莊曜宇教授的著作列表 - Publication List of Eric Y. Chuang

Publication List of 莊曜宇 Eric Y. Chuang

Journal articles & book chapters:

  1. C.S. Hsieh, P.S. Huang, S.N. Chang, C.K. Wu, J.J. Hwang, E.Y. Chuang*, C.T. Tsai, “Genome-Wide Copy Number Variation Association Study of Atrial Fibrillation Related Thromboembolic Stroke,” J. Clin. Med, 8(3), 332, Mar. 2019
  2. P.H. Ko, Y.C. Shen, K. Murugan, C.W. Huang, G. Sivakumar, P. Pal, C.C. Liao, K.S. Luo, E.Y. Chuang, M.H. Tsai, L.C. Lai, “Macrophage Migration Inhibitory Factor Acts as the Potential Target of a Newly Synthesized Compound, 1-(9′-methyl-3′-carbazole)-3, 4-dihydro-β-carboline,” Scientific Reports, Feb. 2019
  3. C.Y. Shen, Y.C. Chang, L.H. Chen, W.C. Lin, Y.H. Lee, S.T. Yeh, H.K. Chen, W. Fang, C.P. Hsu, J.M. Lee, T.P. Lu, P.W. Hsiao, L.C. Lai, M.H. Tsai, E.Y. Chuang*, “The extracellular SEMA domain attenuates intracellular apoptotic signaling of semaphorin 6A in lung cancer cells,” Oncogenesis, Dec. 2018
  4. W.C. Lin, L.H. Chen, Y.C. Hsieh, P.W. Yang, L.C. Lai, E.Y. Chuang, J.M. Lee, M.H. Tsai, “miR-338-5p inhibits cell proliferation, colony formation, migration, and cisplatin resistance in esophageal squamous cancer cells by targeting FERMT2,” Carcinogenesis, bgy189, Dec. 2018
  5. C.S. Hsieh, C.T. Tsai, Y.H. Chen, S.N. Chang, J.J. Hwang, E.Y. Chuang*, I.H. Wu, “Global Expression Profiling Identifies a Novel Hyaluronan Synthases 2 Gene in the Pathogenesis of Lower Extremity Varicose Veins,” J. Clin. Med, 7(12), 537, Dec. 2018
  6. C.Y. Lee, P.H. Hsieh, L.M. Chiang, A. Chattopadhyay, K.Y. Li, Y.F. Lee, T.P. Lu, L.C. Lai, E.C. Lin, H. Lee, S.T. Ding, M.H. Tsai, C.Y. Chen, E.Y. Chuang*, “Whole-Genome De Novo Sequencing Reveals Unique Genes that Contributed to the Adaptive Evolution of the Mikado Pheasant,” Gigascience, 7(5), May 2018
  7. T.H. Hsiao, Y.H. Chen, H.I. Chen, Y.C. Chiu, E.Y. Chuang*, Y. Chen, “Utilizing Cancer–Functional Gene set–Compound Networks to Identify Putative Drugs for Breast Cancer,” Comb Chem High T Scr, 21(2), 74-83, Feb. 2018
  8. Y.F. Lee, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, E.Y. Chuang*, “CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system,” DATABASE-OXFORD, Jan. 2018
  9. Y.C. Chiu, L.J. Wang, T.H. Hsiao, E.Y. Chuang*, Y. Chen, “Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer,” BMC Genomics, Oct. 2017
  10. S.C. Wei, H.F. Yang-Yen, P.N. Tsao, M.T. Weng, C.C. Tung, L.C.H. Yu, L.C. Lai, J.H. Hsiao, E.Y. Chuang, C.T. Shun, Y.H. Ni, R.J. Xavier, “D.K. Podolsky, J.J.Y. Yen, J.M. Wong, SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway,” Inflamm Bowel Dis, Oct. 2017
  11. K.L. Chiu, Y.S. Lin, T.T. Kuo, C.C. Lo, Y.K. Huang, H.F. Chang, E.Y. Chuang, C.C. Lin, W.C. Cheng, Y.N. Liu, L.C. Lai, Y.P. Sher, “ADAM9 enhances CDCP1 by inhibiting miR-1 through EGFR signaling activation in lung cancer metastasis,” Oncotarget, Jul. 2017
  12. A.L. Woolston, P.C. Hsiao, P.H. Kuo, S.H. Wang, Y.J. Lien, C.M. Liu, H.G. Hwu, T.P. Lu, E.Y. Chuang, L.C. Chang, C.H. Chen, J.Y. Wu, M.T. Tsuang, W.J. Chen, “Genetic loci associated with an earlier age at onset in multiplex schizophrenia,” Scientific Reports, Jul. 2017
  13. G.L., M.H. Tsai, H.C. Lin, J.H. Hsiao, Y.C. Lee, T.P. Lu, J.M. Lee, C.P. Hsu, L.C. Lai, E.Y. Chuang*, “Identification of Methylation-Driven, Differentially Expressed STXBP6 as a Novel Biomarker in Lung Adenocarcinoma,” Scientific Reports, Feb. 2017
  14. Y.C. Chiu, L.J. Wang, T.P. Lu, T.H. Hsiao, E.Y. Chuang*, Y. Chen, “Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival,” BMC Bioinformatics, Feb. 2017
  15. Y.P. Lai, L.B. Wang, W.A. Wang, L.C. Lai, M.H. Tsai, T.P. Lu, E.Y. Chuang*, “iGC—an integrated analysis package of gene expression and copy number alteration,” BMC Bioinformatics, Jan. 2017
  16. C.Y. Shen, L.H. Chen, Y.F. Lin, L.C. Lai, E.Y. Chuang, M.H. Tsai, “Mitomycin C treatment induces resistance and enhanced migration via phosphorylated Akt in aggressive lung cancer cells,” Oncotarget, Nov. 2016
  17. Yu-Ching Hsu, Yu-Chiao Chiu, Wei-Yi Liu, Chia-Yang Cheng, Tzu-Hung Hsiao, Mong-Hsun Tsai, “A simple gene set-based analysis accurately predicts the synergy of drug pairs.,” BMC Systems Biology, Aug. 2016
  18. H.L. Wu, T.H. Hsiao, P.J. Chen, S.H. Wong, J.H. Kao, D.S. Chen, J.Y. Lu, T.P. Lu, Y. Chen, E.Y. Chuang, H.C. Tu, C.J. Liu, “Liver Gene Expression Profiles Correlate with Virus Infection and Response to Interferon Therapy in Chronic Hepatitis B Patients,” SCIENTIFIC REPORTS, Aug. 2016
  19. W.A. Wang, L.C. Lai, M.H. Tsai, T.P. Lu, E.Y. Chuang*, “Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs,” Oncotarget, May 2016
  20. Chi-Yun Wu, E.Y. Chuang*, Tzu-Pin Lu, “Low correlation of lncRNA and target gene expression in microarray data,” Transl Cancer Res, Apr. 2016
  21. Govinda Lenka, Mong-Hsun Tsai, Jen-Hao Hsiao, Liang-Chuan Lai, E.Y. Chuang, “Overexpression of methylation-driven DCC suppresses proliferation of lung cancer cells.,” Transl Cancer Res, Apr. 2016
  22. Yi-Hsuan Chang, Yu-Chiao Chiu1, Yu-Ching Hsu, Hui-Mei Tsai, E.Y. Chuang*, Tzu-Hung Hsiao, “Applying gene set analysis to characterize the activities of immune cells in estrogen receptor positive breast cancer.,” Transl Cancer Res, Apr. 2016
  23. Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, E.Y. Chuang, “Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs,” Oncotarget, Mar. 2016
  24. T.H. Hsiao, Y.C. Chiu, P.Y. Hsu, T.P. Lu, L.C. Lai, M.H. Tsai, T.H. Huang, E.Y. Chuang*, Y. Chen, “Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers,” Scientific Reports, Mar. 2016
  25. E.Y. Li, W.Y. Huang, Y.C. Chang, M.H. Tsai, E.Y. Chuang, Q.Y. Kuok, S.T. Bai, L.Y. Chao, Y.P. Sher, and L.C. Lai, “Aryl Hydrocarbon Receptor Activates NDRG1 Transcription under Hypoxia in Breast Cancer Cells.,” Sci Rep, Feb. 2016
  26. C.T. Tsai, C.S. Hsieh, S.N. Chang, E.Y. Chuang, K.C. Ueng, C.F. Tsai, T.H. Lin, C.K. Wu, J.K. Lee, L.Y. Lin, Y.C. Wang, C.C. Yu, L.P. Lai, C.D. Tseng, J.J. Hwang, F.T. Chiang, J.L. Lin, “Genome-wide screening identifies a KCNIP1 copy number variant as a genetic predictor for atrial fibrillation,” Nature Communications, Feb. 2016
  27. Chiu YC, Tsai MH, Chou WC, Liu YC, Kuo YY, Hou HA, Lu TP, Lai LC, Chen Y, Tien HF, Chuang EY*, “Prognostic significance of NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia.,” Leukemia, Feb. 2016
  28. Chuang MK, Chiu YC, Chou WC, Hou HA, Tseng MH, Kuo YY, Chen Y, Chuang EY*, Tien HF, “An mRNA Expression Signature for Prognostication in De Novo Acute Myeloid Leukemia Patients with Normal Karyotype.,” Oncotarget, Nov. 2015
  29. Woolston A, Sintupisut N, Lu TP, Lai LC, Tsai MH, Chuang EY, Yeang CH, “Putative effectors for prognosis in lung adenocarcinoma are ethnic and gender specific.,” Oncotarget, Jun. 2015
  30. Hsu, FM, Cheng, JCH, Chang, YL, Lee, JM , Koong, AC, Chuang, EY*, “Circulating mRNA Profiling in Esophageal Squamous Cell Carcinoma Identifies FAM84B As A Biomarker In Predicting Pathological Response to Neoadjuvant Chemoradiation.,” Sci Rep, 5:10291, May 2015
  31. Hsu YC, Chiu YC, Chen Y, Hsiao TH, Chuang EY*, “A gene-set approach to analyze copy number alterations in breast cancer.,” Translational Cancer Research, 4(3), 291-302, May 2015
  32. Lu TP, Hsiao CK, Lai LC, Tsai MH, Hsu CP, Lee JM, Chuang EY*, “Identification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma.,” BMC Res Notes, 8:92, Mar. 2015
  33. Chang YY, Kuo WH, Hung JH, Lee CY, Lee YH, Chang YC, Lin WC, Shen CY, Huang CS, Hsieh FJ, Lai LC, Tsai MH, Chang KJ, Chuang EY*, “Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing.,” Molecular Cancer, 14:36, Feb. 2015
  34. Chiu YC, Hsiao TH, Chen Y, Chuang EY*, “Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers.,” BMC Genomics, 16(Suppl 4), S1, Feb. 2015
  35. Tsai CT, Hsieh CS, Chang SN, Chuang EY, Juang JM, Lin LY, Lai LP, Hwang JJ, Chiang FT, Lin JL, “Next-generation sequencing of nine atrial fibrillation candidate genes identified novel de novo mutations in patients with extreme trait of atrial fibrillation.,” J Med Genet, 52(1), 28-36, Jan. 2015
  36. Chiu Y.C., Wu C.T., T.H. Hsiao, Y.P. Lai, C.K. Hsiao, Y. Chen, E.Y. Chuang*, “Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes.,” BMC Genomics, 16(Suppl 7), S19, 2015
  37. Chuang M, Chiu Y, Chou W, Hou H, Chuang EY, Tien H, “A 3-microRNA scoring system for prognostication in de novo acute myeloid leukemia patients.,” Leukemia, 29, 1051-1059, Dec. 2014
  38. Juang JM, Lu TP, Lai LC, Ho CC, Liu YB, Tsai CT, Lin LY, Yu CC, Chen WJ, Chiang FT, Yeh SF, Lai LP, Chuang EY, Lin JL, “Disease-targeted sequencing of ion channel genes identifies de novo mutations in patients with non-familial Brugada syndrome.,” Sci Rep, 4:6733, Oct. 2014
  39. Huang CC, Tu SH, Lien HH, Huang CS, Huang CJ, Lai LC, Tsai MH, Chuang EY*, “Refinement of breast cancer risk prediction with concordant leading edge subsets from prognostic gene signatures.,” Breast Cancer Res Tr, 147(2), 353-370, Sept. 2014
  40. Lu TP, Hsu YY, Lai LC, Tsai MH, Chuang EY*, “Identification of gene expression biomarkers for predicting radiation exposure.,” Sci Rep, 4:6293, Sept. 2014
  41. Luo EC, Chang YC, Sher YP, Huang WY, Chuang LL, Chiu YC, Tsai MH, Chuang EY, Lai LC, “MicroRNA-769-3p down-regulates NDRG1 and enhances apoptosis in MCF-7 cells during reoxygenation.,” Sci Rep, 4:5908, Aug. 2014
  42. Liu, C.-C., Wang, Y.-H., Chuang, E. Y., Tsai, M.-H., Chuang, Y.-H., Lin, C.-L., Liu, C.-J., Hsiao, B.-Y., Lin, S.-M., Liu, L.-Y. and Yu, M.-W, “Identification of a liver cirrhosis signature in plasma for predicting hepatocellular carcinoma risk in a population-based cohort of hepatitis B carriers.,” Mol. Carcinog, 53, 58-66, Aug. 2014
  43. Rosenstein BS, West CM, Bentzen SM, Alsner J, Andreassen CN, Azria D, Barnett GC, Baumann M, Burnet N, Chang-Claude J, Chuang EY, Coles CE, Dekker A, De Ruyck K, De Ruysscher D, Drumea K, Dunning AM, Easton D, Eeles R, Fachal L, Gutiérrez-Enríq, “Radiogenomics: radiobiology enters the era of big data and team science.,” Int J Radiat Oncol, 89(4), 709-713, Jul. 2014
  44. Yang YC, Wang DY, Cheng HF, Chuang EY, Tsai MH, “A reliable multiplex genotyping assay for HCV using a suspension bead array.,” Microb Biotechnol, 8(1), 93-102, Jul. 2014
  45. Wei SC, Tan YY, Weng MT, Lai LC, Hsiao JH, Chuang EY, Shun CT, Wu DC, Kao AW, Chuang CS, Ni YH, Shieh MJ, Tung CC, Chen Y, Wang CY, Xavier RJ, Podolsky DK, Wong JM, “SLCO3A1, a Novel Crohn's Disease-Associated Gene, Regulates NF-κB Activity and Associates with Intestinal Perforation.,” PLoS One, 9(6), e100515, Jun. 2014
  46. Sher YP, Wang LJ, Chuang LL, Tsai MH, Kuo TT, Huang CC, Chuang EY, Lai LC, “ADAM9 Up-Regulates N-Cadherin via miR-218 Suppression in Lung Adenocarcinoma Cells.,” PLoS One, 9(4, e94065, Apr. 2014
  47. Lai LC, Tsai MH, Chen PC, Chen LH, Hsiao JH, Chen SK, Lu TP, Lee JM, Hsu CP, Hsiao CK, Chuang EY*, “SNP rs10248565 in HDAC9 as a novel genomic aberration biomarker of lung adenocarcinoma in non-smoking women.,” J Biomed Sci, 21:24, Mar. 2014
  48. Lu TP, Chen KT, Tsai MH, Kuo KT, Hsiao CK, Lai LC, Chuang EY*, “Identification of genes with consistent methylation levels across different human tissues.,” Sci Rep, 4:4351, Mar. 2014
  49. Huang CC, Tu SH, Lien HH, Jeng JY, Liu JS, Huang CS, Lai LC, Chuang EY*, “Estrogen receptor status prediction by gene component regression: a comparative study.,” Int J Data Min Bioi, 9(2), 149-171, Feb. 2014
  50. Juang JM, Lu TP, Lai LC, Hsueh CH, Liu YB, Tsai CT, Lin LY, Yu CC, Hwang JJ, Chiang FT, Yeh SS, Chen WP, Chuang EY*, Lai LP, Lin JL, “Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome,” Sci Rep, 4:3850, Jan. 2014
  51. Lu TP, Chuang EY, Chen JJ, “Identification of reproducible gene expression signatures in lung adenocarcinoma.,” BMC Bioinformatic, 14:371, Dec. 2013
  52. Huang CC, Tu SH, Huang CS, Lien HH, Lai LC, Chuang EY*, “Multiclass prediction with partial least square regression for gene expression data: applications in breast cancer intrinsic taxonomy.,” Biomed Res Int, 2013:248648, Dec. 2013
  53. Huang CC, Tu SH, Lien HH, Jeng JY, Huang CS, Huang CJ, Lai LC, Chuang EY*, “Concurrent gene signatures for han chinese breast cancers.,” PLoS One, 8(10), e76421, Oct. 2013
  54. Lai TY, Wu SD, Tsai MH, Chuang EY, Chuang LL, Hsu LC, Lai LC, “Transcription of Tnfaip3 Is Regulated by NF-κB and p38 via C/EBPβ in Activated Macrophages.,” PLoS One, 8(9), e73153, Sept. 2013
  55. Wang IJ, Chen SL, Lu TP, Chuang EY, Chen PC, “Prenatal smoke exposure, DNA methylation, and childhood atopic dermatitis.,” Clin Exp Allergy, 43(5), 535-543, May 2013
  56. Liu YJ, Lin YF, Chen YF, Luo EC, Sher YP, Tsai MH, Chuang EY, Lai LC, “MicroRNA-449a enhances radiosensitivity in CL1-0 lung adenocarcinoma cells.,” PLoS One, 8(4), e62383, Apr. 2013
  57. Flores M, Hsiao TH, Chiu YC, Chuang EY, Huang Y, Chen Y, “Gene regulation, modulation, and their applications in gene expression data analysis.,” Adv Bioinformatics, 2013, 360678, Mar. 2013
  58. Huang CC, Jeng JY, Tu SH, Lien HH, Huang CS, Lai LC, Chuang EY*, “A preliminary study of concurrent gains and losses across gene expression profiles and comparative genomic hybridization in Taiwanese breast cancer patients.,” Transl Cancer Res, 2(1), 18-24, Feb. 2013
  59. Chi-Cheng Huang, Shin-Hsiu Tu, Eric Y. Chuang*, “Dissecting the Heterogeneity of Luminal Subtype Breast Cancer Using Gene Component Analysis.,” Journal of Medical Research and Development(JMRD), Vol. 2 Iss. 1, 21-27, Jan. 2013
  60. Chen PC, Lu TP, Chang JC, Lai LC, Tsai MH, Hsiao CK, Chuang EY*, “Concurrent analysis of copy number variation and gene expression: application in paired non- smoking female lung cancer patients.,” Int J Data Min Bioinform, 8(1), 92-104, 2013
  61. Huang CC, Tu SH, Lien HH, Jeng JY, Liu JS, Huang CS, Wu YY, Liu CY, Lai LC, Chuang EY*, “Prediction consistency and clinical presentations of breast cancer molecular subtypes for Han Chinese population.,” J Transl Med, 10 Suppl 1, S10, Sept. 2012
  62. Kuo, W.H., Y.Y. Chang, L.C. Lai, M.H. Tsai, C.K. Hsiao, K.J. Chang, and E.Y. Chuang*, “Molecular characteristics and metastasis predictor genes of triple-negative breast cancer: a clinical study of triple-negative breast carcinomas.,” PLoS One, 7(9), e45831, Sept. 2012
  63. Lu, T.P., C.Y. Lee, M.H. Tsai, Y.C. Chiu, C.K. Hsiao, L.C. Lai, and E.Y. Chuang*, “miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.,” PLoS One, 7(8), e42390, Aug. 2012
  64. Lin, S.Y., S.C. Hsieh, Y.C. Lin, C.N. Lee, M.H. Tsai, L.C. Lai, E.Y. Chuang, P.C. Chen, C.C. Hung, L.Y. Chen, W.S. Hsieh, D.M. Niu, Y.N. Su, and H.N. Ho, “A whole genome methylation analysis of systemic lupus erythematosus: hypomethylation of the IL10 and IL1R2 promoters is associated with disease activity.,” Genes Immun, 13(3), 214-220, Apr. 2012
  65. Chen, L.H., W.H. Kuo, M.H. Tsai, P.C. Chen, C.K. Hsiao, E.Y. Chuang, L.Y. Chang, F.J. Hsieh, L.C. Lai, and K.J. Chang, “Identification of prognostic genes for recurrent risk prediction in triple negative breast cancer patients in Taiwan.,” PLoS One, 6(11), e28222, Dec. 2011
  66. Hsu, F.H., H.I. Chen, M.H. Tsai, L.C. Lai, C.C. Huang, S.H. Tu, E.Y. Chuang*, and Y. Chen, “A model-based circular binary segmentation algorithm for the analysis of array CGH data.,” BMC Res Notes, 4(1), 394, Oct. 2011
  67. Chen, H., T.H. Chen, T.F. Tseng, J.T. Lu, C.C. Kuo, S.C. Fu, W.J. Lee, Y.F. Tsai, Y.Y. Huang, E.Y. Chuang, Y.J. Hwang, and C.K. Sun, “High-sensitivity in vivo THz transmission imaging of early human breast cancer in a subcutaneous xenograft mouse model.,” Opt Express, 19(22), 21552-21562, Oct. 2011
  68. Lai, L.C., Y.Y. Su, K.C. Chen, M.H. Tsai, Y.P. Sher, T.P. Lu, C.Y. Lee, and E.Y. Chuang*, “Down-Regulation of NDRG1 Promotes Migration of Cancer Cells during Reoxygenation.,” PLoS One, 6(8), e24375, Sept. 2011
  69. Lu, T.P., L.C. Lai, M.H. Tsai, P.C. Chen, C.P. Hsu, J.M. Lee, C.K. Hsiao, and E.Y. Chuang*, “Integrated analyses of copy number variations and gene expression in lung adenocarcinoma.,” PLoS One, 6(9), e24829, Sept. 2011
  70. Kuo, H.C., P.Y. Lin, T.C. Chung, C.M. Chao, L.C. Lai, M.H. Tsai, and E.Y. Chuang*, “DBCAT: database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells.,” J Comput Biol, 18(8), 1013-1017, Aug. 2011
  71. Chen, P.C., Y.C. Chen, L.C. Lai, M.H. Tsai, S.K. Chen, P.W. Yang, Y.C. Lee, C.K. Hsiao, J.M. Lee, and E.Y. Chuang*, “The Use of Germline Polymorphisms in Predicting Concurrent Chemoradiotherapy Response in Esophageal Cancer.,” Int J Radiat Oncol Biol Phys, 82(5), 1996-2003, May 2011
  72. Hsiao, T.H., C.H. Lin, T.T. Lee, J.Y. Cheng, P.K. Wei, E.Y. Chuang*, and K. Peck, “Verifying expressed transcript variants by detecting and assembling stretches of consecutive exons.,” Nucleic Acids Res, 38(20), e187, Nov. 2010
  73. Lu, T.P., M.H. Tsai, J.M. Lee, C.P. Hsu, P.C. Chen, C.W. Lin, J.Y. Shih, P.C. Yang, C.K. Hsiao, L.C. Lai, and E.Y. Chuang*, “Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women.,” Cancer Epidemiol Biomarkers Prev, 19(10), 2590-2597, Oct. 2010
  74. Lu, T.P., L.C. Lai, B.I. Lin, L.H. Chen, T.H. Hsiao, H.L. Liber, J.A. Cook, J.B. Mitchell, M.H. Tsai, and E.Y. Chuang*, “Distinct signaling pathways after higher or lower doses of radiation in three closely related human lymphoblast cell lines.,” Int J Radiat Oncol Biol Phys, 76(1), 212-219, Jan. 2010
  75. Kassis, J.N., V.M. Virador, E.A. Guancial, D. Kimm, A.S. Ho, M. Mishra, E.Y. Chuang, J. Cook, D. Gius, and E.C. Kohn, “Genomic and phenotypic analysis reveals a key role for CCN1 (CYR61) in BAG3-modulated adhesion and invasion.,” J Pathol, 218(4), 495-504, Aug. 2009
  76. Lin, Y.F., H. Nagasawa, Y. Peng, E.Y. Chuang, and J.S. Bedford, “Comparison of several radiation effects in human MCF10A mammary epithelial cells cultured as 2D monolayers or 3D acinar stuctures in matrigel.,” Radiat Res, 171(6), 708-715, Jun. 2009
  77. Chen, H.I., F.H. Hsu, Y. Jiang, M.H. Tsai, P.C. Yang, P.S. Meltzer, E.Y. Chuang*, and Y. Chen, “A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.,” Bioinformatics, 24(16), 1749-1756, Aug. 2008
  78. Guo, Z., M.H. Tsai, Y.H. Shiao, L.H. Chen, M.L. Wei, X. Lv, D. Gius, J.B. Little, J.B. Mitchell, and E.Y. Chuang*, “DNA (cytosine-5)-methyltransferase 1 as a mediator of mutant p53-determined p16(ink4A) down-regulation.,” J Biomed Sci, 15(2), 163-168, Mar. 2008
  79. Gius, D., M.C. Funk, E.Y. Chuang, S. Feng, P.C. Huettner, L. Nguyen, C.M. Bradbury, M. Mishra, S. Gao, B.M. Buttin, D.E. Cohn, M.A. Powell, N.S. Horowitz, B.P. Whitcomb, and J.S. Rader, “Profiling microdissected epithelium and stroma to model genomic signatures for cervical carcinogenesis accommodating for covariates.,” Cancer Res, 67(15), 7113-7123, Aug. 2007
  80. Lin, Y.F., C.Y. Chen, M.H. Tsai, M.S. Wu, Y.C. Wang, E.Y. Chuang, J.T. Lin, P.C. Yang, and L.P. Chow, “Duodenal ulcer-related antigens from Helicobacter pylori: immunoproteome and protein microarray approaches.,” Mol Cell Proteomics, 6(6), 1018-1026, Jun. 2007
  81. Tsai, M.H., J.A. Cook, G.V. Chandramouli, W. DeGraff, H. Yan, S. Zhao, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Gene expression profiling of breast, prostate, and glioma cells following single versus fractionated doses of radiation.,” Cancer Res, 67(8), 3845-3852, Apr. 2007
  82. Cook, J.A., E.Y. Chuang, M.H. Tsai, D. Coffin, W. Degraff, A.L. Sowers, and J.B. Mitchell, “Radiation-induced changes in gene-expression profiles for the SCC VII tumor cells grown in vitro and in vivo.,” Antioxid Redox Signal, 8(7-8), 1263-1272, Aug. 2006
  83. Zhao, W., E.Y. Chuang, M. Mishra, R. Awwad, K. Bisht, L. Sun, P. Nguyen, J.D. Pennington, T.J. Wang, C.M. Bradbury, L. Huang, Z. Chen, G. Bar-Sela, M.E. Robbins, and D. Gius, “Distinct effects of ionizing radiation on in vivo murine kidney and brain normal tissue gene expression.,” Clin Cancer Res, 12(12), 3823-3830, Jun. 2006
  84. Chuang, E.Y., X. Chen, M.H. Tsai, H. Yan, C.Y. Li, J.B. Mitchell, H. Nagasawa, P.F. Wilson, Y. Peng, M.M. Fitzek, J.S. Bedford, and J.B. Little, “Abnormal gene expression profiles in unaffected parents of patients with hereditary-type retinoblastoma.,” Cancer Res, 66(7), 3428-3433, Apr. 2006
  85. Tsai, M.H., X. Chen, G.V. Chandramouli, Y. Chen, H. Yan, S. Zhao, P. Keng, H.L. Liber, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Transcriptional responses to ionizing radiation reveal that p53R2 protects against radiation-induced mutagenesis in human lymphoblastoid cells.,” Oncogene, 25(4), 622-632, Jan. 2006
  86. Stuart, J.R., H. Kawai, K.K. Tsai, E.Y. Chuang, and Z.M. Yuan, “c-Abl regulates early growth response protein (EGR1) in response to oxidative stress.,” Oncogene, 24(55), 8085-8092, Dec. 2005
  87. Jazaeri, A.A., C.S. Awtrey, G.V. Chandramouli, Y.E. Chuang, J. Khan, C. Sotiriou, O. Aprelikova, C.J. Yee, K.K. Zorn, M.J. Birrer, J.C. Barrett, and J. Boyd, “Gene expression profiles associated with response to chemotherapy in epithelial ovarian cancers.,” Clin Cancer Res, 11(17), 6300-6310, Sept. 2005
  88. Tsai, K.K., E.Y. Chuang, J.B. Little, and Z.M. Yuan, “Cellular mechanisms for low-dose ionizing radiation-induced perturbation of the breast tissue microenvironment.,” Cancer Res, 65(15), 6734-6744, Aug. 2005
  89. Tsai, M.H., H. Yan, X. Chen, G.V. Chandramouli, S. Zhao, D. Coffin, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays.,” Mol Biotechnol, 29(3), 221-224, Mar. 2005
  90. Samuni, A.M., U. Kasid, E.Y. Chuang, S. Suy, W. Degraff, M.C. Krishna, A. Russo, and J.B. Mitchell, “Effects of hypoxia on radiation-responsive stress-activated protein kinase, p53, and caspase 3 signals in TK6 human lymphoblastoid cells.,” Cancer Res, 65(2), 579-586, Jan. 2005
  91. Lu, M., J. Suen, C. Frias, R. Pfeiffer, M.H. Tsai, E. Chuang, and S.L. Zeichner, “Dissection of the Kaposi's sarcoma-associated herpesvirus gene expression program by using the viral DNA replication inhibitor cidofovir.,” Virol, 78(24), 13637-13652, Dec. 2004
  92. Dodd, L.E., E.L. Korn, L.M. McShane, G.V. Chandramouli, and E.Y. Chuang, “Correcting log ratios for signal saturation in cDNA microarrays.,” Bioinformatics, 20(16), 2685-2693, Nov. 2004
  93. Gius, D., H. Cui, C.M. Bradbury, J. Cook, D.K. Smart, S. Zhao, L. Young, S.A. Brandenburg, Y. Hu, K.S. Bisht, A.S. Ho, D. Mattson, L. Sun, P.J. Munson, E.Y. Chuang, J.B. Mitchell, and A.P. Feinberg, “Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach.,” Cancer Cell, 6(4), 361-371, Oct. 2004
  94. Rosenwald, A., E.Y. Chuang, R.E. Davis, A. Wiestner, A.A. Alizadeh, D.C. Arthur, J.B. Mitchell, G.E. Marti, D.H. Fowler, W.H. Wilson, and L.M. Staudt, “Fludarabine treatment of patients with chronic lymphocytic leukemia induces a p53-dependent gene expression response.,” Blood, 104(5), 1428-1434, Sept. 2004
  95. Loercher, A., T.L. Lee, J.L. Ricker, A. Howard, J. Geoghegen, Z. Chen, J.B. Sunwoo, R. Sitcheran, E.Y. Chuang, J.B. Mitchell, A.S. Baldwin, Jr., and C. Van Waes, “Nuclear factor-kappaB is an important modulator of the altered gene expression profile and malignant phenotype in squamous cell carcinoma.,” Cancer Res, 64(18), 6511-6523, Sept. 2004
  96. Lu, X., W.E. Burgan, M.A. Cerra, E.Y. Chuang, M.H. Tsai, P.J. Tofilon, and K. Camphausen, “ranscriptional signature of flavopiridol-induced tumor cell death.,” Mol Cancer Ther, 3(7), 861-872, Jul. 2004
  97. Goley, E.M., S.J. Anderson, C. Menard, E. Chuang, X. Lu, P.J. Tofilon, and K. Camphausen, “Microarray analysis in clinical oncology: pre-clinical optimization using needle core biopsies from xenograft tumors.,” BMC Cancer, 4, 20, May 2004
  98. Ge, H., Y.Y. Chuang, S. Zhao, M. Tong, M.H. Tsai, J.J. Temenak, A.L. Richards, and W.M. Ching, “Comparative genomics of Rickettsia prowazekii Madrid E and Breinl strains.,” J Bacteriol, 186(2), 556-565, Jan. 2004
  99. Su, H., N. Hu, J. Shih, Y. Hu, Q.H. Wang, E.Y. Chuang, M.J. Roth, C. Wang, A.M. Goldstein, T. Ding, S.M. Dawsey, C. Giffen, M.R. Emmert-Buck, and P.R. Taylor, “Gene expression analysis of esophageal squamous cell carcinoma reveals consistent molecular profiles related to a family history of upper gastrointestinal cancer.,” Cancer Res, 63(14), 3872-3876, Jul. 2003
  100. Ge, H., Y.Y. Chuang, S. Zhao, J.J. Temenak, and W.M. Ching, “Genomic studies of Rickettsia prowazekii virulent and avirulent strains.,” Ann N Y Acad Sci, 990, 671-677, Jun. 2003
  101. Samuni, A.M., E.Y. Chuang, M.C. Krishna, W. Stein, W. DeGraff, A. Russo, and J.B. Mitchell, “Semiquinone radical intermediate in catecholic estrogen-mediated cytotoxicity and mutagenesis: chemoprevention strategies with antioxidants.,” Proc Natl Acad Sci U S A, 100(9), 5390-5395, Apr. 2003
  102. Chuang, Y.Y., Y. Chen, Gadisetti, V.R. Chandramouli, J.A. Cook, D. Coffin, M.H. Tsai, W. DeGraff, H. Yan, S. Zhao, A. Russo, E.T. Liu, and J.B. Mitchell, “Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells.,” Cancer Res, 62(21), 6246-6254, Nov. 2002
  103. Chuang, Y.Y., Q. Chen, J.P. Brown, J.M. Sedivy, and H.L. Liber, “Radiation-induced mutations at the autosomal thymidine kinase locus are not elevated in p53-null cells.,” Cancer Res, 59(13), 3073-3076, Jul. 1999
  104. Y.Y. Chuang, Q.C.a.H.L.L., “The construction of a p53-null cell line from human lymphoblast cells for mutagenesis studies.,” Environ. Mol. Mutagen, 31(Suppl. 29), 65, 1998
  105. Y.C. and H.L. Liber, “Mutational spectra at the thymidine kinase locus of spontaneously-arising and mitomycin C (MMC)-induced mutants in two closely related human lymphoblast cell lines.,” Environ. Mol. Mutagen, 29(Suppl. 28), 9, 1997
  106. Chuang, Y.Y. and H.L. Liber, “Effects of cell cycle position on ionizing radiation mutagenesis. I. Quantitative assays of two genetic loci in a human lymphoblastoid cell line.,” Radiat Res, 146(5), 494-500, Nov. 1996
  107. Y.Y. Chuang, W.C.C.a.H.L.L., “A DNA cross-linking agent (MMC) induces systematic differences in toxicity and mutagenicity in two closely related human lymphoblast cell lines.,” Environ. Mol. Mutagen, 27(Suppl. 27), 13, 1996
  108. Liu, S.C., B. Ogretmen, Y.Y. Chuang, and B.C. Stark, “Selection and characterization of alpha-amylase-overproducing recombinant Escherichia coli containing the bacterial hemoglobin gene.,” Appl Microbiol Biotechnol, 38(2), 239-242, Nov. 1992

Conference & proceeding papers:

  1. Wu CT, Tsai MH, Lu TP, Lai LC, Chuang EY, “Performances evaluation of algorithms for identifying differently expressed genes in RNA-seq data.,” 2015 AACR annual meeting, Abstract 2123, Philadelphia, PA, USA, Apr. 2015
  2. Wang WA, Lai LC, Tsai MH, Lu TP, Chuang EY, “Survival prediction model with long non-coding RNA profile in lung adenocarcinoma cancer.,” 2015 AACR annual meeting, Abstract 419, Philadeplhia, PA, USA, Apr. 2015
  3. Hsu YC, Chiu YC, Chen Y, Chuang EY, and Hsiao TH, “A gene set approach to analyze copy number alterations profiles of breast cancer.,” International Conference on Intelligent Biology and Medicine (ICIBM2014), San Antonio, TX, USA, Dec. 2014
  4. Chiu YC, Wu CT, Hsiao TH , Lai YP , Hsiao CK, Yidong Chen Y, Chuang EY, “Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes.,” International Conference on Intelligent Biology and Medicine (ICIBM2014), San Antonio, TX, USA, Dec. 2014
  5. Chuang MK, Chiu YC, Chou WC, Hou HA, Chuang EY, Tien HF, “A Simple, Powerful, and Widely Applicable Micro-RNA Scoring System in Prognostication of De Novo Myeloid Leukemia Patients.,” 56th ASH® Annual Meeting and Exposition, 71, San Francisco, CA, USA, Dec. 2014
  6. Lai LC, Sher YP, Wang LJ, Tsai MH, Kuo TT, Chuang EY, “ADAM9 up-regulates N-Cadherin via miR-218 suppression in lung adenocarcinoma cells.,” Human Genome Meeting 2014, 204-204, Geneva, Switzerland, Apr. 2014
  7. Tsai MH*, Chou WC, Chiu YC, Tien HF, Chuang EY, “Investigation of Dynamic Cross-talk between miRNA and mRNA in Acute Myeloid Leukemia.,” Human Genome Meeting 2014, 128, Geneva, Switzerland, Apr. 2014
  8. Chiu YC, Chuang EY, Hsiao TH, Chen Y, “Modeling competing endogenous RNA regulatory networks in glioblastoma multiforme.,” 2013 IEEE International Conference on Bioinformatics and Biomedicine, 201-204, Shanghai, China, Dec. 2013
  9. Chiu YC, Chuang EY*, Hsiao TH, Chen Y, “Characterization of conditions for competing endogenous RNA regulation in GBM. ” Oral presentation at 2013 IEEE International Workshop on Genomic Signal Processing and Statistics.,” 2013 IEEE Internatioal Workshop on Genomic Signal Processing and Statistics, 23, Houston, USA, Nov. 2013
  10. Liu YJ, Lin YF, Chen YF, Luo EC, Sher YP, Tsai MH, Chuang EY, and Liang LC, “MicroRNA-449a enhances radiosensitivity in lung adenocarcinoma cells.,” AACR 104th Annual Meeting 2013, Abstract 4166, Washington, DC, USA, Apr. 2013
  11. Lu TP, Chuang EY, Chen JJ, “Identification of universal survival predictors in lung adenocarcinoma.,” 2013 AACR annual meeting, Abstract 4028, Washington D.C., USA, Apr. 2013
  12. Chen YH, Hsiao TH, Chen HIH, Chen Y, Chuang EY, “An integrative analysis to identify putative drugs for acute myeloid leukemia.,” 2013 AACR annual meeting, Abstract 2904, Washington D.C., USA, Apr. 2013
  13. Chiu YC, Hsiao TH, Gu F, Chen Y, Huang THM, Chuang EY*, “Identification of estrogen receptor modulated gene methylation network in breast cancer.,” 2013 AACR annual meeting, Abstract 2889, Washington D.C., USA, Apr. 2013
  14. Lee CY, Wang LB, Tsai MH, Lai LC, Chuang EY, “Identification of novel miRNAs in breast data of the next generation sequencing using miRDeep2 and Galaxy.,” 2013 AACR annual meeting, Abstract 2903, Washington D.C., USA, Apr. 2013
  15. Eric Y. Chuang, “Combination of Genomic Technologies and Bioinformatics for Exploring New Cancer Biomarkers” , Princeton, NJ, 2012,” EITA 2012-BIO, Princeton, NJ, Oct. 2012
  16. Shen CY, Li YH, Lu TP, Lai LC, Chuang EY, Tsai MH, “Semaphorin 6A inhibits the cell migration in lung adenocarcinoma cells.,” 2011 AACR annual meeting, Abstract 1444, Orlando, Florida, USA, Apr. 2011
  17. Eric Y. Chuang, “Radiogenomics: An Emerging Field for Personalized Radiation Therapy.,” 2011 International Symposium on Radiation Medicine: The Future Research and Development of Radiation Medicine, Taipei, Taiwan, 2011
  18. Liu YC, Lu TP, Hsaio TH, Lu JY,Hsu FM, Cheng JCH, Yang PC, Lai LC, Chuang EY, Tsai MH, “Differential cytokine-related signaling pathways responded to ionizing radiation in two lung adenocarcinoma cell lines.,” 2010 AACR annual meeting, Abstract1326, Washington D.C.,USA, Apr. 2010
  19. Eric Y. Chuang, “Microarray Gene Expression Data Analysis in Cancer Research,” The 28th World Congress of Internal Medicine, Taipei, Taiwan, 2006
  20. M.H. Tsai, X. Chen, G.V.R. Chandramouli, Y. Chen, H. Yan, S. Zhao, H.L. Liber, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang, “Gene Expression Profiles Following Radiation in Different p53 status Human Lymphoblast Cell Lines Revealed p53R2 Protein Plays a Role in Radiation-Induced Mutagenesis.,” 34th Annual Meeting of the European Environmental Mutagen Society, Maastricht, the Netherlands, 2004

Books:

  1. 莊曜宇,王志軒, “別瞎忙了!健康的關鍵就在腸道菌,” AME publishing company, Hong Kong, 2017, ISBN:978-988-77840-4-3
  2. Jie He, Rafael Rosell, Eric Y. Chuang, “Lung Cancer Precision Medicine,” AME Publishing Company, Hong Kong, 2016, ISBN:978-988-14028-1-3 Hardback
  3. Huang Giap, Eric Y Chuang, Gary Y Yang, “Particle Beam Therapy: contemporary trends and reviews,” AME Publishing Company, Hong Kong, 291 pages, 2014, ISBN:978-988-12997-4-1
  4. 熊映美、莊曜宇, “金屬奈米微粒暴露與勞工過敏發炎指標分析研究,” 行政院勞委會勞工安全研究所, 臺灣, 57 pages, Mar. 2008
  5. 熊映美、莊曜宇、蔡孟勳, “極細微粒二氧化鈦之細胞毒性與基因毒性之探討,” 行政院勞委會勞工安全研究所, 臺灣, 67 pages, Mar. 2006, ISBN:9789860048872

Patents:

  1. 劉韋驛、邱育賢、徐仁徽、謝嘉珊、蔡孟勳、盧子彬、賴亮全、莊曜宇、蕭暉議, “藥物組合療效預測篩選系統與方法,” 中華民國第I622012號, Apr. 2018
  2. 鄭佳揚、徐仁徽、劉韋驛、蔡孟勳、盧子彬、賴亮全、莊曜宇, “用以分析細菌菌種之定序資料的系統及其方法,” 中華民國第I582631號, May 2017
  3. 鄭少樺、邱育賢、莊曜宇、盧子彬、董恆元, “次世代定序分析系統及其次世代定序分析方法,” 中華民國第I571763號, Feb. 2017
  4. 周文堅、田蕙芬、莊曜宇、邱鈺喬、莊名凱, “利用三個微小核糖核酸之評分系統以預測急性骨髓性白血病之預後,” 中華民國第I531655號, May 2016
  5. 陳佩君、 程蘊菁、 賴亮全、 蔡孟勳、 陳星光、 楊珮雯、 李章銘、 莊曜宇、 蕭朱杏, “預測食道癌病患對於化學暨放射線療法之反應的方法及套組,” 中華民國第I380018號, Dec. 2012
  6. Chen, Pei-Chun; Chen, Yen-Ching; Lai, Liang-Chuan; Tsai, Mong-Hsun; Chen, Shin-Kuang; Yang, Pei-Wen; Lee, Jang-Ming; Chuang, Eric Y; Hsiao, Chuhsing K, “Biomarkers for predicting response of esophageal cancer patient to chemoradio therapy,” USA US 8,268,562 B2, Sept. 2012