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2013
[j33]
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Hsueh-Ting Chu, William W. L. Hsiao, Jen-Chih Chen, Tze-Jung Yeh, Mong-Hsun Tsai, Han Lin, Yen-Wenn Liu, Sheng-An Lee, Chaur-Chin Chen, Theresa Tsao, Cheng-Yan Kao:
EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. Bioinform. 29(8): 1004-1010 (2013)
2012
[j32]
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Chien-Hao Su, Tse-Yi Wang, Ming-Tsung Hsu, Francis Cheng-Hsuan Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai:
The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes. IEEE ACM Trans. Comput. Biol. Bioinform. 9(2): 619-628 (2012)
2011
[j31]
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Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Sufeng Chiang, Jen-Hao Cheng, Francis C. Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai:
MetaABC - an integrated metagenomics platform for data adjustment, binning and clustering. Bioinform. 27(16): 2298-2299 (2011)
[j30]
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Chien-Hsiang Hsu, Tse-Yi Wang, Hsueh-Ting Chu, Cheng-Yan Kao, Kuang-Chi Chen:
A quantitative analysis of monochromaticity in genetic interaction networks. BMC Bioinform. 12(S-13): S16 (2011)
[j29]
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Sheng-An Lee, Theresa Tsao, Ko-Chun Yang, Han Lin, Yu-Lun Kuo, Chien-Hsiang Hsu, Wen-Kuei Lee, Kuo-Chuan Huang, Cheng-Yan Kao:
Construction and analysis of the protein-protein interaction networks for schizophrenia, bipolar disorder, and major depression. BMC Bioinform. 12(S-13): S20 (2011)
2009
[j28]
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Sheng-An Lee, Chen-hsiung Chan, Tzu-Chi Chen, Chia-Ying Yang, Kuo-Chuan Huang, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F. Huang:
POINeT: protein interactome with sub-network analysis and hub prioritization. BMC Bioinform. 10 (2009)
[j27]
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Shun-Fu Chen, Yue-Li Juang, Wei-Kang Chou, Jin-Mei Lai, Chi-Ying F. Huang, Cheng-Yan Kao, Feng-Sheng Wang:
Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis. BMC Syst. Biol. 3: 110 (2009)
[j26]
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Un-Gian Iunn, Jia-hung Tai, Kiat-Gak Lau, Cheng-Yan Kao, Keh-Jiann Chen:
Modeling Taiwanese POS Tagging Using Statistical Methods and Mandarin Training Data. Int. J. Comput. Linguistics Chin. Lang. Process. 14(3) (2009)
2008
[j25]
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Sheng-An Lee, Chen-hsiung Chan, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F. Huang:
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinform. 9(S-12) (2008)
[j24]
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Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chiang Chen, Yuh-Jyh Hu, Jinn-Moon Yang:
Evolutionary conservation of DNA-contact residues in DNA-binding domains. BMC Bioinform. 9(S-6) (2008)
2007
[j23]
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Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen, Gen-Cher Lee, D. T. Lee, Yow-Ling Shiue, Chang-Wei Yeh, Chao-Hui Chang, Cheng-Yan Kao, Chi-Ying F. Huang:
Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC Bioinform. 8 (2007)
[j22]
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Tao-Wei Huang, Chung-Yen Lin, Cheng-Yan Kao:
Reconstruction of human protein interolog network using evolutionary conserved network. BMC Bioinform. 8 (2007)
[j21]
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Un-Gian Iunn, Kiat-Gak Lau, Hong-Giau Tan-Tenn, Sheng-An Lee, Cheng-Yan Kao:
Modeling Taiwanese Southern-Min Tone Sandhi Using Rule-Based Methods. Int. J. Comput. Linguistics Chin. Lang. Process. 12(4) (2007)
[j20]
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Chia-Hung Chang, Yu-Chung Chang, Anthony Underwood, Chien-Shun Chiou, Cheng-Yan Kao:
VNTRDB: a bacterial variable number tandem repeat locus database. Nucleic Acids Res. 35(Database-Issue): 416-421 (2007)
2006
[j19]
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Ming-Hui Jin, D. Frank Hsu, Cheng-Yan Kao:
Compact Genetic Algorithm for Performance Improvement in Hierarchical Sensor Networks Management. J. Interconnect. Networks 7(1): 101-116 (2006)
2005
[j18]
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  - journals/bioinformatics/ZhaoLTTCK05
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East Zhao, Hsuan-Liang Liu, Chi-Hung Tsai, Huai-Kuang Tsai, Chen-hsiung Chan, Cheng-Yan Kao:
Cysteine separations profiles on protein sequences infer disulfide connectivity. Bioinform. 21(8): 1415-1420 (2005)
[j17]
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Kuang-Chi Chen, Tse-Yi Wang, Huei-Hun Tseng, Chi-Ying F. Huang, Cheng-Yan Kao:
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinform. 21(12): 2883-2890 (2005)
[j16]
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  - journals/bioinformatics/HuangCCYCCK05
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Yu-Cheng Huang, Chun-Fan Chang, Chen-hsiung Chan, Tze-Jung Yeh, Ya-Chun Chang, Chaur-Chin Chen, Cheng-Yan Kao:
Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens. Bioinform. 21(24): 4330-4337 (2005)
[j15]
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Chi-Hung Tsai, Bo-Juen Chen, Chen-hsiung Chan, Hsuan-Liang Liu, Cheng-Yan Kao:
Improving disulfide connectivity prediction with sequential distance between oxidized cysteines. Bioinform. 21(24): 4416-4419 (2005)
2004
[j14]
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Tao-Wei Huang, An-Chi Tien, Wen-Shien Huang, Yuan-Chii G. Lee, Chin-Lin Peng, Huei-Hun Tseng, Cheng-Yan Kao, Chi-Ying F. Huang:
POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinform. 20(17): 3273-3276 (2004)
[j13]
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Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fan Tsai, Cheng-Yan Kao:
Some issues of designing genetic algorithms for traveling salesman problems. Soft Comput. 8(10): 689-697 (2004)
[j12]
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Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fan Tsai, Cheng-Yan Kao:
An Evolutionary Approach for Gene Expression Patterns. IEEE Trans. Inf. Technol. Biomed. 8(2): 69-78 (2004)
[j11]
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Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fang Tsai, Cheng-Yan Kao:
An evolutionary algorithm for large traveling salesman problems. IEEE Trans. Syst. Man Cybern. Part B 34(4): 1718-1729 (2004)
2003
[j10]
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Han-Yu Chuang, Huai-Kuang Tsai, Yuan-Fan Tsai, Cheng-Yan Kao:
Ranking Genes for Discriminability on Microarray Data. J. Inf. Sci. Eng. 19(6): 953-966 (2003)
2001
[j9]
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Jinn-Moon Yang, Jorng-Tzong Horng, Chih-Jen Lin, Cheng-Yan Kao:
Optical Coating Designs Using the Family Competition Evolutionary Algorithm. Evol. Comput. 9(4): 421-443 (2001)
[j8]
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Jorng-Tzong Horng, Ying-Ping Chen, Cheng-Yan Kao:
A Theoetical Aspect of a Stochastic Sketching Method for Global Optimization. J. Inf. Sci. Eng. 17(1): 47-71 (2001)
[j7]
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Jinn-Moon Yang, Cheng-Yan Kao:
A Robust Evolutionary Algorithm for Training Neural Networks. Neural Comput. Appl. 10(3): 214-230 (2001)
2000
[j6]
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Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao:
A Genetic Algorithm with Adaptive Mutations and Family Competition for Training Neural Networks. Int. J. Neural Syst. 10(5): 333-352 (2000)
[j5]
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Jinn-Moon Yang, Cheng-Yan Kao:
Flexible ligand docking using a robust evolutionary algorithm. J. Comput. Chem. 21(11): 988 (2000)
[j4]
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Jinn-Moon Yang, Cheng-Yan Kao:
Integrating adaptive mutations and family competition into genetic algorithms as function optimizer. Soft Comput. 4(2): 89-102 (2000)
[j3]
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Jinn-Moon Yang, Cheng-Yan Kao:
A family competition evolutionary algorithm for automated docking of flexible ligands to proteins. IEEE Trans. Inf. Technol. Biomed. 4(3): 225-237 (2000)
1999
[j2]
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Ying-Ping Chen, Jorng-Tzong Horng, Cheng-Yan Kao:
Stochastic sketching: a new method for global optimization. Soft Comput. 3(2): 101-110 (1999)
1993
[j1]
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  - journals/tsmc/LinKH93
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Feng-Tse Lin, Cheng-Yan Kao, Ching-Chi Hsu:
Applying the genetic approach to simulated annealing in solving some NP-hard problems. IEEE Trans. Syst. Man Cybern. 23(6): 1752-1767 (1993)

Conference and Workshop Papers

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2013
[c51]
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Chia-Hung Liu, Tzu-Chi Chen, Chun-Houh Chen, Cheng-Yan Kao, Chi-Ying F. Huang:
Differential network biology reveals a positive correlation between a novel protein-protein interaction and cancer cells migration. EMBC 2013: 2700-2703
2012
[c50]
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  - conf/asunam/ShenLLLHKLL12
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Chia-Ping Shen, Chia-Hung Liu, Feng-Sheng Lin, Han Lin, Chi-Ying F. Huang, Cheng-Yan Kao, Feipei Lai, Jeng-Wei Lin:
A Multiclass Classification Tool Using Cloud Computing Architecture. ASONAM 2012: 765-770
2009
[c49]
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  - conf/bibe/WangCHK09
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Tse-Yi Wang, Kuang-Chi Chen, D. Frank Hsu, Cheng-Yan Kao:
Combining Agent-Based Models with Stochastic Differential Equations for Gene Regulatory Networks. BIBE 2009: 405-409
2008
[c48]
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  - conf/imsccs/ChangLKY08
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Yao-Lin Chang, I-Hsin Liu, Cheng-Yan Kao, Jinn-Moon Yang:
Evolutionary Conservation and Interacting Preference for Identifying Protein-DNA Interactions. IMSCCS 2008: 1-8
[c47]
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  - conf/rocling/IunnTLCK08
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Un-Gian Iunn, Chia-Hung Tai, Kiat-Gak Lau, Keh-Jiann Chen, Cheng-Yan Kao:
利用統計方法及中文訓練資料處理台語文詞性標記 (Modeling Taiwanese POS tagging with statistical methods and Mandarin training data) [In Chinese]. ROCLING 2008
[c46]
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Yen-Hsi Lin, Zhao-Ming Gao, Cheng-Yan Kao:
中文名詞組的辨識：監督式與半監督式學習法的實驗 (Chinese NP Chunking: Experiments with Supervised, and Semisupervised Learning) [In Chinese]. ROCLING 2008
2007
[c45]
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  - conf/gecco/WangSJFLCK07
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Chi-Way Wang, Lei-Ming Sun, Ming-Hui Jin, Chung-Jung Fu, Li Liu, Chen-hsiung Chan, Cheng-Yan Kao:
A genetic algorithm for resident physician scheduling problem. GECCO 2007: 2203-2210
[c44]
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  - conf/imsccs/ChangTKCY07
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Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chiang Chen, Jinn-Moon Yang:
Evolutionary Conservation of DNA-Contact residues in DNA-binding Domains. IMSCCS 2007: 9-16
[c43]
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Tzu-Hsiang Chou, Ming-Hui Jin, Chi-Chung Chen, Cheng-Yan Kao:
Positioning System in Taipei Children's Museum of Transportation and Communication. ISPA Workshops 2007: 77-86
[c42]
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Tu-Bin Chu, Ming-Hui Jin, Li-Xin Xu, Jong-Tsong Chiang, Cheng-Yan Kao:
Portable Patient Information Integration System for Patient Safety Improvement. ISPA Workshops 2007: 87-95
2006
[c41]
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  - conf/crv/ChenKCCC06
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Chaur-Chin Chen, Cheng-Yan Kao, Chun-Fan Chang, Hsueh-Ting Chu, Chiung-Nien Chen:
Simple Software for Microarray Image Analysis. CRV 2006: 46
[c40]
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Pei-Ying Huang, Tzung-Pei Hong, Cheng-Yan Kao:
Combining Single-pass and Multiple-pass Heuristics for Group Flexible Flow-shop Scheduling Problems. SMC 2006: 3901-3906
2005
[c39]
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Yen-Chih Chen, Jinn-Moon Yang, Chi-Hung Tsai, Cheng-Yan Kao:
GEMPLS: A New QSAR Method Combining Generic Evolutionary Method and Partial Least Squares. EvoWorkshops 2005: 125-135
[c38]
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Chen-hsiung Chan, Sheng-An Lee, Cheng-Yan Kao, Huai-Kuang Tsai:
Improving EAX with restricted 2-opt. GECCO 2005: 1471-1476
[c37]
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  - conf/gecco/JinKHHLL05
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Ming-Hui Jin, Cheng-Yan Kao, Yu-Cheng Huang, D. Frank Hsu, Ren-Guey Lee, Chih-Kung Lee:
Compact genetic algorithm for active interval scheduling in hierarchical sensor networks. GECCO 2005: 2205-2206
[c36]
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  - https://dblp.org/rec/conf/icpads/JinLKWWHDH05
Ming-Hui Jin, Ren-Guey Lee, Cheng-Yan Kao, You-Rui Wu, D. Frank Hsu, Tse-Ping Dong, Kuan-Tsae Huang:
Sensor Network Design and Implementation for Health Telecare and Diagnosis Assistance Applications. ICPADS (2) 2005: 407-411
[c35]
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Ming-Hui Jin, Win-Zing Li, D. Frank Hsu, Cheng-Yan Kao:
Compact Genetic Algorithm for Performance Improvement in Hierarchical Sensor Networks Management. ISPAN 2005: 406-413
[c34]
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  - electronic edition @ aclanthology.org (open access)
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Un-Gian Iunn, Kiat-Gak Lau, Sheng-an Li, Cheng-Yan Kao:
A Study on Implementation of Southern-Min Taiwanese Tone Sandhi System. PACLIC 2005
[c33]
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Un-Gian Iunn, Sheng-an Li, Kiat-Gak Lau, Cheng-Yan Kao:
台語變調系統實作研究 (A Study on Implementation of Taiwanese Tone Sandhi System) [In Chinese]. ROCLING 2005
2004
[c32]
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  - conf/bibe/ChuangLBMKH04
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Han-Yu Chuang, Hongfang Liu, Stuart M. Brown, Cameron McMunn-Coffran, Cheng-Yan Kao, D. Frank Hsu:
Identifying Significant Genes from Microarray Data. BIBE 2004: 358-365
[c31]
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  - conf/bibe/ChangCCCLK04
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Chia-Hung Chang, Han-Yu Chuang, Yi-Hung Chiang, Chien-Shun Chiou, Hsueh-I Lu, Cheng-Yan Kao:
Automatically Predicting Possible Loci of Variable Number of Tandem Repeats. BIBE 2004: 475-482
[c30]
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Yen-Chih Chen, Jinn-Moon Yang, Chi-Hung Tsai, Cheng-Yan Kao:
Comparative Molecular Binding Energy Analysis of HIV-1 Protease Inhibitors Using Genetic Algorithm-Based Partial Least Squares Method. GECCO (2) 2004: 385-386
[c29]
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Han-Yu Chuang, Huai-Kuang Tsai, Cheng-Yan Kao:
Optimal Designs for Microarray Experiments. ISPAN 2004: 619-624
[c28]
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Han-Yu Chuang, Hongfang Liu, Fang-An Chen, Cheng-Yan Kao, D. Frank Hsu:
Combination Methods in Microarray Analysis. ISPAN 2004: 625-630
[c27]
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  - conf/metmbs/ChiuCTHK04
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Hua-Sheng Chiu, Han-Yu Chuang, Huai-Kuang Tsai, Tao-Wei Huang, Cheng-Yan Kao:
Discovering Statistically Significant Clusters by Using Iterative Genetic Algorithms in Gene Expression Data. METMBS 2004: 243-249
[c26]
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Chia-Wen Chang, Mao-Yen Chen, Wen-Chang Chang, Cheng-Yan Kao:
Exploring of Radiation Resistance from Bacterium Deinococcus radiodurans R1 by Amino Acid Compositions of Proteins: View from Comparative Whole Protein Sequences. METMBS 2004: 314-321
[c25]
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Chi-Hung Tsai, Huai-Kuang Tsai, Shih-Chieh Chen, Cheng-Yan Kao:
Disulfide Connectivity Prediction Using Support Vector Machine and Novel Features. METMBS 2004: 391-395
[c24]
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Yu-Cheng Huang, Yu-Chih Chao, Shwu-Bin Lin, Huai-Kuang Tsai, Chun-Fan Chang, Sheng-An Lee, Cheng-Yan Kao:
A Tool to Determine the Specificity of Antisense Oligonucleotide. METMBS 2004: 447-449
[c23]
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Yu-Cheng Huang, Han-Yu Chuang, Huai-Kuang Tsai, Chun-Fan Chang, Cheng-Yan Kao:
Designing Multiple-Use Primer Set for Multiplex PCR by Using Compact GAs. PPSN 2004: 511-521
2003
[c22]
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  - conf/bibe/HuangCTLKH03
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Hsien-Da Huang, Huei-Lin Chang, Tsung-Shan Tsou, Baw-Jhiune Liu, Cheng-Yan Kao, Jorng-Tzong Horng:
A Data Mining Method to Predict Transcriptional Regulatory Sites Based on Differentially Expressed Genes in Human Genome. BIBE 2003: 297-304
2002
[c21]
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Huai-Kuang Tsai, Jinn-Moon Yang, Cheng-Yan Kao:
Solving traveling salesman problems by combining global and local search mechanisms. IEEE Congress on Evolutionary Computation 2002: 1290-1295
[c20]
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Huai-Kuang Tsai, Jinn-Moon Yang, Cheng-Yan Kao:
Applying Genetic Algorithms To Finding The Optimal Gene Order In Displaying The Microarray Data. GECCO 2002: 610-617
2001
[c19]
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Hsien-Da Huang, Shu-Fen Fang, Jorng-Tzong Horng, Cheng-Yan Kao:
Discovering Common Structural Motifs from SSU 16 S Ribosomal RNA Secondary Structures. BIBE 2001: 104-111
[c18]
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Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao:
Integrating adaptive mutations and family competition with differential evolution for flexible ligand docking. CEC 2001: 473-480
[c17]
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Jorng-Tzong Horng, Hsien-Da Huang, Cho-Chun Huang, Cheng-Yan Kao:
Mining Putative Regulatory Elements in Gene Promoter Regions. German Conference on Bioinformatics 2001: 90-95
[c16]
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Jorng-Tzong Horng, Ching-Mei Lin, Bing-He Yang, Cheng-Yan Kao:
A Genetic Algorithm for Multiple Sequence Alignment. German Conference on Bioinformatics 2001: 167-170
2000
[c15]
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Huai-Kuang Tsai, Cheng-Yan Kao, Jinn-Moon Yang:
A Genetic Algorithm for Physical Mapping Problems. GECCO 2000: 375
[c14]
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Jorng-Tzong Horng, Yu-Jan Chang, Baw-Jhiune Liu, Cheng-Yan Kao:
Materialized View Selection in a Data Warehouse Using Evolutionary Algorithms. GECCO 2000: 385
[c13]
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Jorng-Tzong Horng, Ching-Mei Lin, Baw-Jhiune Liu, Cheng-Yan Kao:
Using Genetic Algorithms to Solve Multiple Sequence Alignments. GECCO 2000: 883-
[c12]
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Jinn-Moon Yang, Cheng-Yan Kao:
An Evolutionary Algorithms to Training Neural Networks for a Two-Spiral Problem. GECCO 2000: 1025-1032
1999
[c11]
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Jorng-Tzong Horng, Li-Yi Lin, Baw-Jhiune Liu, Cheng-Yan Kao:
Resolution of simple plant location problems using an adapted genetic algorithm. CEC 1999: 1186-1193
[c10]
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Jorng-Tzong Horng, Yu-Jan Chang, Baw-Jhiune Liu, Cheng-Yan Kao:
Materialized view selection using genetic algorithms in a data warehouse system. CEC 1999: 2221-2230
1998
[c9]
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  - conf/icra/YangHK98
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Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao:
A New Evolutionary Approach to Developing Neural Autonomous Agents. ICRA 1998: 1411-1416
[c8]
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  - conf/ictai/ChenWKOC98
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Chien-Cheng Chen, Leuo-hong Wang, Cheng-Yan Kao, Ming Ouhyoung, Wen-Chin Chen:
Molecular binding in structure-based drug design: a case study of the population-based annealing genetic algorithms. ICTAI 1998: 328-335
[c7]
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Jinn-Moon Yang, Cheng-Yan Kao:
An Evolutionary Algorithm for Synthesizing Optical Thin-Film Designs. PPSN 1998: 947-958
1997
[c6]
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  - conf/eps/YangCHK97
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Jinn-Moon Yang, Ying-Ping Chen, Jorng-Tzong Horng, Cheng-Yan Kao:
Applying Family Competition to Evolution Strategies for Constrained Optimization. Evolutionary Programming 1997: 201-211
[c5]
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  - conf/icga/YangHK97
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Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao:
A Continuous Genetic Algorithm for Global Optimization. ICGA 1997: 230-237
1996
[c4]
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  - conf/icec/YangK96a
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Jinn-Moon Yang, Cheng-Yan Kao:
A Combined Evolutionary Algorithm for Real Parameters Optimization. International Conference on Evolutionary Computation 1996: 732-737
1994
[c3]
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  - conf/icec/HorngLK94
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Jorng-Tzong Horng, Baw-Jhiune Liu, Cheng-Yan Kao:
A Genetic Algorithm for Database Query Optimization. International Conference on Evolutionary Computation 1994: 350-355
[c2]
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  - conf/icec/HuangKH94
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Wen-Chih Huang, Cheng-Yan Kao, Jorng-Tzong Horng:
A Genetic Algorithm Approach for Set Covering Problems. International Conference on Evolutionary Computation 1994: 569-574
[c1]
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Leuo-hong Wang, Cheng-Yan Kao, Ming Ouhyoung, Wen-Chin Chen:
Using an Annealing Genetic Algorithm to Solve Global Energy Minimazation Problem. ICTAI 1994: 404-410

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