Publications
core publications
2007
1. Tsai CA, Chen DT, Chen JJ, Balch CM, Thompson JF, Soong SJ. (2007) An integrated tree-based classification approach to prognostic grouping with application to localized melanoma patients. Journal of Biopharmaceutical statistics. 17:3, 445-460.
2. Chen HY, Yu SL, Chen CH, Chang GC, Chen CY, Yuan A, Cheng CL, Wang CH, Terng HJ, Kao SF, Chan WK, Li HN, Liu CC, Singh S, Chen WJ, Chen JJ, Yang PC. (2007) A five-gene signature and clinical outcome in non-small-cell lung cancer. New England Journal of Medicine. 356:1, 11-12.
3. Hsu CN, Lai JM, Liu CH, Tseng HH, Lin CY, Lin KT, Yeh HH, Sung TY, Hsu WL, Su LJ, Lee SA, Chen CH, Lee GC, Lee DT, Shiue YL, Yeh CW, Chang CH, Kao CY, Huang CY. (2007) Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC Bioinformatics. 8:66.
4. Chen JJ, Tsai CA, Tzeng S, Chen CH. (2007) Gene selection with multiple ordering criteria. BMC Bioinformatics. 8:74.
5. Chang KP, Hao SP, Tsang NM, Chang YL, Cheng MH, Liu CT, Lee, YS, Tsai CL, Lee TJ, Wang TH, Tsai CN. (2007) Promoter polymorphisms of DNMT3B and the risk of head and neck squamous cell carcinoma in Taiwan: A case-control study. Oral Oncology. 43:4, 345-351.
6. Leu JH, Chang CC, Wu JL, Hsu CW, Hirono I, Aoki T, Juan HF, Lo CF, Kou GH, Huang HC. (2007) Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon. BMC Genomics. 8:120.
7. Tsai CA, Chen JJ. (2007) Kernel estimation for adjusted p-values in multiple testing. Computational Statistics and Data Analysis. 51:8, 3885-3897.
8. Su LJ, Chang CW, Wu YC, Chen KC, Lin CJ, Liang SC, Lin CH, Jacqueline WP, Hsu SL, Chen CH, Huang CY. (2007) Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC Genomics. 8:140.
9. Chen JJ, Lee T, Delongchamp RR, Chen T, Tsai CA. (2007) Significance analysis of groups of genes in expression profiling studies. Bioinformatics. 23:16, 2104-2112.
10. Chen SY, Chang YC, LeeYS, Chao HC, Tsao KC, Lin TY, Ko TY, Tsai CN, Chiu CH. (2007) Molecular epidemiology and clinical manifestations of viral gastroenteritis in hospitalized pediatric patients in northern Taiwan. Journal of Clinical Mirobiology. 45:6, 2054-2057.
11. Huang TC, Huang HC, Chang CC, Chang HY, Ou CH, Hsu CH, Chen ST, Juan HF. (2007) An apoptosis-related gene network induced by novel compound-cRGD in human breast cancer cells. FEBS Letters. 581:18, 3517-3522.
12. Lin CT, Chung IF, Ko LW, Chen YC, Liang SF, Duann JR. (2007) EEG-based assessment of driver cognitive responses in a dynamic virtual-reality driving environment. IEEE Transactions on Biomedical Engineering: Communications. 54:7, 1349-1352.
13. Lin CJ, Chung IF, Chen CH. (2007) An entropy-based quantum neuro-fuzzy inference system for classification applications. Neurocomputing. 70:12-15, 2502-2516.
<>14. Chen JJ, Lee T, Delongchamp RR, Chen T, Tsai CA. (2007) Significance analysis of groups of genes in expression profiling studies. Bioinformatics. 23:16, 2104-2112.
15. Juang CF, Chung IF, Hsu CH. (2007) Automatic construction of feedforward/recurrent fuzzy systems by clustering-aided simplex particle swarm optimization. Fuzzy Sets and Systems. 158:18, 1979-1996.
16. Juang CF, Chung IF. (2007) Recurrent fuzzy network design using hybrid evolutionary learning algorithms. Neurocomputing. 70:16-18, 3001-3010.
17. Lin CC, Tsai YS, Lin YS, Chiu TY, Hsiung CC, Lee MI, Simpson JC, Hsu CN. (2007) Boosting multiclass learning with repeating codes and weak detectors for protein subcellular localization. Bioinformatics. 23:24, 3374-3381.
18. Cheng KC, Huang HC, Chen JH, Hsu JW, Cheng HC, Ou CH, Yang WB, Chen ST, Wong CH, Juan HF. (2007) Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction. BMC Genomics. 8:1, 411.
19. Chen CC, Bai YY, Huang GH, Tang ST. (2007) Revisiting the concept of malnutrition in older people. Journal of Clinical Nursing. 16:11, 2015-2026
20. Fang YC, Huang HC, Juan HF. (2007) MeInfoText: associated gGene methylation and cancer information from text mining. BMC Bioinformatics. 9:1, 22.
21. Tantoso E, Li KB. (2007) AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices. Amino Acids. 0939-4451.
22. Lee CT, Amaro C, Wu KM, Valiente E, Chang YF, Tsai SF, Chang CH, Hor LI. (2007) A common virulence plasmid in biotype 2 Vibrio vulnificus and its dissemination aided by a conjugal plasmid. Journal of Bacteriology. 10, 1128.
23. George F Mayhew, Lyric C Bartholomay, Hang-Yen Kou, Thomas A Rocheleau, Jeremy F Fuchs, Matthew T Aliota, I-Yu Tsao, Chiung-Yen Huang, Tze-Tze Liu, Kwang-Jen Hsiao, Shih-Feng Tsai, Ueng-Cheng Yang, Nicole T Perna, Wen-Long Cho, Bruce M Christensen and Cheng-Chen Chen. (2007) Construction and characterization of an expressed sequenced tag library for the mosquito vector Armigeres subalbatus. BMC Genomics. 8:462
2006
1. Hsiang-you Yuan, Jen-Jie Chiou, Wen-Hsien Tseng, Chia-Hung Liu, Chuan-Kun Liu, Yi-Jung Lin, Hui-Hung Wang, Adam Yao, Yuan-Tsong, Chen, Chun-Nan Hsu. (2006) FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Research.34, 635-641.
2. Jinn Ho, Wen-Liang Hwang, Henry Horn-Shing Lu, and Der-Tsai Lee. (2006) Gridding spot centers of smoothly distorted microarray images. IEEE TRANSACTIONS ON IMAGE PROCESSING. 15:2, 342-353.
3. Huai-Kuang Tsai, Grace Tzu-Wei Huang, Meng-Yuan Chou, Henry Horng-Shing Lu and Wen-Hsiung Li. (2006) Method for identifying transcription factor binding sites in yeast. Bioinformatics. 22:141, 675-1681.
4. Wen-Harn Pan, Ke-Shiuan Lynn, Chun-Houh Chen, Yi-Lin Wu, Chung-Yen Lin, and Hsing-Yi Chang. (2006) Using endophenotypes for pathway clusters to map complex disease genes. Genetic Epidemiology. 30:2, 143-154.
5. Chun-Nan Hsu, Han-Shen Huang, Bo-Hou Yang. (2006) Global and componentwise extrapolation for accelerating data mining from large incomplete data sets with the EM algorithm. IEEE Int’l Conference on Data Mining. 265-274.
6. Yi-Feng Chang, Chuan-Hsiung Chang. (2006) CAGO: a cross platform for cross-genome mining and hypothesis testing on genome organization. BMC Bioinformatics.
7. Yi-Shin Pan, Yun-Shien Lee, Yung-Lin Lee, Wei-Chen Lee, Sen-Yung Hsieh. (2006) Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach. BMC Genomics.7:131
8. Angel Chao, Tzu-Hao Wang, Yun-Shien Lee, Swei Hsueh, An-Shine Chao, Ting-Chang Chang, Wei-Hsiang Kung, Shang-Lang Huang, Fang-Yu Chao, Min-Li Wei and Chyong-Huey Lai. (2006) Molecular characterization of adenocarcinoma and squamous carcinoma of the uterine cervix using microarray analysis of gene expression. International Journal of Cancer. 119:1, 91-98.
9. Tzu-Hao Wang, Y-H Chan, C-W Chen, Wei-Hsiang Kung, Yun-Shien Lee, S-T Wang, Ting-Chang Chang, and H-S Wang. (2006) Paclitaxel (Taxol) upregulates expression of functional interleukin-6 in human ovarian cancer cells through multiple signaling pathways. Oncogene. 25:35, 4857-4866.
10. Han-Shen Huang, Bo-Hou Yang, Chun-Nan Hsu. (2006) Triple jump aitken’s acceleration for the EM algorithm and its extrapolation-based variants. Journal of Machine Learning Research.
2005
1. Lin CT, Chung IF, Ko LW, Chen YC, Liang SF, Duann JR. (2005) Reconfigurable web wrapper agents for biological information integration. Journal of the American Society for Information Science and Technology. 56, 505-517.
2. Chi-Ming Wu, Yun-Shien Lee, Tzu-Hao Wang, Li-Yu Lee, Wei Hsiang Kong, En-Shin Chen, Min-Li Wei, Ying Liang, and Tsann-Long Hwang. (2005) Identification of differential gene expression between intestinal and diffuse gastric cancer using cDNA microarray. Oncology Report. 15:1, 57-64.
user publications
2007
1. Su LJ, Chang CW, Wu YC, Chen KC, Lin CJ, Liang SC, Lin CH, Whang-Peng J, Hsu SL, Chen CH, Huang CY. (2007) Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC Genomics.
2. Lubomirov R, Csajka C, Telenti A. (2007) ADME pathway approach for pharmacogenetic studies of anti-HIV therapy. Pharmacogenomics. 8:6.
3. Zhu H, Enaw JO, Ma C, Shaw GM, Lammer EJ, Finnell RH. (2007) Association between CFL1 gene polymorphisms and spina bifida risk in a California population. BMC medical genetics.
4. Arning L, Saft C, Wieczorek S, Andrich J, Kraus PH, Epplen JT. (2007) NR2A and NR2B receptor gene variations modify age at onset in Huntington disease in a sex-specific manner. Human Genetics. 122:2, 175-182.
5. Mayhew GF, Bartholomay LC, Kuo HY, Rocheleau TA, Fuchs JF, Aliota MT, Tsao IY, Huang CY, Liu TT, Hsiao KJ, Tsai SF, Yang UC, Perna NT, Cho WL, Christensen BM, Chen CC. (2007) Construction and characterization of an expressed sequenced tag library for the mosquito vector Armigeres subalbatus. BMC Genomics. 8:462, 1471-2164.
2006
1. Yi-Shin Pan, Yun-Shien Lee, Yung-Lin Lee, Wei-Chen Lee, Sen-Yung Hsieh. (2006) Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach. BMC Genomics. 7:131.
2. Angel Chao, Tzu-Hao Wang, Yun-Shien Lee, Swei Hsueh, An-Shine Chao, Ting-Chang Chang, Wei-Hsiang Kung, Shang-Lang Huang, Fang-Yu Chao, Min-Li Wei and Chyong-Huey Lai. (2007) Molecular characterization of adenocarcinoma and squamous carcinoma of the uterine cervix using microarray analysis of gene expression. International Journal of Cancer. 119:1, 91-98.
3. Chi-Ming Wu, Yun-Shien Lee, Tzu-Hao Wang, Li-Yu Lee, Wei Hsiang Kong, En-Shin Chen, Min-Li Wei, Ying Liang, and Tsann-Long Hwang. (2007) Identification of differential gene expression between intestinal and diffuse gastric cancer using cDNA microarray. Oncology Report. 15:1, 57-64.
4. Tzu-Hao Wang, Y-H Chan, C-W Chen, Wei-Hsiang Kung, Yun-Shien Lee, S-T Wang, Ting-Chang Chang, and H-S Wang. Paclitaxel (Taxol) upregulates expression of functional interleukin-6 in human ovarian cancer cells through multiple signaling pathways. Oncogene. 25:35, 4857-4866.
5. C. J. Chang, J. H. Chiu, L. M. Tseng, C. H. Chang, T. M. Chien, C. W. Wu, W. Y. Lui. (2007) Modulation of HER2 expression by ferulic acid on human breast cancer MCF7 cells. European Journal of Clinical Investigation. 36:8, 588-596.
6. Chang, C.-J. Chiu, J.-H. Tseng, L.-M. Chang, C.-H. Chien, T.-M. Chen, C.-C. Wu, C.-W. Lui, W.-Y. (2007) Si-Wu-Tang and its constituents promote mammary duct cell proliferation by up-regulation of HER-2 signaling. MENOPAUSE NEW YORK. 13:6, 567-976.
2005
1. Hsiang-Yu Yuan, Jin-Jer Chen, M.T. Michael Lee, Ju-Chieh Wung, Ying-Fu Chen, Min-Ji Charng, Ming-Jen Lu, Chi-Ren Hung, Chun-Yu Wei, Chien-Hsiun Chen, Jer-Yuarn Wu and Yuan-Tsong Chen. (2005) A novel functional VKORC1 promoter polymorphism is associated with inter-individual and inter-ethnic differences in warfarin sensitivity. Human Molecular Genetics. 14:13, 1745-1751.