Major Research Areas

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Research Summary

    Eric Y Chuang (莊曜宇), ScD, EMBA

    Eric Y Chuang received his doctorate in cancer biology with toxicology and molecular genetics as two sub-specialties from Harvard University in 1997 and his doctoral thesis was to study radiation-induced mutagenesis in human cells. After graduation, he stayed at Harvard as a postdoctoral fellow for one year. He then joined the Radiation Biology Branch of National Cancer Institute (NCI), National Institutes of Health (NIH) as an IRTA fellow to study radiogenomics in Bethesda, MD, USA. Next, he became the Head of Microarray Laboratory for Radiation Oncology Sciences Program at NCI; his lab was to develop new initiatives that utilized state-of-the-art microarray technologies for studying radiation oncology related research projects. After working at the NIH for several years, he took a faculty position at National Taiwan University (NTU). In 2009, he joined the Radiation Research Program of Division of Cancer Treatment and Diagnosis at NCI as a Program Director to oversee a portfolio of NIH grants that included radiation-induced signaling pathways, molecular mechanisms and normal tissue injuries as well as radiation related genomic studies. In 2011, he returned to NTU and was serving as the Director of Graduate Institute of Biomedical Electronics and Bioinformatics (BEBI) in 2012-2018. Dr. Chuang received his Executive MBA degree in International Business Management from NTU in June 2017. Currently, he is a Professor of BEBI at NTU and serving as the VP & General Director, Biomedical Technology and Device Research Laboratories(BDL), Industrial Technology Research Institute(ITRI), Hsinchu, Taiwan. Being an expert in genomic technologies, bioinformatics, cancer, radiation biology & oncology, biomedical engineering, and precision medicine, he has published more than 168 peer-reviewed papers in related fields. Moreover, Dr. Chuang has been serving as an editorial board member of Scientific Reports and the Editor-in-Chief of Translation Cancer Research.

    Current Research Interests: Radiogenomics, Radiation-induced signaling pathways, Cancer genomics, Bioinformatics, Precision medicine, and Artificial intelligence(AI).

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Journal articles & book chapters

1. Z.Q. Hu, Y.M. Hung, L.H. Chen, L.C. Lai, M.H. Pang, Eric Y. Chuang, M.H. Tsai, “NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition” , IEEE/ACM Transactions on Computational Biology and Bioinformatics , Vol. 21 , 254-264, Mar. 2024

2. Kevin C.Y. Huang, T.W. Ke, C.Y. Lai, W.Z. Hong, H.Y. Chang, C.Y. Lee, C.H. Wu, S.F. Chiang, J.A. Liang, J.Y. Chen, P.C. Yang, William T.L. Chen, Eric Y. Chuang, K.S. Clifford Chao, “Inhibition of DNMTs increases neoantigen-reactive T-cell toxicity against microsatellite-stable colorectal cancer in combination with radiotherapy” , Biomedicine & Pharmacotherapy , Vol. 177 , 116958-undefined, Aug. 2024

3. C.H. Sally Chen, T.H. Yuan, T.P. Lu, H.Y. Lee, Y.H. Chen, L.C. Lai, M.H. Tsai, Eric Y. Chuang*, C.C. Chan, “Exposure-associated DNA methylation among people exposed to multiple industrial pollutants” , Clinical Epigenetics , Vol. 16 , Aug. 2024

4. H.L. Chen, H.Y. Chiang, D. R. Chang, C.F. Cheng, C. C.N. Wang, T.P. Lu, C.Y. Lee, A. Chattopadhyay, Y.T. Lin, C.C. Lin, P.T. Yu, C.F. Huang, C.H. Lin, H.C. Yeh, I.W. Ting, H.K. Tsai, Eric Y. Chuang, A. Tin, F.J. Tsai, C.C. Kuo, “Discovery and prioritization of genetic determinants of kidney function in 297,355 individuals from Taiwan and Japan” , Nature Communications , Vol. 15 , Sep. 2024

5. P.S. Huang, J.F. Cheng, G.W. Li, Eric Y. Chuang, J.J. Chen, F.C. Chiu, C.K. Wu, Y.C. Wang, J.J. Hwang, C.T. Tsai, “Copy number variation of gasdermin D gene is associated with atrial fibrillation-related thromboembolic stroke” , Europace , Vol. 25 , May 2023

6. Chattopadhyay,Lee,Shen,Lu,Hsiao,Lin,Lai,Tsai,Lu,Chuang, “Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data” , Journal of Biomedical Informatics , Vol. 143 , 104423-undefined, Jul. 2023

7. Watson H.S. Tseng, A. Chattopadhyay, N.N. Phan, Eric Y. Chuang, Oscar K. Lee, “Utilizing multimodal approach to identify candidate pathways and biomarkers and predicting frailty syndrome in individuals from UK Biobank” , GeroScience , Vol. 46 , 1211-1228, Jul. 2023

8. W.N. Lyu, M.C. Lin, C.Y. Shen, L.H. Chen, Y.H. Lee, S.K. Chen, L.C. Lai, Eric Y. Chuang, P.J. Lou, M.H. Tsai, “An Oral Microbial Biomarker for Early Detection of Recurrence of Oral Squamous Cell Carcinoma” , ACS Infectious Diseases , Vol. 9 , 1783-1792, Aug. 2023

9. Y.C. Hsu, H.L. Chen, C.F. Cheng, A. Chattopadhyay, P.S. Chen, C.C. Lin, H.Y. Chiang, T.Y. Liu, C.H. Huang, C.C. Kuo, Eric Y. Chuang, T.P. Lu, F.J. Tsai, “The largest genome-wide association study for breast cancer in Taiwanese Han population” , Breast Cancer Research and Treatment , Vol. 203 , 291-306, Oct. 2023

10. Chattopadhyay,Lee,Lee,Liu,Chen,Li,Lai,Tsai,Ni,Chiu,Lu,Chuang, “Twnbiome: a public database of the healthy Taiwanese gut microbiome” , BMC Bioinformatics , Vol. 24 , Dec. 2023

11. C.Y. Lin, W.T. Tseng, Y.Y. Chang, M.H. Tsai, Eric Y. Chuang, T.P. Lu, L.C. Lai, “Lidocaine and Bupivacaine Downregulate MYB and DANCR lncRNA by Upregulating miR-187-5p in MCF-7 Cells” , Frontiers in Medicine , Vol. 8 , Jan. 2022

12. U.N. Wisesty, A. Purwarianti, A. Pancoro, A. Chattopadhyay, N.N. Phan, Eric Y. Chuang, T.R. Mengko, “Join Classifier of Type and Index Mutation on Lung Cancer DNA Using Sequential Labeling Model” , IEEE Access , Vol. 10 , 9004-9021, Jan. 2022

13. M.Z. Chen, L.Y. Su, P.H. Ko, M.H. Hsu, L.L. Chuang, L.H. Chen, T.P. Lu, Eric Y. Chuang, L.P. Chow, M.H. Tsai, H.H. Hsu, L.C. Lai, “Extracellular domain of semaphorin 5A serves a tumor‑suppressing role by activating interferon signaling pathways in lung adenocarcinoma cells” , International Journal of Oncology , Vol. 60 , Feb. 2022

14. P.S. Huang, Y.H. Tseng, C.F. Tsai, J.J. Chen, S.C. Yang, F.C. Chiu, Z.W. Chen, J.J. Hwang , Eric Y. Chuang*, Y.C. Wang, C.T. Tsai, “An Artificial Intelligence-Enabled ECG Algorithm for the Prediction and Localization of Angiography-Proven Coronary Artery Disease” , Biomedicines , Vol. 10 , 394-undefined, Feb. 2022

15. Chiu,Tsai,Huang,Shih,Tsai,Hwang,Wang,Chuang,Tsai,Chang, “The Gut Microbiome, Seleno-Compounds, and Acute Myocardial Infarction” , Journal of Clinical Medicine , Vol. 11 , 1462-undefined, Mar. 2022

16. S. Shivani, C.Y. Kao, A. Chattopadhyay, J.W. Chen, L.C. Lai, W.H. Lin, T.P. Lu I.H. Huang, M.H. Tsai, C.H. Teng, J.J. Wu, Y.H. Hsieh, M.C. Wang, Eric Y. Chuang, “Uremic Toxin-Producing Bacteroides Species Prevail in the Gut Microbiota of Taiwanese CKD Patients: An Analysis Using the New Taiwan Microbiome Baseline” , Frontiers in Cellular and Infection Microbiology , Vol. 12 , Apr. 2022

17. Y.M. Hung, W.N. Lyu, M.L. Tsai, C. Liu, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “To compare the performance of prokaryotic taxonomy classifiers using curated 16S full-length rRNA sequences” , Computers in Biology and Medicine , Vol. 145 , 105416-undefined, Jun. 2022

18. Daniel T.L Chen, S.W. Cheng, Tiffany Chen, Jane P.C. Chang, B.F. Hwang, H.H. Chang, Eric Y. Chuang, C.H. Chen, K.P. Su, “Identification of Genetic Variations in the NAD-Related Pathways for Patients with Major Depressive Disorder: A Case-Control Study in Taiwan” , Journal of Clinical Medicine , Vol. 11 , 3622-undefined, Jun. 2022

19. Y.P. Hsieh, Y.M. Hung, M.H. Tsai, L.C. Lai, Eric Y. Chuang, “16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences” , Frontiers in Bioinformatics , Vol. 2 , Aug. 2022

20. H.H. Chao, J.L. Luo, M.H. Hsu, L.H. Chen, T.P. Lu, M.H. Tsai, Eric Y. Chuang, L.L. Chuang, L.C. Lai, “Regulatory mechanisms and function of hypoxia-induced long noncoding RNA NDRG1-OT1 in breast cancer cells” , Cell Death & Disease , Vol. 13 , Sep. 2022

21. C.S. Huang, M.L. Tsai, T.P. Lu, C.C. Tu, C.Y. Liu, C.J. Huang, Y.S. Ho, S.H. Tu, Eric Y Chuang, L.M. Tseng, C.C. Huang, “The extended concurrent genes signature for disease-free survival in breast cancer” , Journal of the Formosan Medical Association , Vol. 121 , 1945-1955, Oct. 2022

22. A. Chattopadhyay, C.Y. Shih, Y.C. Hsu, J.M. Jimmy Juang, Eric Y. Chuang, T.P. Lu, “CLIN_SKAT: an R package to conduct association analysis using functionally relevant variants” , BMC Bioinformatics , Vol. 23 , Oct. 2022

23. P.W. Yang, M.C. Lin, P.M. Huang, C.P. Wang, T.C. Chen, C.N. Chen, M.H. Tsai, Jason C.H. Cheng, Eric Y. Chuang, M.S. Hsieh, P.J. Lou, J.M. Lee, “Risk Factors and Genetic Biomarkers of Multiple Primary Cancers in Esophageal Cancer Patients” , Frontiers in Oncology , Vol. 10 , Jan. 2021

24. H.C. Chan, A. Chattopadhyay, Eric Y. Chuang, T.P. Lu, “Development of a Gene-Based Prediction Model for Recurrence of Colorectal Cancer Using an Ensemble Learning Algorithm” , Frontiers in Oncology , Vol. 11 , Feb. 2021

25. S. Shivani, A. Chattopadhyay, Eric Y. Chuang, “Targeting the gut microbiome for non-communicable diseases: present and future” , Annals of Translational Medicine , Vol. 9 , 361-361, Mar. 2021

26. C.H. Wu, H.T. Yeh, C.S. Hsieh, C.C. Huang, A. Chattopadhyay, Y.C. Chung, S.H. Tu, Y.H. Li, T.P. Lu, L.C. Lai, M.F. Hou, K.J. Chang, M.H. Tsai, Eric Y. Chuang, “Evolutionary Trajectories and Genomic Divergence in Localized Breast Cancers after Ipsilateral Breast Tumor Recurrence” , Cancers , Vol. 13 , 1821-undefined, Apr. 2021

27. Y.W. Hsiao, C.L. Tao, Eric Y. Chuang, T.P. Lu, “A risk prediction model of gene signatures in ovarian cancer through bagging of GA-XGBoost models” , Journal of Advanced Research , Vol. 30 , 113-122, May 2021

28. J.M. Jimmy Juang, T.P. Lu, M.W. Su, C.W. Lin, J.H. Yang, H.W. Chu, C.H. Chen, Y.W. Hsiao, C.Y. Lee, L.M. Chiang, Q.Y. Yu, C.H. Kate Hsiao, C.Y. Julius Chen, P.E. Wu, C.H. Pai, Eric Y. Chuang*, C.Y. Shen, “Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine” , Journal of Advanced Research , Vol. 30 , 147-158, May 2021

29. C.H. Shih, L.L. Chuang, M.H. Tsai, L.H. Chen, Eric Y. Chuang, T.P. Lu, and L.C. Lai, “Hypoxia-Induced MALAT1 Promotes the Proliferation and Migration of Breast Cancer Cells by Sponging MiR-3064-5p” , Frontiers in Oncology , Vol. 11 , 147-158, May 2021

30. Y.M. Hung, M.H. Tsai, L.C. Lai, Eric Y. Chuang, “ATTRACTIVE – An Auto-Updating Database for Experimental Protocols in Regenerative Medicine” , IEEE Access , Vol. 9 , 75202-75210, May 2021

31. Y.C. Cheng, L.Y. Su, L.H. Chen, T.P. Lu, Eric Y. Chuang, M.H. Tsai, L.L. Chuang, L.C. Lai, “Regulatory Mechanisms and Functional Roles of Hypoxia-Induced Long Non-Coding RNA MTORT1 in Breast Cancer Cells” , Frontiers in Oncology , Vol. 11 , Jun. 2021

32. C. Goswami, A. Chattopadhyay, Eric Y. Chuang, “Rare variants: data types and analysis strategies” , Annals of Translational Medicine , Vol. 9 , 961-961, Jun. 2021

33. C.H. Lin, Ruby Y.J. Huang, T.P. Lu, K.T. Kuo, K.Y. Lo, C.H. Chen, IC. Chen, Y.S. Lu, Eric Y. Chuang, J. P. Thiery, C.S. Huang, A.L. Cheng, “High prevalence of APOA1/C3/A4/A5 alterations in luminal breast cancers among young women in East Asia” , npj Breast Cancer , Vol. 7 , Jul. 2021

34. A. Chattopadhyay, Z.H. Teoh, C.Y. Wu , J.M. J. Juang, L.C. Lai, M.H. Tsai, C.H. Wu, T.P. Lu, Eric Y. Chuang, “CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer” , Database , Vol. 2021 , Jul. 2021

35. Y.M. Hung, T.P. Lu, M.H. Tsai, L.C. Lai, Eric Y. Chuang, “EasyMAP: A user-friendly online platform for analyzing 16S ribosomal DNA sequencing data” , New Biotechnology , Vol. 63 , 37-44, Jul. 2021

36. C.H. Wu, C.S. Hsieh, Y.C. Chang, C.C. Huang, H.T. Yeh, M.F. Hou, Y.C. Chung, S.H. Tu, K.J. Chang, A. Chattopadhyay, L.C. Lai, T.P. Lu, Y.H. Li, M.H. Tsai, Eric Y. Chuang, “Differential whole-genome doubling and homologous recombination deficiencies across breast cancer subtypes from the Taiwanese population” , Communications Biology , Vol. 4 , Sep. 2021

37. N.N. Phan, C.Y. Hsu, C.C. Huang, L.M. Tseng, Eric Y. Chuang, “Prediction of Breast Cancer Recurrence Using a Deep Convolutional Neural Network Without Region-of-Interest Labeling” , Frontiers in Oncology , Vol. 11 , Oct. 2021

38. N.N. Phan, A. Chattopadhyay, T.T. Lee, H,I Yin, T.P. Lu, L.C. Lai, H.L. Hwa, M.H. Tsai, Eric Y Chuang, “High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data” , Briefings in Bioinformatics , Vol. 22 , Nov. 2021

39. W.T. Fang, C.H. Wu, Q.L. Sun, Z.T. Gu, L. Zhu, T. Mao, X.F. Zhang, N. Xu, T.P. Lu, M.H. Tsai, L.H. Chen, L.C. Lai, Eric Y. Chuang, “Novel Tumor-Specific Antigens for Immunotherapy Identified From Multi-omics Profiling in Thymic Carcinomas” , Frontiers in Immunology , Vol. 12 , Nov. 2021

40. C.Y. Lee, Y.F. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes” , New Biotechnology , Vol. 65 , 42-52, Nov. 2021

41. C.H. Lu, C.H. Wu, M.H. Tsai, L.C. Lai, Eric Y Chuang, “MutScape: an analytical toolkit for probing the mutational landscape in cancer genomics” , NAR Genomics and Bioinformatics , Vol. 3 , Dec. 2021

42. N.N. Phan, C.C. Huang, L.M. Tseng, Eric Y. Chuang, “Predicting Breast Cancer Gene Expression Signature by Applying Deep Convolutional Neural Networks From Unannotated Pathological Images” , Frontiers in Oncology , Vol. 11 , Dec. 2021

43. P.H. Ko, G. Lenka, Y.A. Chen, Eric Y. Chuang, M.H. Tsai, Y.P. Sher, L.C. Lai, “Semaphorin 5A suppresses the proliferation and migration of lung adenocarcinoma cells” , International Journal of Oncology , Vol. undefined , Jan. 2020

44. J.M. Jimmy Juang, A. Binda, S.J. Lee, J.J. Hwang, W.J. Chen, Y.B. Liu, L. Y. Lin, C. C. Yu, L. T. Ho, H. C. Huang, C. Y. Julius Chen, T. P. Lu, L. C. Lai, S. F. Sherri Yeh, L. P. Lai, Eric Y. Chuang, I. Rivolta, C. Antzelevitch, “GSTM3 variant is a novel genetic modifier in Brugada syndrome, a disease with risk of sudden cardiac death” , EBioMedicine , Vol. 57 , 102843-undefined, Jul. 2020

45. Jimmy Juang,Liu,Julius Chen,Yu,Chattopadhyay,Lin,Chen,Yu,Huang,Ho,Lai,Hwang,Lin,Liao,Chen,Sherri Yeh,Chuang,Yang,Lin,Lu,Chuang,Ackerman, “Validation and Disease Risk Assessment of Previously Reported Genome-Wide Genetic Variants Associated With Brugada Syndrome” , Circulation: Genomic and Precision Medicine , Vol. 13 , 102843-undefined, Aug. 2020

46. H.C. Lo, D.S. Yu, H.W. Gao, M.H. Tsai, Eric Y. Chuang, “IL-27/IL-27RA signaling may modulate inflammation and progression of benign prostatic hyperplasia via suppressing the LPS/TLR4 pathway” , Translational Cancer Research , Vol. 9 , 4618-4634, Aug. 2020

47. P. S. Huang, C. S. Hsieh, S. N. Chang, J. J. Chen, F. C. Chiu, C. K. Wu, J. J. Hwang, Eric Y Chuang, C. T. Tsai, “Prevalence of sudden arrhythmic death syndrome-related genetic mutations in an Asian cohort of whole genome sequence” , EP Europace , Vol. 22 , 1287-1297, Aug. 2020

48. H.C. Lo, J.H. Hsu, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “MicroRNA-107 enhances radiosensitivity by suppressing granulin in PC-3 prostate cancer cells” , Scientific Reports , Vol. 10 , 1287-1297, Sep. 2020

49. C.C. Chen, W.K. Wu, C.M. Chang, S. Panyod, T.P. Lu, J.M. Liou, Y.J. Fang, Eric Y. Chuang, M.S. Wu, “Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles” , Journal of the Formosan Medical Association , Vol. 119 , 1791-1798, Dec. 2020

50. 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 , Vol. 8(3) , 332-, Mar. 2019

51. P.H. Ko, C.W. Huang, H.H. Chang, Eric Y. Chuang, M.H. Tsai, L.C. Lai, “Identifying the functions and biomarkers of Codonopsis pilosula and Astragalus membranaceus aqueous extracts in hepatic cells” , Chinese Medicine , Vol. 14 , Mar. 2019

52. T.T. Wang, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “anamiR: integrated analysis of MicroRNA and gene expression profiling” , BMC Bioinformatics , Vol. 20 , May 2019

53. C.H. Lin, C.C. Chen, H.L. Chiang, J.M. Liou, C.M. Chang, T.P. Lu, Eric Y. Chuang, Y.C. Tai, C. Cheng, H.Y. Lin, M.S. Wu, “Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson’s disease” , Journal of Neuroinflammation , Vol. 16 , Jun. 2019

54. C.Y. Lee, A. Chattopadhyay, L.M. Chiang, J.M. Jimmy Juang, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases” , Database , Vol. 2019 , Jul. 2019

55. W.C. Lin, L.H. Chen, Y.C. Hsieh, P.W. Yang, L.C. Lai, Eric 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 , Vol. 40 , 883-892, Jul. 2019

56. L.C. Lai, Q.L. Sun, Y.A. Chen, Y.W. Hsiao, T.P. Lu, M.H. Tsai, L. Zhu, Eric Y. Chuang*, W.T. Fang, “Using proteomic profiling to characterize protein signatures of different thymoma subtypes” , BMC Cancer , Vol. 19 , 883-892, Aug. 2019

57. L.H. Chen, C.Y. Liao, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “Semaphorin 6A Attenuates the Migration Capability of Lung Cancer Cells via the NRF2/HMOX1 Axis” , Scientific Reports , Vol. 9 , 883-892, Sep. 2019

58. J.M. Liou, C.C. Chen, C.M. Chang, Y.J. Fang, M.J. Bair, P.Y. Chen, C.Y. Chang, Y.C. Hsu, M.J. Chen, C.C. Chen, J.Y. Lee, T.H. Yang, J.C. Luo, C.Y. Chen, W.F. Hsu, Y.N. Chen, J.Y. Wu, J.T. Lin, TP Lu, Eric Y Chuang, Emad M El-Omar, MS. Wu, “Long-term changes of gut microbiota, antibiotic resistance, and metabolic parameters after Helicobacter pylori eradication: a multicentre, open-label, randomised trial” , The Lancet Infectious Diseases , Vol. 19 , 1109-1120, Oct. 2019

59. 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 , Vol. bgy189 , Jul. 2019

60. 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

61. 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

62. 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 , Vol. 21(2) , 74-83, Feb. 2018

63. 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 , Vol. 7(5) , May 2018

64. 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

65. 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 , Vol. 7(12) , 537-, Dec. 2018

66. 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

67. 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

68. 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

69. 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

70. 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

71. 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

72. 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, Eric 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

73. 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

74. 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

75. 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

76. 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

77. 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

78. 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

79. 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

80. 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

81. 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

82. 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

83. 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

84. 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

85. 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 , Vol. 52(1) , 28-36, Jan. 2015

86. 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 , Vol. 14:36 , Feb. 2015

87. 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 , Vol. 16(Suppl 4) , S1-, Feb. 2015

88. 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 , Vol. 16(Suppl 7) , S19-, Jan. 2015

89. 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 , Vol. 8:92 , Mar. 2015

90. 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

91. 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 , Vol. 5:10291 , May 2015

92. 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 , Vol. 4(3) , 291-302, May 2015

93. 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

94. 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 , Vol. 4:5908 , Aug. 2014

95. 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 , Vol. 147(2) , 353-370, Sep. 2014

96. 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 , Vol. 53 , 58-66, Aug. 2014

97. Lu TP, Hsu YY, Lai LC, Tsai MH, Chuang EY*, “Identification of gene expression biomarkers for predicting radiation exposure.” , Sci Rep , Vol. 4:6293 , Sep. 2014

98. 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 , Vol. 4:6733 , Oct. 2014

99. 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 , Vol. 29 , 1051-1059, Dec. 2014

100. 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 , Vol. 4:3850 , Jan. 2014

101. 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 , Vol. 9(2) , 149-171, Feb. 2014

102. 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 , Vol. 21:24 , Mar. 2014

103. 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 , Vol. 4:4351 , Mar. 2014

104. 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 , Vol. 9(4 , e94065-, Apr. 2014

105. 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 , Vol. 9(6) , e100515-, Jun. 2014

106. 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 , Vol. 89(4) , 709-713, Jul. 2014

107. Yang YC, Wang DY, Cheng HF, Chuang EY, Tsai MH, “A reliable multiplex genotyping assay for HCV using a suspension bead array.” , Microb Biotechnol , Vol. 8(1) , 93-102, Jul. 2014

108. 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. Vol. 2 Iss. 1 , 21-27, Jan. 2013

109. 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 , Vol. 2013 , 360678-, Mar. 2013

110. 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 , Vol. 2(1) , 18-24, Feb. 2013

111. 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 , Vol. 8(4) , e62383-, Apr. 2013

112. Wang IJ, Chen SL, Lu TP, Chuang EY, Chen PC, “Prenatal smoke exposure, DNA methylation, and childhood atopic dermatitis.” , Clin Exp Allergy , Vol. 43(5) , 535-543, May 2013

113. 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 , Vol. 8(1) , 92-104, Jan. 2013

114. 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 , Vol. 8(9) , e73153-, Sep. 2013

115. 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 , Vol. 8(10) , e76421-, Oct. 2013

116. Lu TP, Chuang EY, Chen JJ, “Identification of reproducible gene expression signatures in lung adenocarcinoma.” , BMC Bioinformatic , Vol. 14:371 , Dec. 2013

117. 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 , Vol. 2013:248648 , Dec. 2013

118. 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 , Vol. 13(3) , 214-220, Apr. 2012

119. 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 , Vol. 7(8) , e42390-, Aug. 2012

120. 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 , Vol. 10 Suppl 1 , S10-, Sep. 2012

121. 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 , Vol. 7(9) , e45831-, Sep. 2012

122. 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 , Vol. 82(5) , 1996-2003, May 2011

123. 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 , Vol. 18(8) , 1013-1017, Aug. 2011

124. 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 , Vol. 6(8) , e24375-, Sep. 2011

125. 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 , Vol. 6(9) , e24829-, Sep. 2011

126. 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 , Vol. 4(1) , 394-, Oct. 2011

127. 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 , Vol. 6(11) , e28222-, Dec. 2011

128. 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 , Vol. 19(22) , 21552-21562, Oct. 2011

129. 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 , Vol. 76(1) , 212-219, Jan. 2010

130. 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 , Vol. 38(20) , e187-, Nov. 2010

131. 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 , Vol. 19(10) , 2590-2597, Oct. 2010

132. 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 , Vol. 218(4) , 495-504, Aug. 2009

133. 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 , Vol. 171(6) , 708-715, Jun. 2009

134. 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 , Vol. 15(2) , 163-168, Mar. 2008

135. 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 , Vol. 24(16) , 1749-1756, Aug. 2008

136. 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 , Vol. 6(6) , 1018-1026, Jun. 2007

137. 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 , Vol. 67(8) , 3845-3852, Apr. 2007

138. 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 , Vol. 67(15) , 7113-7123, Aug. 2007

139. 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 , Vol. 25(4) , 622-632, Jan. 2006

140. 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 , Vol. 66(7) , 3428-3433, Apr. 2006

141. 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 , Vol. 12(12) , 3823-3830, Jun. 2006

142. 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 , Vol. 8(7-8) , 1263-1272, Aug. 2006

143. 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 , Vol. 65(2) , 579-586, Jan. 2005

144. 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 , Vol. 29(3) , 221-224, Mar. 2005

145. 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 , Vol. 65(15) , 6734-6744, Aug. 2005

146. 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 , Vol. 24(55) , 8085-8092, Dec. 2005

147. 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 , Vol. 11(17) , 6300-6310, Sep. 2005

148. 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 , Vol. 186(2) , 556-565, Jan. 2004

149. 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 , Vol. 4 , 20-, May 2004

150. 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 , Vol. 104(5) , 1428-1434, Sep. 2004

151. 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 , Vol. 20(16) , 2685-2693, Nov. 2004

152. 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 , Vol. 3(7) , 861-872, Jul. 2004

153. 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 , Vol. 64(18) , 6511-6523, Sep. 2004

154. 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 , Vol. 6(4) , 361-371, Oct. 2004

155. 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 , Vol. 78(24) , 13637-13652, Dec. 2004

156. 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 , Vol. 100(9) , 5390-5395, Apr. 2003

157. 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 , Vol. 990 , 671-677, Jun. 2003

158. 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 , Vol. 63(14) , 3872-3876, Jul. 2003

159. 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 , Vol. 62(21) , 6246-6254, Nov. 2002

160. 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 , Vol. 59(13) , 3073-3076, Jul. 1999

161. 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 , Vol. 31(Suppl. 29) , 65-, Jan. 1998

162. 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 , Vol. 29(Suppl. 28) , 9-, Jan. 1997

163. 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 , Vol. 27(Suppl. 27) , 13-, Jan. 1996

164. 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 , Vol. 146(5) , 494-500, Nov. 1996

165. 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 , Vol. 38(2) , 239-242, Nov. 1992

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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 , 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 , Philadeplhia, PA, USA , Apr. 2015

3. 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 , Geneva, Switzerland , Apr. 2014

4. 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 , San Francisco, CA, USA , Dec. 2014

5. 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 , Geneva, Switzerland , Apr. 2014

6. 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

7. 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

8. Lu TP, Chuang EY, Chen JJ, “Identification of universal survival predictors in lung adenocarcinoma.” , 2013 AACR annual meeting , Washington D.C., USA , Apr. 2013

9. 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 , Washington D.C., USA , Apr. 2013

10. 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 , Washington D.C., USA , Apr. 2013

11. 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 , Washington D.C., USA , Apr. 2013

12. 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 , Houston, USA , Nov. 2013

13. 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 , Shanghai, China , Dec. 2013

14. 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 , Washington, DC, 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. 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 , Jan. 2011

17. 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 , Orlando, Florida, USA , Apr. 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 , 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 , Jan. 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 , Jan. 2004

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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 , 978-988-77840-4-3 , 978-988-77840-4-3 , Hong Kong, 2017

2. Jie He, Rafael Rosell, Eric Y. Chuang, “Lung Cancer Precision Medicine” , AME Publishing Company , 978-988-14028-1-3 Hardback , 978-988-14028-1-3 Hardback , Hong Kong, 2016

3. Huang Giap, Eric Y Chuang, Gary Y Yang, “Particle Beam Therapy: contemporary trends and reviews” , AME Publishing Company , 978-988-12997-4-1 , 978-988-12997-4-1 , 291 , Hong Kong, 2014

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 , 57 , 臺灣, 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 , 9789860048872 , 9789860048872 , 67 , 臺灣, Mar. 2006

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Patents:

1. 蔡孟勳、莊曜宇、華筱玲、潘日南, “一種判別源自不同個體之基因的方法及其深度學習模型” , 中華民國I783699號, Nov. 2022

2. 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

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. 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

5. 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

6. 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

7. 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, Sep. 2012

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