陳倩瑜 | 臺灣大學生物機電工程學系

	專任師資
姓名	陳倩瑜
職稱	教授
電子郵件	chienyuchen@ntu.edu.tw
聯絡電話	02-3366-5334
研究專長	生物資訊資料探勘機器學習
授課領域	電子學電子學實習結構生物資訊學數位電路設計生醫資料探勘
實驗室網站	http://bioinfo.bime.ntu.edu.tw/c4lab/

期刊論文

Chien-Yu Chen, Ting-Ying Chien, Chih-Kang Lin, Chih-Wei Lin, Yi-Zhong Weng, and Darby Tien-Hao Chang*, "Predicting Target DNA Sequences of DNA-binding Proteins Based on Unbound Structures" , PLoS ONE, 7(2):e30446 (SCI), 2012年參考連結
Mei-Ju May Chen, Lih-Ching Chou, Tsung-Ting Hsieh, Ding-Dar Lee, Kai-Wei Liu, Chi-Yuan Yu, Yen-Jen Oyang, Huai-Kuang Tsai*, and Chien-Yu Chen*, "De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae" , Bioinformatics, 28(5):701-708 (SCI), 2012年參考連結
Ting-Ying Chien, Chih-Kang Lin, Chih-Wei Lin, Yi-Zhong Weng, Chien-Yu Chen*, Darby Tien-Hao Chang*, "DBD2BS: connecting a DNA-binding protein with its binding sites" , Nucleic Acids Research, Vol. 40, Web Server issue, pp. W173-179 (SCI), 2012年參考連結
Ju-Chun Hsu, Ting-Ying Chien(§:equal contribution), Chia-Cheng Hu§, Mei-Ju May Chen§, Wen-Jer Wu, Hai-Tung Feng, David S. Haymer and Chien-Yu Chen*, "Discovery of genes related to insecticide resistance in Bactrocera dorsalis by functional genomic analysis of a de novo assembled transcriptome" , PLoS ONE, 7(8): e40950 (SCI), 2012年參考連結
Hsi-Che Liu, Lee-Yung Shih, Mei-Ju May Chen, Chien-Chih Wang, Ting-Chi Yeh, Tung-Huei Lin, Chien-Yu Chen, Chih-Jen Lin, and Der-Cherng Liang*, "Expression of HOXB genes is significantly different in acute myeloid leukemia with a partial tandem duplication of MLL vs. a MLL translocation: a cross-laboratory study" , Cancer Genetics, 204(5):252-259 (SCI), 2011年參考連結
Chih-Min Liu, Cathy S-J Fann, Chien-Yu Chen, Yu-Li Liu, Yen-Jen Oyang, Wei-Chih Yang, Chien-Ching Chang, Chun-Chiang Wen, Wei J. Chen, Tzung-Jeng Hwang, Ming-Hsien Hsieh, Chen-Chung Liu, Stephen V. Faraone, Ming T. Tsuang, and Hai-Gwo Hwu*,"ANXA7, PPP3CB, DNAJC9, and ZMYND17 Genes at Chromosome 10q22 Associated with the Subgroup of Schizophrenia with Deficits in Attention and Executive Function" , Biological Psychiatry, 70(1):51-58 (SCI), 2011年參考連結
Chen-Ming Hsu, Chien-Yu Chen*, and Baw-Jhiune Liu, "WildSpan: Mining Structured Motifs from Protein Sequences" , Algorithms for Molecular Biology, 6:6 (SCI), 2011年參考連結
Chien-Chih Wang and Chien-Yu Chen*, "Predicting DNA-binding Locations and Orientation on Proteins Using Knowledge-based Learning of Geometric Properties" , Proteome Science, 9(Suppl 1):S11 (SCI), 2011年參考連結
Li-Yu Daisy Liu, Chien-Yu Chen, Mei-Ju May Chen, Ming-Shian Tsai, Cho-Han Sam Lee, Tzu L. Phang, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Huang-Chun Lien, Shih-Ming Jung, Yi-Shing Lin, King-Jen Chang, and Fon-Jou Hsieh*, "Statistical identification of gene association by CID in application of constructing ER regulatory network" , BMC Bioinformatics, 10:85 (SCI), 2009年
Darby Tien-Hao Chang, Ting-Ying Chien, and Chien-Yu Chen*, "seeMotif: exploring and visualizing sequence motifs in 3D structures" , Nucleic Acids Research, Vol. 37, Web Server issue, pp. W552–W558 (SCI), 2009年
Chien-Yu Chen, Huai-Kuang Tsai, Chen-Ming Hsu, Mei-Ju May Chen, Hao-Geng Hung, Grace Tzu-Wei Huang, and Wen-Hsiung Li*, "Discovering gapped binding sites of yeast transcription factors" , Proceedings of the National Academy of Sciences, Vol. 105(7), pp. 2527-2532 (SCI), 2008年
Hsi-Che Liu, Chien-Yu Chen, Yu-Ting Liu, Cheng-Bang Chu, Der-Cherng Liang, Lee-Yung Shih and Chih-Jen Lin, "Cross-generation and Cross-laboratory Predictions of Affymetrix Microarrays by Rank-based Methods" , Journal of Biomedical Informatics, Vol. 41, Issue 4, pp. 570-579 (SCI), 2008年
Ting-Ying Chien, Darby Tien-Hao Chang*, Chien-Yu Chen, Yi-Zhong Weng, and Chen-Ming Hsu, "E1DS: catalytic site prediction based on 1D signatures of concurrent conservation", Nucleic Acids Research, Vol. 36, Web Server issue, pp. W291-W296 (SCI), 2008年
Chung-Tsai Su, Chien-Yu Chen*, and Chen-Ming Hsu, "iPDA: Integrated Protein Disorder Analyzer" , Nucleic Acids Research, Vol. 35, Web Server issue, pp. W465-W472 (SCI), 2007年
Chen-Ming Hsu, Chien-Yu Chen*, Baw-Jhiune Liu, Chih-Chang Huang, Min-Hung Laio, Chien-Chieh Lin, and Tzung-Lin Wu, "Identification of Hot Regions in Protein-Protein Interactions by Sequential Pattern Mining" , BMC Bioinformatics, 8(Suppl 5):S8 (SCI), 2007年
Chen-Ming Hsu, Chien-Yu Chen*, and Baw-Jhiune Liu, "MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences" , Nucleic Acids Research, Vol. 34, Web Server Issue, pp. W356-W361 (SCI), 2006年
Chung-Tsai Su, Chien-Yu Chen, and Yu-Yen Ou, "Protein disorder prediction by condensed PSSM considering propensity for order or disorder" , BMC Bioinformatics 2006, 7:319. (SCI), 2006年
Chien-Yu Chen, Wen-Chin Chung, and Chung-Tsai Su, "Exploiting Homogeneity in Protein Sequence Clusters for Construction of Protein Family Hierarchies" , Pattern Recognition, Vol. 39(12), pp. 2356-2369 (SCI) (EI), 2006年
Tsun-Chen Lin, Ru-Sheng Liu*, Chien-Yu Chen, Ya-Ting Chao, and Shu-Yuan Chen,"Pattern classification in DNA microarray data of multiple tumor types" , Pattern Recognition, Vol. 39(12), pp. 2426-2438 (SCI) (EI), 2006年
Chien-Yu Chen*, Shien-Ching Hwang, and Yen-Jen Oyang., "Statistics-Based Approach to Control the Quality of Subclusters in Incremental Gravitational Clustering" , Pattern Recognition, Vol. 38(12), pp. 2256-2269 (SCI) (EI), 2005年
Chien-Yu Chen, Shien-Ching Hwang, and Yen-Jen Oyang, "Analysis and Summarization of Correlations in Data Cubes and its Applications in Microarray Data Analysis" , Intelligent Data Analysis, Vol. 9(1), pp. 43-58., 2005年
Yen-Jen Oyang, Shien-Ching Hwang, Yu-Yen Ou, Chien-Yu Chen, and Zhi-Wei Chen,"Data Classification with the Radial Basis Function Network Based on a Novel Kernel Density Estimation Algorithm" , IEEE transactions on neural networks, Vol. 16, No. 1, pp225-236 (SCI) (EI), 2005年
Chien-Yu Chen, Shien-Ching Hwang, and Yen-Jen Oyang., "A Statistics-Based Approach to Control the Quality of Subclusters in Incremental Gravitational Clustering" , Pattern Recognition, Vol. 38(12), pp. 2256-2269 (SCI) (EI), 2005年
Chien-Yu Chen, Yen-Jen Oyang, and Hsueh-Fen Juan, "Incremental Generation of Summarized Clustering Hierarchy for Protein Family Analysis" , Bioinformaitcs, 2004, Vol. 20(16), pp. 2586-2596. (SCI), 2004年
Darby Tien-Hau Chang, Chien-Yu Chen, Wen-Chin Chung, Yen-Jen Oyang, Hsueh-Fen Juan, and Hsuan-Cheng Huang, "ProteMiner-SSM: A Web Server for Identifying Possible Protein-Ligand Interactions Based on Analysis of Protein Tertiary Substructures" , Nucleic Acids Research, 2004, Vol. 32, Web Server issue, pp. W76-W82. (SCI), 2004年

Mei-Ju Chen and Chien-Yu Chen, "Identification of Transcription Factor Interacting Pairs by Mining ChIP-chip Data" , Poster of 16th Annual International Conference Intelligent Systems for Molecular Biology, 2008年
Ting-Ying Chien, Darby Tien-Hao Chang, Chien-Yu Chen, Yi-Zhong Weng, and Chen-Ming Hsu,, "E1DS: catalytic site prediction based on 1-dimensional signatures of concurrent conservation" , Poster of 16th Annual International Conference Intelligent Systems for Molecular Biology, 2008年
Chien-Chih Wang and Chien-Yu Chen, "Tracking DNA Routes by Basic Residues in Predicted Functional Regions of Protein Structures" , Poster of 7th Annual International Conference on Computational Systems Bioinformatics, 2008年
Ting-Ying Chien, Darby Tien-Hao Chang, Chien-Yu Chen, Yi-Zhong Weng, and Chen-Ming Hsu, "Catalytic site prediction using E1DS server" , Poster of 7th Annual International Conference on Computational Systems Bioinformatics, 2008年
Ai-Mi Chen and Chien-Yu Chen, "Prediction of DNA-binding Regions from Sequence Conservation and Composition" , Poster of 8th European conference in Computational Biology and Bioinformatics, 2008年
Chien-Yu Chen, Ai-Mi Chen, Chen-Ming Hsu, Chung-Tsai Su, Yung-Chia Chen, and Baw-Jhiune Liu, "Prediction of DNA-binding Regions by Detecting Intra-molecular Interactions with Pattern Mining" , Poster of 11th Research in Computational Molecular Biology (RECOMB), 2007年
Ting-Ying Chien, Chein-Yu Chen, Darby Tien-Hao Chang, and Chen-Ming Hsu, "Deriving Functional Signatures from Protein Sequences by Iterative Pattern Mining" , Poster of 11th Research in Computational Molecular Biology (RECOMB), 2007年
Chung-Tsai Su, Tong-Ming Hsu, Chien-Yu Chen, Yu-Yen Ou, Yen-Jen Oyang, "Enhancing Protein Disorder Detection by Refined Secondary Structure Prediction" , 1st International Conference on Bioinformatics Research and Development (BIRD-2007), Berlin, 2007年
Chen-Ming Hsu, Chien-Yu Chen, Ching-Chi Hsu, Baw-Jhiune Liu, "Efficient Discovery of Structural Motifs from Protein Sequences with Combination of Flexible Intra- and Inter-block Gap Constraints" , in Proceedings of 10th Pacific Area Conference on Knowledge Discovery and Data Mining (PAKDD-2006), Singapore (EI), 2006年
Chen-Ming Hsu, Chien-Yu Chen, Ching-Chi Hsu, and Baw-Jhiune Liu, "Identification of Hot Regions in Protein-Protein Interactions by Sequential Pattern Mining" , Poster of 10th Research in Computational Molecular Biology (RECOMB), 2006年
Chien-Yu Chen, Guan-Hau Chen, Tien-Hau Darby Chang, Ya-Ting Chao, Ru-Sheng Liu, Shu-Yuan Chen, and Yu-Yen Ou, "Removing Noisy Relations to Reduce Side-Effect of Exploiting Homology Transitivity" , Poster of 10th Research in Computational Molecular Biology (RECOMB), 2006年
Yen-Jen Oyang, Darby Tien-Hau Chang, Yu-Yen Ou and Chien-Yu Chen, "On the Convergence of the Locally Relaxed Kernel Density Estimator" , HICStatistics-2006 (5th Annual Hawaii International Conference on Statistics, Mathematics and Related Fields), 2006年
Yen-Jen Oyang, Yu-Yen Ou, Shien-Ching Hwang, Chien-Yu Chen and Darby Tien-Hau Chang, "On the Convergence Rate of the Locally Relaxed Variable Kernel Density Estimator" , HICStatistics-2006 (5th Annual Hawaii International Conference on Statistics, Mathematics and Related Fields), 2006年
Yen-Jen Oyang, Yu-Yen Ou, Shien-Ching Hwang, Chien-Yu Chen, and Darby Tien-Hau Chang, "Data Classification with a Relaxed Model of Variable Kernel Density Estimation" , in Proceedings of International Joint Conference on Neural Networks, July 31-August 4 (EI), 2005年
Yu-Yen Ou, Chien-Yu Chen, and Yen-Jen Oyang, "A Novel Radial Basis Function Network Classifier with Hierarchical Clustering Approach" , in Proceedings of International Joint Conference on Neural Networks, July 31-August 4 (EI), 2005年
Tsun-Chen Lin, Ru-Sheng Liu, Chen-Chung Liu, Chieh-Yu Chen, Shu-Yuan Chen, "Genetic Algorithms and Silhouette Measures Applied to Microarray Data Classification" , in Proceedings of the Third Asia-Pacific Bioinformatics Conference, Singapore., 2005年
Ssu-Hua Huang, Ru-Sheng Liu, Chien-Yu Chen, Ya-Ting Chao, Shu-Yuan Chen, "Prediction of Outer Membrane Proteins by Support Vector Machines Using Combinations of Gapped Amino Acid Pair Compositions" , in Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE-2005), Minneapolis, Minnesota, USA (EI), 2005年
Darby Tien-Hau Chang, Chien-Yu Chen, Yen-Jen Oyang, Hsueh-Fen Juan, and Hsuan-Cheng Huang, "An Efficient Mechanism for Prediction of Protein-Ligand Interactions Based on Analysis of Protein Tertiary Substructures" , in Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE-2004), Taichung, Taiwan, May 19-21 (EI), 2004年
Chien-Yu Chen, Hsueh-Fen Juan, Po-Jen Hsiao, Shui-Tein Chen, Hsiang-Wen Tseng, and Yen-Jen Oyang, "Design of an Incremental Clustering Package for Protein Function and Family Analysis" , in Proceedings of IEEE 5th International Symposium on Multimedia Software Engineering, Taichung, Taiwan, 2003年
Yen-Jen Oyang, DarbyTien-Hau Chang, Chien-Yu Chen, and Shien-Ching Hwang,"Expediting Protein Structural Analysis with an Efficient Kernel Density Estimation Algorithm" , in Proceedings of IEEE 5th International Symposium on Multimedia Software Engineering, Taichung, Taiwan., 2003年
Yu-Yen Ou, Chien-Yu Chen, Shien-Ching Hwang, and Yen-Jen Oyang, "Expediting Model election for Support Vector Machines Based on Data Reduction" , in Proceedings of IEEE nternational Conference on Systems, Man and Cybernetics (EI), 2003年
Yen-Jen Oyang, Shien-Ching Hwang, Yu-Yen Ou, Chien-Yu Chen, and Zhi-Wei Chen, "A Novel Learning Algorithm for Data Classification with Radial Basis Function Networks" , in Proceedings of 9th International Conference on Neural Information Processing (ICONIP-2002), Singapore, Nov. 18-22., 2002年
Chien-Yu Chen, Shien-Ching Hwang, and Yen-Jen Oyang, "An Incremental Hierarchical Data Clustering Algorithm Based on Gravity Theory" , in Proceedings of 6th Pacific Area Conference on Knowledge Discovery and Data Mining (PAKDD-2002), Taipei, Taiwan, May 6-8, 2002. (LNAI 2336) (SCI Expanded) (EI), 2002年
Chien-Yu Chen, Shien-Ching Hwang, and Yen-Jen Oyang, "Analysis and Summarization of Correlations in Data Cubes" , in Proceedings of SPIE Vol. 4730 Data Mining and Knowledge Discovery: Theory, Tools, and Technology IV, Orlando. Florida, USA, April 1-5 (EI), 2002年
Yen-Jen Oyang, Chien-Yu Chen, and Tsui-Wei Yang, "A Study on the Hierarchical Data Clustering Algorithm Based on Gravity Theory" , in Proceedings of 5th European Conference on Principles and Practice of Knowledge Discovery in Databases, PKDD-2001, Freiburg, Germany, September 3-5, 2001年

農委會研究計畫一覽
年度	計畫名稱	參與人	擔任之工作	計畫時間	補助/委託機構	附件檔案/ 參考連結	備註
100	RFID在平飼種禽集蛋設備與性能檢定之應用	陳倩瑜		2010年01月 ~ 2012年12月			100農科-6.3.1-牧-U1(2) 101農科-7.3.1-牧-U1

國科會研究計畫一覽
年度	計畫名稱	參與人	擔任之工作	計畫時間	備註
101	沉香有用代謝物之試管內操縱與基因組體分析	陳倩瑜	共同主持人	2012年08月 ~ 2013年07月	101-2313-B-001-002-
100	以自動知識擷取為基礎之計算功能性蛋白質體學－子計畫4-整合序列、結構與蛋白質交互作用資訊預測蛋白質-DNA結合專一性(3/3)	陳倩瑜	計畫主持人	2011年08月 ~ 2012年07月	100-2627-B-002-002-
100	台灣重要作物害蟲對有機磷劑抗藥性發生之基因體學及其功能分析－有機磷抗性基因之篩選、蛋白質結構預測以及有機磷分子嵌合模擬之研究	陳倩瑜	子計畫主持人	2011年08月 ~ 2014年07月	100-2313-B-002-018-MY3
99	以自動知識擷取為基礎之計算功能性蛋白質體學－子計畫4-整合序列、結構與蛋白質交互作用資訊預測蛋白質-DNA結合專一性(2/3)	陳倩瑜	計畫主持人	2010年08月 ~ 2011年07月	99-2627-B-002-004-
98	酵母菌轉錄因子與其DNA鍵結區域互動模式之預測與分析(二)	陳倩瑜	計畫主持人	2009年08月 ~ 2011年10月	98-2221-E-002-137-MY2
98	以自動知識擷取為基礎之計算功能性蛋白質體學－子計畫4-整合序列、結構與蛋白質交互作用資訊預測蛋白質-DNA結合專一性(1/3)	陳倩瑜	計畫主持人	2009年08月 ~ 2010年10月	98-2627-B-002-011-
97	酵母菌轉錄因子與其DNA鍵結區域互動模式之預測與分析	陳倩瑜	計畫主持人	2008年08月 ~ 2009年07月	97-2221-E-002-184-
97	計算生物學先導型研究計畫-子計畫一:系統生物學與生物網路	陳倩瑜	共同主持人	2008年04月 ~ 2009年03月
96	結合序列分群與特徵探勘演算法提昇兼職蛋白質預測之可靠度(2/2)	陳倩瑜	計畫主持人	2007年08月 ~ 2008年07月
95	結合序列分群與特徵探勘演算法提昇兼職蛋白質預測之可靠度(1/2)	陳倩瑜	計畫主持人	2006年08月 ~ 2007年07月
94	多功能性蛋白質之預測與特性分析	陳倩瑜	計畫主持人	2005年08月 ~ 2006年07月
93	複合式蛋白質序列分群演算法之研究	陳倩瑜	計畫主持人	2004年08月 ~ 2005年07月

計畫期間

學校名稱	國別	系所	學位	起迄年月
國立台灣大學	中華民國 (台灣)	資訊工程學研究所	博士	1999年09月 ~ 2003年07月
史丹福大學	美國	電機工程學研究所	碩士	1996年09月 ~ 1998年01月
國立台灣大學	中華民國 (台灣)	電機工程學系	學士	1992年09月 ~ 1996年06月

服務機關	職稱	部門/系所	擔任職務	起迄年月
國立台灣大學	助理教授	生物產業機電工程學系	Research & Education	2005年08月 ~ 2008年07月
元智大學	助理教授	生物科技暨生物資訊研究所	Research & Education	2004年02月 ~ 2005年07月

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臺灣大學生物機電工程學系