of Oncidium 'Gower Ramsey' Transcriptomes using 454 GS-FLX Pyrosequencing and Their Application to the Identification of Genes Associated with Flowering Time, Plant and Cell Physiology, 52(9): 1532-1545 (SCI: 4.319, Co-first Author)
  • Hui-Fuang Ng, Zeng-Wei Hong and Yen-Wei Chu (2008) "Pose and Expression Invariant Face Recognition from a Single Training Sample Using Similarity Vector", Journal of Cybernetics and Systems, 1(1): 21-26. (International Journal)
  • Yen-Wei Chu* and Chuen-Tsai Sun (2007) Problem-based Approach for Bioinformatics. International Journal of Instructional Media,Vol. 34 #4. (International Journal)
  • Yen-Wei Chu*, Chuen-Tsai Sun, and Chung-Yuan Huang (2006) Regularity of Protein Secondary Structures and Its Prediction. WSEAS Transactions on Systems, 2(5), pp. 380-387. (EI).
  • Chung-Yuan Huang, Chuen-Tsai Sun, and Yen-Wei Chu (2006) A Co-adaptive Approach to XCS Classifier Systems. WSEAS Transactions on Systems, 2(5), pp. 388-394. (EI).
  • Yen-Wei Chu* and. Jinn-Moon Yang (2003) Finding Regularity in Various Types of Secondary Protein Structures, Journal of Information Science and Engineering, vol. 19, pp.943-952. (SCI)

Conference (*Invited speaker) :

  • Shih-Huan Lin, Liang-Yu Hsia, Chen-Hua Liu and Yen-Wei Chu* (2019) Using Artificial Intelligence Approaches for Predicting The Risk of Hepatic Decompensation Induced by Prod, ANIMH 2nd International Conference on Modern Trends in Engineering, Applied Sciences, IT and Communication Technologies, Hong Kong.
  • Yu-Tai Laing, Chun-Chieh Chen, Shuen-Fang Lo, Tuan-Hua David Ho, Su-May Yu and Yen-Wei Chu* (2019) Using Artificial Intelligence Approaches for Developing Wisdom Irrigation System for Crops, ANIMH 2nd International Conference on Modern Trends in Engineering, Applied Sciences, IT and Communication Technologies, Hong Kong.
  • Chen Chi-Wei, Chin-Hau Tu and Yen-Wei Chu* (2018) SUMOylation Sites Prediction by Machine Learning Approaches, IEEE International Conference on Consumer Electronics-Taiwan. (http://edas.info/p24335#S1569554145)
  • Kai-Po Chang, Chi-Chang Chang, Yen-Wei Chu* and John Wang* (2018) BreastExtractor: A Word/Phrase Matching-Based Text Mining Program for Automatic Extraction of Hormone Receptor Data from Free-text Pathology Reports on Breast Cancer, the second International Conference on Medical and Health Informatics. (Best Paper Award)
  • Kai-Po Chang, John Wang* and Yen-Wei Chu* (2016) Big data in pathologists’ office: large-scale extraction and analysis of immunohistochemical study result in free-text pathology reports by a client-side Python script, Paper presented at 2016 Annual Meeting of Taiwan Society Of Pathology, Taipei, Taiwan.
  • Ci-Jhou Liao, Liang-Jwu Chen, Yen-Wei Chu* (2014) Using machine learning approach to predict the flanking genes expression in T-DNA insertion activation-tagged rice lines, Summer Workshop on Plant Molecular Biology, Nantou County, Taiwan, July 4-6.
  • Chi-Wei Chen, Hui-Chih Hung, Yen-Wei Chu* (2014) Citrullination Sites Prediction by Machine Learning Approaches, Proceedings of the 25th International Conference on Information Management (ICIM 2014), pp. 1-13. (Best Paper Award)
  • Chi-Wei Chen, Hui-Chih Hung, Yen-Wei Chu* (2013) Feature Model Integration by Evolutionary Computation for Predicting Protein Citrullination sites, Proceedings of the Taiwan Academic Network Conference 2013 (TANet 2013), pp. 1047-1052.
  • Hao-Chen Chang and Yen-Wei Chu* (2013) Gelatinase Substrate Cleavage Sites Prediction Using Machine Learning and Feature Selection, Proceedings of the Taiwan Academic Network Conference 2013 (TANet 2013), pp. 1053-1058.
  • Chi-Wei Chen, Jerome Lin, Yen-Wei Chu* (2013) iStable: Off-the-shelf Predictor Integration for Predicting Protein Stability Changes, The Eleventh Asia Pacific Bioinformatics Conference, Vancouver, BC, Canada, January 21-23.
  • Wen-Pin Hu, Chi-Wei Chen, Jian-Shiun Chen, and Yen-Wei Chu* (2012) Evaluating various machine learning approaches for the sunspot number prediction. Symposium of university league in Changhua, Yunlin, and Chiayi, Taiwan, December 7.
  • Yu-Yun Chang, Yen-Wei Chu, Wei-Ming Leu and Chang-Hsien Yang* (2011) Characterization of Oncidium 'Gower Ramsey' transcriptome for using GS-FLX 454 pyrosequencing and its application for studies of flowering time associate genes. The International Conference Plant Gene Discovery Technologies. Venue. February 23- 26.
  • Yu-Yun Chang, Yen-Wei Chu, Hsing-Fun Hsu, Chi-Wei Chen, Wei-Ming Leu and Chang-Hsien Yang* (2011) Characterization of Oncidium 'Gower Ramsey' transcriptomes using 454 GS-FLX pyrosequencing and their application to theidentification of genes associated with flowering time. 2011 Canadian Plant Genomics Workshop, Niagara Falls, Ontario. Canada, August 22-25.
  • Wei-Jie Pan, Chi-Wei Chen and Yen-Wei Chu* (2011) High efficacy siRNA selection using machine learning approach, Proceedings of 2011 Joint Conference on 7th Taiwan Software Engineering (TCSE) and 22nd Object-Oriented Technology and Applications (OOTA), pp. 94-99
  • Qiu-Hui Lin, Chi-Wei Chen, Zeng-Wei Hong,* and Yen-Wei Chu* (2009) PredPhosGrid - A Grid-based Phosphorylation Prediction System by Reengineering off-the-shelf Bioinformatic Websites, Proceedings of the 20th Workshop on Object-Oriented Technology and Applications, pp. 1-6.
  • Cheng-Yu Liao, Wei-Fu Lu and Yen-Wei Chu* (2009) Using Genetic Algorithms to Assist the Classification of Biological Documents: An Example of Mushroom and Toadstool Data, Information Management and Commerce Technology Conference, pp. 559, Yunlin, Taiwan.
  • Yen-Wei Chu*, Chin-Sheng Yu. and Hui-Fuang Ng. (2008) Protein Secondary Structures Prediction Using Data Fusion Approach, Proceedings of the 7th IEEE World Congress on Intelligent Control and Automation (WCICA), v. 4, pp. 1885-1890. (EI, NSC 96-2218-E-468-001)
  • Hui-Fuang Ng* and Yen-Wei Chu (2008) Illumination Invariant Color Model for Image Matching and Object Recognition, The Eighth International Conference on Intelligent Systems Design and Applications.(EI)
  • Yen-Wei Chu*, Chin-Sheng Yu., Chia-Hsiang Pai and You-Ting Wu (2007) Protein Phosphorylation Site Prediction Using Data Fusion Approach, National Computer Symposium, v1, pp. 1-8 (NSC 96-2218-E-468-001)
  • Yen-Wei Chu*, Chin-Sheng Yu., Chih-Ying Chen and Kun-Chang Hsieh (2007) Applying Sequence Conservation Strategy to Predict Protein Phosphorylation Site, National Computer Symposium, v1, pp.9-15 (NSC 96-2218-E-468-001)
  • Ting-Yi Chang*, Yi-Ting Chen, and Yen-Wei Chu (2007) 'Develop the Peer Assessment of Cooperative Learning in e-Learning — Using Consistent Fuzzy Preference Relation, National Computer Symposium, pp. 554-561
  • Hui-Fuang Ng*, Ding-Fu Wang and Yen-Wei Chu (2007) Illumination invariant color descriptors for image matching. The 20th IPPR Conference on Computer Vision, Graphics and Image Processing, Miaoli, Taiwan.
  • Yen-Wei Chu* and Chuen-Tsai Sun (2006) A Hybrid Genetic Algorithm Approach for Protein Secondary Structures, Proceedings of the 6th IEEE World Congress on Intelligent Control and Automation (WCICA), v. 4, pp. 3320-3324. (EI)
  • Yen-Wei Chu*, Chuen-Tsai Sun, and Chung-Yuan Huang (2005) Finding Regularity in Protein Secondary Structures using a Cluster-based Genetic Algorithm. In Proceedings of International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics (CIMMACS'05), Miami, Florida, USA, pp. 179-183. (IEE, EI)
  • Chung-Yuan Huang*, Chuen-Tsai Sun, and Yen-Wei Chu (2005) Using a Coevolution Mechanism with a Dyna Architecture for Parameter Adaptation in XCS Classifier Systems. In Proceedings of International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics (CIMMACS'05), Miami, Florida, USA, pp. 173-178. (IEE, EI)
  • Yen-Wei Chu* and Chuen-Tsai Sun (2004) Regularity of secondary protein structures: A genetic algorithm approach, Proceedings of the 5th IEEE World Congress on Intelligent Control and Automation (WCICA), v. 3, pp. 2104-2108. (EI)
  • Chuen-Tsai Sun* and Yen-Wei Chu (1997) Hysteresis Behavior in Fuzzy Perception: A Preliminary Experiment. Second International ICSC Symposium on Intelligent Industrial Automation and Soft Computing, Nimes, France, Sep. 1997.

Books :

  • Chu Y.W. (2006) Finding Protein Secondary Structure Regularity and Related Applications: National Chiao Tung University, Hsinchu, Taiwan. (Dissertation)
  • Chu Y.W. (1998) Studies on Hysteresis: Human Perception and Time Series Prediction: National Chiao Tung University, Hsinchu, Taiwan. (Master Thesis)