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

朱彥煒

研究室:自然計算與生物資訊核心實驗室

簡要經歷

 

職稱 服務單位 起訖年月
Review Editor Frontiers in Digital Public Health 2021/07 – present
Guest Editor Frontiers in Genetics 2021 – present
Editor Journal of Biochemistry and Molecular Biology Research 2014/10 – present
Lead Guest Editor Journal of Neuroscience and Neuroengineering 2012 – 2013
教授 國立中興大學 基因體暨生物資訊學研究所 2019/08 -present
副教授 國立中興大學 基因體暨生物資訊學研究所 2012/08 -2019/07
研究發展組組長 國立中興大學 計算機及資訊網路中心 2013/08 – 2015/08
助理教授 國立中興大學 基因體暨生物資訊學研究所 2008/08 – 2012/07
咨詢審查委員 中華民國 行政院 衛生署 2006 – present
助理教授 亞洲大學 生物資訊學系 2006/08 – 2008/07
專任講師 元培科技大學 資訊管理學系 2005/08 – 2006/07
專任講師 中國科技大學 資訊管理系 2003/09 – 2005/07
顧問 台璧實業股份有限公司 資訊處 1998/03 – 2000/03
專任講師 台灣電子化多元教育協會 電子化學校 1997/03 – 1999/06
博士 國立交通大學 資訊工程研究所 1998/09 – 2006/07
碩士 國立交通大學 資訊科學研究所 1996/09 – 1998/07
學士 國立交通大學 資訊科學系 1992/09 – 1996/07

榮譽

時間 內容
2022 榮獲本校111學年度特聘教授
2022 參加「水資料應用競賽」以「使用人工智慧演算法開發全方位水庫智慧管理級預警平台」榮獲「佳作」
2021 「應用作物生理指標建立需水超前預警系統」入圍「2021未來科技獎」參展技術
2021 榮獲中興大學110學年度產學績優教師
2018 榮獲中興大學107學年度優聘教師
2018 國際會議The second International Conference on Medical and Health Informatics榮獲最佳論文獎
2015 榮獲教育部教育部生技產業創新創業人才培育計畫生技創新創業獎最佳人氣獎
2014 國際會議 25th International Conference on Information Management 榮獲最佳論文獎

教學與研究

研究方向
  1. 生物資訊演算法
  2. 計算表觀遺傳學
  3. 生醫資訊學
  4. 演化式計算
  5. 類神經網路
  6. 模糊系統
  7. 資料探勘
  8. 智慧計算
  9. 自然計算

教授課程:

課程名稱

自然計算應用特論(基資所)、機器學習(資工系)、生物資訊發展現況(分生所)、 生物資訊程式設計(基資所)、生物資訊學暨實習(生科系)、應用基因體學及生物 資訊學暨實習(基資所)

著作

期刊論文 (*Corresponding author)
  1. Chi-Hua Tung, Yi-Sheng Chang, Kai-Po Chang and Yen-Wei Chu* (2021) NIgPred: Class-Specific Antibody Prediction for Linear B-Cell Epitopes Based on Heterogeneous Features and Machine-Learning Approaches，Viruses, 13(8), 1531.
  2. Chi-Wei Chen, Lan-Ying Huang, Chia-Feng Liao, Kai-Po Chang and Yen-Wei Chu* (2020) GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System, International Journal of Molecular Sciences, 21(21):7891.(SCI)
  3. Ching-Hsuan Chien, Chi-Chang Chang, Shih-Huan Lin, Chi-Wei Chen, Zong-Han Chang and Yen-Wei Chu* (2020 )N-GlycoGo: Predicting Protein N-glycosylation Sites on Imbalanced Data Sets by Using Heterogeneous and Comprehensive Strategy, IEEE Access, doi:10.1109/ACCESS.2020.3022629. (SCI)
  4. Kai-Po Chang, John Wang, Chi-Chang Chang,and Yen-Wei Chu* (2020) Development of a Novel Tool for the Retrieval and Analysis of Hormone Receptor Expression Characteristics in Metastatic Breast Cancer via Data Mining on Pathology Reports, BioMed Research International, 2020(7):2654815.(SCI)
  5. Yen-Wei Chu, Ching-Hsuan Chien, Mei-I Sung, Chi-Wei Chen, and Yu-Ting Chen (2020) dBMHCC: a comprehensive Hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers, PLoS ONE, 15(6): e0234084. (SCI)
  6. Chi-Hua Tung, Ching-Hsuan Chien, Chi-Wei Chen, Lan-Ying Huang, Yu-Nan Liu and Yen-Wei Chu* (2020) QUATgo: Protein quaternary structural attributes predicted by two-stage machine learning approaches with heterogeneous feature encoding, PLoS ONE, 15(4): e0232087. (SCI)
  7. Chi-Wei Chen, Meng-Han Lin, Chi-Chou Liao, Hsung-Pin Chang and Yen-Wei Chu* (2020) iStable 2.0: Predicting protein thermal stability changes by integrating various characteristic modules, Computational and Structural Biotechnology Journal, 18:622-630. (SCI: 6.018)
  8. Yen-Wei Chu, Kai-Po Chang, Chi-Wei Chen, Yu-Tai Liang, Zhi Thong Soh and Li‐Ching Hsieh* (2020) miRgo: integrating various off-the-shelf tools for identification of microRNA–target interactions by heterogeneous features and a novel evaluation indicator, Scientific Reports, 10:1466. (SCI)
  9. Jehn-Hwa Kuo, Chi-Chang Chang, Chi-Wei Chen, Heng-Hao Liang, Chih-Yen Chang and Yen-Wei Chu* (2020) Sequence-Based Structural B-cell Epitope Prediction by Using Two Layer SVM Model and Association Rule Features, Current Bioinformatics, 15(3), doi:10.2174/1574893614666181123155831 (SCI)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. 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)
  16. 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)
  17. 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)
  18. 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)
  19. 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)
  20. 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)
  21. 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)
  22. 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)
  23. 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)
  24. 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%)
  25. 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%)
  26. 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%)
  27. 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
  28. 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)
  29. 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)
  30. 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)
  31. Yen-Wei Chu* and Chuen-Tsai Sun (2007) Problem-based Approach for Bioinformatics. International Journal of Instructional Media,Vol. 34 #4. (International Journal)
  32. 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)
  33. 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)
  34. 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)

 

學術研討會論文 (*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.
專書與專書論文
  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)