國立中興大學基因體暨生物資訊學研究所

　　

　　 　　

　　　　　　　

　　　　　　　

　　　　　　　

基因體暨生物資訊學研究所

Graduate Institute of Genomics and Bioinformatics

Chinese
English

興大首頁

National Chung Hsing University

醫科博班

Doctoral Program in Medical Biotechnology

生命科學院

College of Life Sciences

Chu, Yen-Wei

Lab: Natural Computing & Bioinformatics Laboratory

Experience

Title Department Period
Review Editor Frontiers in Digital Public Health 2021/07 – present
Editor International Journal of Genomics, Proteomics, Metabolomics & Bioinformatics 2017/12 – present
Editor International Journal of Pharmacology, Phytochemistry & Ethnomedicine 2015/11 – present
Editor Journal of Biochemistry and Molecular Biology Research 2014/10 – present
Editor Journal of Computation in Biosciences and Engineering 2013/11 – present
Lead Guest Editor Journal of Neuroscience and Neuroengineering 2012 – 2013
Professor NCHU, Institute of Genomics and Bioinformatics 2019/08 -present
Associate Professor NCHU, Institute of Genomics and Bioinformatics 2012/08 -2019/07
Assistant Professor NCHU, Institute of Genomics and Bioinformatics 2008/08 – 2012/07
Advisory Committee Member ROC, Ministry of Health and Welfare 2006 – present
Assistant Professor Asia University, Department of Bioinformatics and Medical Engineering 2006/08 – 2008/07
Lecturer YUMT, Department of Information Management 2005/08 – 2006/07
Lecturer CUTE, Department of Information Management 2003/09 – 2005/07
Consultant IT Division, Transformer Bobbin Industrial Co., LTD 1998/03 – 2000/03
Lecturer Association of Electronic Multi-education, R.O.C. 1997/03 – 1999/06
PhD NCTU, Department of Computer Science 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

Research Interests
  1. Bioinformatics Algorithms
  2. Computational Epigenetics
  3. Artificial Intelligence
  4. Intelligent Systems

Lectures:

Course

Special Topics in The Application of Natural Computing, Machine Learning, Current Approaches in Bioinformatics, Bioinformatics Programming, Bioinformatics: Lecture and Experiment, Applied Genomics and Bioinformatics: Lecture and Experiment

Publications

Journal (*Corresponding author)
  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. 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%)
  16. 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, ranking: 25%)
  17. 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, ranking: 25%)
  18. 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
  19. 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)
  20. 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)
  21. 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)
  22. Yen-Wei Chu* and Chuen-Tsai Sun (2007) Problem-based Approach for Bioinformatics. International Journal of Instructional Media,Vol. 34 #4. (International Journal)
  23. 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)
  24. 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)
  25. 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)
  1. 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)
  2. 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)
  3. 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.
  4. 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.
  5. 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)
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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
  13. 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.
  14. 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.
  15. 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)
  16. 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)
  17. 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)
  18. 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)
  19. 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
  20. 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.
  21. 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)
  22. 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)
  23. 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)
  24. 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)
  25. 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:
  1. Chu Y.W. (2006) Finding Protein Secondary Structure Regularity and Related Applications: National Chiao Tung University, Hsinchu, Taiwan. (Dissertation)
  2. Chu Y.W. (1998) Studies on Hysteresis: Human Perception and Time Series Prediction: National Chiao Tung University, Hsinchu, Taiwan. (Master Thesis)