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, 15, Sept. 2024
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, 177, 116958-undefined, Aug. 2024
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, 16, Aug. 2024
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, 21, 254-264, Mar. 2024
Chattopadhyay,Lee,Lee,Liu,Chen,Li,Lai,Tsai,Ni,Chiu,Lu,Chuang, “Twnbiome: a public database of the healthy Taiwanese gut microbiome,” BMC Bioinformatics, 24, Dec. 2023
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, 203, 291-306, Oct. 2023
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, 9, 1783-1792, Aug. 2023
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, 143, 104423-undefined, Jul. 2023
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, 46, 1211-1228, Jul. 2023
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, 25, May 2023
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, 121, 1945-1955, Oct. 2022
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, 23, Oct. 2022
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, 13, Sept. 2022
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, 2, Aug. 2022
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, 145, 105416-undefined, Jun. 2022
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, 11, 3622-undefined, Jun. 2022
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, 12, Apr. 2022
Chiu,Tsai,Huang,Shih,Tsai,Hwang,Wang,Chuang,Tsai,Chang, “The Gut Microbiome, Seleno-Compounds, and Acute Myocardial Infarction,” Journal of Clinical Medicine, 11, 1462-undefined, Mar. 2022
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, 60, Feb. 2022
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, 10, 394-undefined, Feb. 2022
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, 8, Jan. 2022
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, 10, 9004-9021, Jan. 2022
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, 3, Dec. 2021
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, 11, Dec. 2021
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, 22, Nov. 2021
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, 12, Nov. 2021
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, 65, 42-52, Nov. 2021
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, 11, Oct. 2021
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, 4, Sept. 2021
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, 7, Jul. 2021
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, 2021, Jul. 2021
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, 63, 37-44, Jul. 2021
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, 11, Jun. 2021
C. Goswami, A. Chattopadhyay, Eric Y. Chuang, “Rare variants: data types and analysis strategies,” Annals of Translational Medicine, 9, 961-961, Jun. 2021
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, 30, 113-122, May 2021
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, 30, 147-158, May 2021
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, 11, 147-158, May 2021
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, 9, 75202-75210, May 2021
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, 13, 1821-undefined, Apr. 2021
S. Shivani, A. Chattopadhyay, Eric Y. Chuang, “Targeting the gut microbiome for non-communicable diseases: present and future,” Annals of Translational Medicine, 9, 361-361, Mar. 2021
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, 11, Feb. 2021
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, 10, Jan. 2021
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, 119, 1791-1798, Dec. 2020
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, 10, 1287-1297, Sept. 2020
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, 13, 102843-undefined, Aug. 2020
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, 9, 4618-4634, Aug. 2020
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, 22, 1287-1297, Aug. 2020
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, 57, 102843-undefined, Jul. 2020
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, undefined, Jan. 2020
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, 19, 1109-1120, Oct. 2019
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, 9, 883-892, Sept. 2019
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, 19, 883-892, Aug. 2019
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, 2019, Jul. 2019
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, 40, 883-892, Jul. 2019
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, Jul. 2019
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, 16, Jun. 2019
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, 20, May 2019
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, 14, Mar. 2019
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Lu TP, Chuang EY, Chen JJ, “Identification of reproducible gene expression signatures in lung adenocarcinoma.,” BMC Bioinformatic, 14:371, Dec. 2013
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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:
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Eric Y. Chuang, “Combination of Genomic Technologies and Bioinformatics for Exploring New Cancer Biomarkers” , Princeton, NJ, 2012,” EITA 2012-BIO, Princeton, NJ, Oct. 2012
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
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
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
Eric Y. Chuang, “Microarray Gene Expression Data Analysis in Cancer Research,” The 28th World Congress of Internal Medicine, Taipei, Taiwan, 2006
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:
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
Jie He, Rafael Rosell, Eric Y. Chuang, “Lung Cancer Precision Medicine,” AME Publishing Company, Hong Kong, 2016, ISBN:978-988-14028-1-3 Hardback
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
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
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