Publications

Publications:

1. Chu HT, Lin H, Tsao TT, Chang CF, Hsiao WW, Yeh TJ, Chang CM, Liu YW, Wang TY, Yang KC, Chen TJ, Chen JC, Chen KC, Kao CY. Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data. BMC Med Genomics. 2013 Sep 12;6(1):31.

2. Chu HT, Hsiao WW, Chen JC, Yeh TJ, Tsai MH, Lin H, Liu YW, Lee SA, Chen CC, Tsao TT, Kao CY. EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. Bioinformatics. 2013 Apr 15;29(8):1004-10.

3. Chu HT, Hsiao WW, Tsao TT, Hsu DF, Chen CC, Lee SA, Kao CY. SeqEntropy: genome-wide assessment of repeats for short read sequencing. PLoS One. 2013;8(3):e59484.

4. Chu HT, Hsiao WW, Tsao TT, Chang CM, Liu YW, Fan CC, Lin H, Chang HH, Yeh TJ, Chen JC, Huang DM, Chen CC, Kao CY. Quantitative assessment of mitochondrial DNA copies from whole genome sequencing. BMC Genomics. 2012;13 Suppl 7:S5.

5. Chia-Hung Liu, Tzu-Chi Chen, Gar-Yang Chau, Yi-Hua Jan, Chun-Houh Chen, Chun-Nan Hsu, Kuan-Ting Lin, Yue-Li Juang, Pei-Jung Lu, Hui-Chuan Cheng, Ming-Huang Chen, Chia-Fen Chang, Yu-Shan Ting, Cheng-Yan Kao, Michael Hsiao, Chi-Ying F. Huang, Analysis of protein-protein interactions in cross-talk pathways reveals CRKL protein as a novel prognostic marker in hepatocellular carcinoma, Mol Cell Proteomics, 2013 12: 1335-1349.

6. Sheng-An Lee1., Theresa Tsun-Hui 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 interactio networks for schizophrenia, bipolar disorder, and major depression BMC Bioinformatics, 2011.(SCI)

7. Chen MH, Yang WL, Lin KT, Liu CH, Liu YW, Huang KW, Chang PM, Lai JM, Hsu CN, Chao KM, Kao CY, Huang CY. Gene expression-based chemical genomics identifies potential therapeutic drugs in hepatocellular carcinoma. PLOS One, 2011.(SCI)

8. Chien-Hsiang Hsu1., Tse-Yi Wang2., Hsueh-Ting Chu, Cheng-Yan Kao* and Kuang-Chi Chen5* A quantitative analysis of monochromaticity in genetic interaction networks BMC Bioinformatics, 12(Suppl 13):S16, 2011.(SCI) (NSC99-2221-E-002-168-MY2)

9. Chia-Hung Liu, Kuan-Ting Lin, Chi-Ying F Huang, Yih-Jyh Shann, Yu-Shi Lin, Cheng-Yan Kao and Chun-Nan Hsu Genome-Wide Detection of Putative Oncofetal Genes in Human Hepatocellular Carcinoma by Splicing Pattern Comparison iConcept Transaction on Computational Intelligence in Bioinformatics (TCIB), 1:1, 2010.(其它)

10. Shun-Fu Chen,#1 Yue-Li Juang,#2 Wei-Kang Chou,1 Jin-Mei Lai,3 Chi-Ying F Huang,4 Cheng-Yan Kao,5 and Feng-Sheng Wang1 Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis BMC Syst Biol., 3: 110, 2009.(SCI)

11. Chen TC, Lee SA, Hong TM, Shih JY, Lai JM, Chiou HY, Yang SC, Chan CH, Kao CY, Yang PC, Huang CY*. From midbody protein-protein interaction network construction to novel regulators in cytokinesis. J Proteome Res., 8 (11), pp 4943–4953, 2009.(SCI)

12. Chen TC, Lee SA, Chan CH, Juang YL, Hong YR, Huang YH, Lai JM, Kao CY, Huang CY Cliques in mitotic spindle network bring kinetochore-associated complexes to form dependence pathway Proteomics, 9(16):4048-62, 2009.(SCI)

13. H. K. Tsai, P. Y. Huang, C. Y. Kao, and D. Wang Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome. International Journal of Molecular Sciences, Vol. 10, pp. 3658-3670, 2009.(SCI)

14. 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 and Chi-Ying F Huang POINeT: protein interactome with sub-network analysis and hub prioritization BMC Bioinformatics, 10:114, 2009.(SCI)

15. Lee Sheng-An, Chan Cheng-hsiung, Tsai Chi-Hung, Lai Jin-Mei, Wang Feng-Sheng, Kao Cheng-Yan and Huang Chi-Ying Ortholog-based protein-protein interaction prediction and its application to inter-species interactions BMC Bioinformatics, 9(Suppl 12): S11, 2008.(SCI)

16. Chang, Y. L., Tsai, H. K., Kao, C. Y.*, Chen, Y. C., Yang, J. M. Evolutionary Conservation of DNA-Contact residues in DNA-binding Domains. BMC Bioinformatics, 2008.(SCI)

17. Huang, T. W., Lin, C. Y., and Kao, C. Y.* Reconstruction of human protein interaction network using evolutionary conserved network. BMC Bioinformatics., 2007.(SCI)

18. 高成炎 Bioinformatics approaches for disulfide connectivity prediction. Curr Protein Pept Sci., 2007.(SCI)

19. Chang, C. H., Chang, Y. C., Underwood, A., Chiou, C. S., and Kao, C. Y.* VNTRDB: a bacterial variable number tandem repeat locus database Nucleic Acids Res., 2007.(SCI)

20. Hsu C. N., Lai J. M., Liu C. H., Tseng H. H., Lin C. Y., Lin K. T., Yeh H. H., Sung T. Y., Hsu W. L., Su L. J., Lee S. A., Chen C. H., Lee G. C., Lee D. T., Shiue Y. L., Yeh C. W., Chang C. H., Kao C. Y. , and Huang C. Y. (2007) “Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online).” BMC Bioinformatics 8 , 66.

21. Lee, Y. C. G., Hwang, Y. C., Chen, K. C., Lin, Y. S., Huang, D. Y., Huang, T. W., Kao, C. Y. , Wu, H. C., Lin, C. T., Huang, C. Y. F. (2007) “Effect of Epstein-Barr Virus Infection on Global Gene Expression in Nasopharyngeal Carcinoma”, Functional and Integrative Genomics 7 , 79-93

22. Chang, C. H., Chang, Y. C., Underwood, A., Chiou, C. S., and Kao, C. Y. (2007) “VNTRDB: a bacterial variable number tandem repeat locus database”, Nucleic Acid. Res. , 35 , D416-D421. (SCI)

23. Chen, B. J., Tsai, C. H., Chan, C. H., and Kao, C. Y. (2006) “Disulfide connectivity prediction with 70% accuracy using two-level models”, Proteins , 64 , 246-252. (SCI)

24. Huang, Y. C., Chang, C. F., Chan, C. H., Yeh, T. J., Chang, Y. C., and Kao, C. Y. (2005) “Integrated Minimum Set Primers and Unique Probes Design Algorithms for Differential Detection of Symptom-Related Pathogens.”, Bioinformatics , 21 , 4330-4337. (SCI)

25. Tsai, C. H., Chen, B. J., Chan, C. H., Liu, H. L., and Kao, C. Y. (2005) “Improving Disulfide Connectivity Prediction with Sequential Distance between Oxidized Cysteines”, Bioinformatics , 21 , 4416-4419. (SCI)

26. Chen, Y. C., Yang, J. M., Tsai, C. H., and Kao, C. Y. (2005) “GEMPLS: A New QSAR Method Combining Generic Evolutionary Method and Partial Least Squares”, LNCS , vol. 3449, pp. 125. (SCI)

27. Chen, K. C., Wang, T. Y., Tseng, H. H., Huang, C. Y., and Kao, C. Y. , (2005) “A Stochastic Differential Equation Model for Quantifying Transcriptional Regulatory Network in Saccharomyces cerevisiae ”, Bioinformatics , vol. 21, pp. 2883-2890. (SCI)

28. Zhao, E., Liu, H. L., Tsai, C. H., Tsai, H. K., Chan, C. H. and Kao, C. Y. , (2005). “Cysteine separations profiles (CSP) on protein sequences infer disulfide connectivity”, Bioinformatics , vol. 21 , pp. 1415-1420. (SCI)

29. Huang, T. W., Tien, A. C., Huang, W. S., Lee, Y. C., Peng, C. L., Tseng, H. H., Kao, C. Y. and Huang, C. Y. (2004). “ POINT: a database for the p rediction o f protein-protein int eractions based on the orthologous interactome.” Bioinformatics, vol. 20 , pp. 3273-3276. (SCI)

30. Jin, M. H., Horng J. T., Wu H. K., and Kao C. Y. (2004) “Location Query Based on Moving Behaviors,” International Journal of Information System. (Revision)

31. Tsai , H. K. , Yang , J. M., Tsai, Y. F., and Kao, C. Y. (2004) “An evolutionary approach for gene expression,” IEEE Transactions on Information Technology and BioMedicine , vol. 8 , pp. 69-78. (SCI)

32. Tsai , H. K. , Yang , J. M., Tsai, Y. F., and Kao, C. Y. (2004) “A genetic algorithm for large traveling salesman problems,” IEEE Transactions on Systems, Man and Cybernetics -PartB , vol. 34 , pp. 1718-1729. (SCI)

33. Tsai, H. K., Yang, J. M., Tsai, Y. F., and Kao, C. Y. "Critical factors of Genetic Algorithm for Traveling Salesman Problems", Soft Computing , .

34. Tsai, Y. F., Tsai, H. K., and Kao, C. Y. "Clustering Analysis of Debris Flow Streams", International Journal of Sediment Research , .（ EI）

35. Tsai, H. K., Yang, J. M., and Kao, C. Y. "Entropy Selection Genetic Algorithms for Traveling Salesman Problems", Engineering Optimization , vol. 35 , no. 3, pp. 297-311, 2003. (SCI)

36. Chuang, H. Y., Tsai, H. K., Tsai, Y. F., and Kao, C. Y. "Ranking genes for discriminability on Microarray Data", Journal of Information Science and Engineering, special issues on Bioinformatics , vol. 19 , pp. 953-966, 2003. (SCI)

37. Yang, J. M., Tsai, C. H., Hwang, M. J., Tsai, H. K., Hwang, J. K., and Kao, C. Y. , “GEM: a Guassian Evolutionary Method for predicting protein Side-chain conformations,” Protein Science , vol. 11 , no. 8, pp. 1897-1907, 2002. (SCI)

38. Yang, J. M, Lin, C. J., and Kao, C. Y. , “A robust evolutionary algorithm for global optimization”, Engineering Optimization , vol. 34, no. 5, pp. 405-427, 2002. (SCI)

39. Yang, J. M. and Kao, C. Y. , “An efficient evolutionary algorithm for the thin-film synthesis of inhomogeneous optical coatings,” Applied Optics , vol. 40, no. 19, pp. 3256-3267, 2001. (SCI)

40. Yang, J. M., Horng, J. T, Lin C. J., and Kao, C. Y. , “Optical coating designs using an evolutionary algorithm”, Evolutionary Computation , vol. 9, no.4, pp. 421-443, 2001.

41. Horng, J. T., Chen, Y. P., and Kao, C. Y. , “A Theoretical Aspect of a Stochastic Sketching for Global Optimization,” Journal of Information Science and Engineering , Vol. 17, No. 1, 2001.

42. Yang, J. M. and Kao, C. Y. , “An evolutionary algorithm for the synthesis of multilayer coatings at oblique light incidence,” IEEE/OSA Journal of Lightwave Technology, vol. 19, no. 4, pp. 559-570, 2001 . (SCI)

43. Yang, J. M. and Kao, C. Y. , “A robust evolutionary algorithm for training neural networks,” Neural Computing and Application, vol. 10, no. 3, pp. 214-230, 2001 . (SCI)

44. Yang, J. M. and Kao, C. Y. , “An efficient evolutionary algorithm for the thin-film synthesis of inhomogeneous optical coatings,” Applied Optics, vol. 40, no. 19, pp. 3256-3267, 2001. (SCI)

45. Yang, J. M., Horng, J. T, Lin, C. J. , and Kao, C. Y. , “Optical coating designs using an evolutionary algorithm”, Evolutionary Computation, vol. 9, no.4, pp. 421-443, 2001.