*Corresponding author is marked with an asterisk (*) mark.
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, J FORMOS MED ASSOC (impact factor: 3.871, journal ranking: 35%), OCT 01 2022, 121(10):1945-1955, DOI: 10.1016/j.jfma.2022.01.022
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 DIS (impact factor: 9.696, journal ranking: 18%), SEP 20 2022, 13(9):807, DOI: 10.1038/s41419-022-05253-2
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 (impact factor: X.XXX, journal ranking: XX%), AUG 03 2022, 2:905489, DOI: 10.3389/fbinf.2022.905489
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, J CLIN MED (impact factor: 4.964, journal ranking: 31%), JUN 23 2022, 11(13):3622, DOI: 10.3390/jcm11133622
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, COMPUT BIOL MED (impact factor: 6.698, journal ranking: 11%), JUN 2022, 145:105416, DOI: 10.1016/j.compbiomed.2022.105416
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, FRONT CELL INFECT MI (impact factor: 6.073, journal ranking: 24%), APR 26 2022, 12:726256, DOI: 10.3389/fcimb.2022.726256
F.C. Chiu, C.F. Tsai, P.S. Huang, C.Y. Shih, M.H. Tsai, J.J. Hwang, Y.C. Wang, Eric Y. Chuang, C.T. Tsai, S.N. Chang, The Gut Microbiome, Seleno-Compounds, and Acute Myocardial Infarction, J CLIN MED (impact factor: 4.964, journal ranking: 31%),MAR 7 2022, 11(5):1462, DOI: 10.3390/jcm11051462
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 (impact factor: 4.757, journal ranking: 31%), FEB 07 2022, 10(2):394, DOI: 10.3390/biomedicines10020394
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, INT J ONCOL (impact factor: 5.884, journal ranking: 30%), FEB 2022, 60(2):21, DOI: 10.3892/ijo.2022.5311
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 (impact factor: 3.476, journal ranking: 38%), JAN 13 2022, 10:9004-9021, DOI: 10.1109/ACCESS.2022.3142925
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, FRONT MED-LAUSANNE (impact factor: 5.058, journal ranking: 30%), JAN 13 2022, 8:732817, DOI: 10.3389/fmed.2021.732817
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, FRONT ONCOL (impact factor: 5.738, journal ranking: 32%), DEC 01 2021, 11:769447, DOI: 10.3389/fonc.2021.769447
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 Genom Bioinform (impact factor:XXXX, journal ranking: XX%), DEC 2021, 3(4):lqab099, DOI: 10.1093/nargab/lqab099
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 BIOTECHNOL (impact factor: 6.490, journal ranking: 11%), NOV 25 2021,65:42-52, DOI: 10.1016/j.nbt.2021.08.002
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, FRONT IMMUNOL (impact factor: 8.786, journal ranking: 20%), NOV 16 2021, 12:748820, DOI: 10.3389/fimmu.2021.748820
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, BRIEF BIOINFORM (impact factor: 13.994, journal ranking: 2%), NOV 05 2021, 22(6):bbab283, DOI: 10.1093/bib/bbab283
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, FRONT ONCOL (impact factor: 5.738, journal ranking: 32%), OCT 21 2021, 11:734015, DOI: 10.3389/fonc.2021.734015
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, COMMUN BIOL (impact factor: 6.548, journal ranking: 16%), SEP 09 2021, 4:1052(2021), DOI: 10.1038/s42003-021-02597-x
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 BIOTECHNOL (impact factor: 6.490, journal ranking: 11%), JUL 25 2021, 63(2021):37-44, DOI: 10.1016/j.nbt.2021.03.001
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-OXFORD (impact factor: 4.462, journal ranking: 19%), JUL 14 2021, 2021:baab044, DOI: 10.1093/database/baab044
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 (impact factor: 7.519, journal ranking: 20%), JUL 05 2021, 7:88(2021), DOI: 10.6084/m9.figshare.14696499
C. Goswami, A. Chattopadhyay, Eric Y. Chuang*, Rare variants: data types and analysis strategies, Ann Transl Med (impact factor: 3.616, journal ranking: 61%), JUN 01 2021, 9(12):961, DOI: 10.21037/atm-21-1635
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, FRONT ONCOL (impact factor: 5.738, journal ranking: 32%), JUN 01 2021, 11:663114, DOI:10.3389/fonc.2021.663114
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 (impact factor: 3.476, journal ranking: 38%), MAY 20 2021, 9:75202-75210, DOI: 10.1109/ACCESS.2021.3082403
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, FRONT ONCOL (impact factor: 5.738, journal ranking: 32%), MAY 03 2021, 11:658151, DOI: 10.3389/fonc.2021.658151
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, J ADV RES (impact factor: 12.822, journal ranking: 11%), MAY 2021, 30(2021):147-158, DOI: 10.1016/j.jare.2020.12.003
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, J ADV RES (impact factor: 12.822, journal ranking: 11%), MAY 2021, 30(2021):113-122, DOI: 10.1016/j.jare.2020.11.006
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 (impact factor: 6.575, journal ranking: 24%), APR 11 2021, 13(8):1821, DOI: 10.3390/cancers13081821
S. Shivani, A. Chattopadhyay, Eric Y. Chuang*, Targeting the gut microbiome for non-communicable diseases: present and future, Ann Transl Med (impact factor: 3.616, journal ranking: 61%), MAR 05 2021, 9(5):361, DOI: 10.21037/atm-21-144
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, FRONT ONCOL (impact factor: 5.738, journal ranking: 32%), FEB 22 2021, 11:631056, DOI: 10.3389/fonc.2021.631056
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, FRONT ONCOL (impact factor: 5.738, journal ranking: 32%), JAN 22 2021, 10:585621, DOI: 10.3389/fonc.2020.585621
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, J FORMOS MED ASSOC (impact factor: 3.871, journal ranking: 35%), DEC 2020, 119(12):1791-1798, DOI: 10.1016/j.jfma.2020.01.013
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, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), SEP 03 2020, 10(1):14584(2020), DOI:10.1038/s41598-020-71128-1
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, EUROPACE (impact factor: 5.486, journal ranking: 32%), AUG 01 2020, 22(8):1287-1297, DOI: 10.1093/europace/euaa092
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, TRANSL CANCER RES (impact factor: 0.496, journal ranking: 99%), AUG 2020, 9(8):4618-4634, DOI: 10.21037/tcr-20-1509
J.M. Jimmy Juang, Y.B. Liu, C.Y. Julius Chen, Q.Y. Yu, A. Chattopadhyay, L.Y. Lin, W.J. Chen, C.C. Yu, H.C. Huang, L.T. Ho, L.P. Lai, J.J. Hwang, T.T. Lin, M.C. Liao, J.J. Chen, S.F. Sherri Yeh, J.Y. Chuang, D.H. Yang, J.L. Lin, T.P. Lu, Eric Y. Chuang, M.J. Ackerman, Validation and Disease Risk Assessment of Previously Reported Genome-Wide Genetic Variants Associated with Brugada Syndrome: SADS-TW BrS Registry, CIRC-CARDIOVASC GENE (impact factor: 4.534, journal ranking: 19%), AUG 2020, 13(4):e002797, DOI: 10.1161/CIRCGEN.119.002797
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 (impact factor: 11.205, journal ranking: 10%), JUL 07 2020, 57(2020):102843, DOI: 10.1016/j.ebiom.2020.102843
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, INT J ONCOL (impact factor: 5.884, journal ranking: 30%), JAN 2020, 56(1):165-177, DOI: 10.3892/ijo.2019.4932
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, LANCET INFECT DIS (impact factor: 71.421, journal ranking: 2%), OCT 01 2019, 19(10):1109-1120, DOI: 10.1016/S1473-3099(19)30272-5
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, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), SEP 16 2019,9:13302(2019), DOI: 10.1038/s41598-019-49874-8
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 (impact factor: 4.638, journal ranking: 44%), AUG 13 2019, 19(1):796(2019), DOI: 10.1186/s12885-019-6023-4
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 (impact factor: 4.741, journal ranking: 42%), JUL 20 2019, 40(7):883-892, DOI: 10.1093/carcin/bgy189
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-OXFORD (impact factor: 4.462, journal ranking: 19%), JUL 17 2019, 2019:baz075, DOI: 10.1093/database/baz075
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, J NEUROINFLAMM (impact factor: 9.594, journal ranking: 9%), JUN 27 2019, 16(1):129, DOI: 10.1186/s12974-019-1528-y
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 (impact factor: 3.328, journal ranking: 35%), MAY 14 2019, 20:239, DOI: 10.1186/s12859-019-2870-x
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, CHIN MED-UK (impact factor: 4.546, journal ranking: 20%), MAR 20 2019, 14:10(2019), DOI: 10.1186/s13020-019-0233-1
C.S. Hsieh, P.S. Huang, S.N. Chang, C.K. Wu, J.J. Hwang, Eric Y. Chuang*, C.T. Tsai, Genome-Wide Copy Number Variation Association Study of Atrial Fibrillation Related Thromboembolic Stroke, J CLIN MED (impact factor: 4.964, journal ranking: 31%), MAR 09 2019, 8(3):332, DOI: 10.3390/jcm8030332.
P.H. Ko, Y.C. Shen, K. Murugan, C.W. Huang, G. Sivakumar, P. Pal, C.C. Liao, K.S. Luo, Eric 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, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), FEB 14 2019, 9(1):2147, DOI: 10.1038/s41598-019-38590-y
C.S. Hsieh, C.T. Tsai, Y.H. Chen, S.N. Chang, J.J. Hwang, Eric 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 (impact factor: 4.964, journal ranking: 31%), DEC 11 2018, 7(12):537, DOI: 10.3390/jcm7120537
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, Eric Y. Chuang*, The extracellular SEMA domain attenuates intracellular apoptotic signaling of semaphorin 6A in lung cancer cells, ONCOGENESIS (impact factor: 6.524, journal ranking: 25%), DEC 05 2018, 7(12):95, DOI: 10.1038/s41389-018-0105-z
C.C. Yeh, J.L. Luo, N.N. Phan, Y.C. Cheng, L.P. Chow, M.H. Tsai, Eric Y. Chuang, L.C. Lai, Different effects of long noncoding RNA NDRG1-OT1 fragments on NDRG1 transcription in breast cancer cells under hypoxia, RNA BIOL (impact factor: 4.766, journal ranking: 41%), DEC 04 2018, 15(12):1487-1498, DOI: 10.1080/15476286.2018.1553480
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, Eric Y. Chuang*, Whole-Genome De Novo Sequencing Reveals Unique Genes that Contributed to the Adaptive Evolution of the Mikado Pheasant, GIGASCIENCE (impact factor: 7.658, journal ranking: 18%), MAY 02 2018, 7(5):giy044, DOI: 10.1093/gigascience/giy044
H.C. Lin, C.C. Yeh, L.Y. Chao, M.H. Tsai, H.H. Chen, Eric Y. Chuang, L.C. Lai, The hypoxia-responsive lncRNA NDRG-OT1 promotes NDRG1 degradation via ubiquitin-mediated proteolysis in breast cancer cells, ONCOTARGET, FEB 13 2018, 9(12):10470-10482, DOI: 10.18632/oncotarget.23732
T.H. Hsiao, Y.H. Chen, H.I. Chen, Y.C. Chiu, Eric Y. Chuang*, Y. Chen, Utilizing Cancer–Functional Gene set–Compound Networks to Identify Putative Drugs for Breast Cancer, COMB CHEM HIGH T SCR (impact factor: 1.714, journal ranking: 69%), FEB 2018, 21(2):74-83, DOI: 10.2174/1574888X13666180105 125347
S.H. Huang, Y.S. Chang, J.M. Jimmy Juang, K.W. Chang, M.H. Tsai, T.P. Lu, L.C. Lai, Eric Y. Chuang, N.T. Huang, An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases, ANALYST (impact factor: 5.227, journal ranking: 21%), JAN 17 2018, 143:1367-1377, DOI: 10.1039/C7AN01648D
Y.F. Lee, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang*, CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system, DATABASE-OXFORD (impact factor: 4.462, journal ranking: 19%), JAN 12 2018, 2018:bax101, DOI: 10.1093/ database/bax101
Y.C. Chiu, L.J. Wang, T.H. Hsiao, Eric Y. Chuang*, Y. Chen, Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer, BMC GENOMICS (impact factor: 4.560, journal ranking: 29%), OCT 03 2017, 18(Suppl 6):679, DOI: 10.1186/s12864-017-4028-4
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 (impact factor: 7.290, journal ranking: 24%), OCT 01 2017, 23(10):1730-1740, DOI: 10.1097/MIB. 0000000000001250
A.L. Woolston, P.C. Hsiao, P.H. Kuo, S.H. Wang, Y.J. Lien, C.M. Liu, H.G. Hwu, T.P. Lu, Eric 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, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), JUL 25 2017, 7:6486, DOI: 10.1038/s 41598-017-06795-8
K.L. Chiu, Y.S. Lin, T.T. Kuo, C.C. Lo, Y.K. Huang, H.F. Chang, Eric 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 08 2017, 8(29):47365-47378, DOI: 10.18632/oncotarget.17648
Y.C. Chiu, L.J. Wang, T.P. Lu, T.H. Hsiao, Eric Y. Chuang*, Y. Chen, Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival, BMC BIOINFORMATICS (impact factor: 3.328, journal ranking: 35%), FEB 28 2017, 18:132, DOI: 10.1186/s12859-017-1557-4
G. Lenka, M.H. Tsai, H.C. Lin, J.H. Hsiao, Y.C. Lee, T.P. Lu, J.M. Lee, C.P. Hsu, L.C. Lai, Eric Y. Chuang*, Identification of Methylation-Driven, Differentially Expressed STXBP6 as a Novel Biomarker in Lung Adenocarcinoma, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), FEB 15 2017, 7:42573, DOI: 10.1038/srep42573
Y.P. Lai, L.B. Wang, W.A. Wang, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang*, iGC—an integrated analysis package of gene expression and copy number alteration, BMC BIOINFORMATICS (impact factor: 3.328, journal ranking: 35%), JAN 14 2017, 18:35, DOI: 10.1186/s12859-016-1438-2
C.Y. Shen, L.H. Chen, Y.F. Lin, L.C. Lai, Eric Y. Chuang, M.H. Tsai., Mitomycin C treatment induces resistance and enhanced migration via phosphorylated Akt in aggressive lung cancer cells, ONCOTARGET, NOV 29 2016, 7(48):79995-80007, DOI: 10.18632/oncotarget.13237
Y.C. Hsu, Y.C. Chiu, Y.D. Chen, T.H. Hsiao, Eric Y. Chuang*, A simple gene set-based method accurately predicts the synergy of drug pairs, BMC SYST BIOL, AUG 26 2016, 10(Suppl 3):66, DOI: 10.1186/s 12918-016-0310-3
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, Eric 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, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), AUG 22 2016, 6:31349, DOI: 10.1038/srep31349
W.A. Wang, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang*, Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs, ONCOTARGET, MAY 03 2016, 7(18):26739-26750, DOI: 10.18632/oncotarget.8496
Y.H. Chang, Y.C. Chiu, Y.C. Hsu, H.M. Tsai, Eric Y. Chuang*, T.H. Hsiao, Applying gene set analysis to characterize the activities of immune cells in estrogen receptor positive breast cancer, TRANSL CANCER RES (impact factor: 0.496, journal ranking: 99%), APR 2016, 5(2):176-185, DOI: 10.21037/tcr.2016.04.09
G. Lenka, M.H. Tsai, J.H. Hsiao, L.C. Lai, Eric Y. Chuang*, Overexpression of methylation-driven DCC suppresses proliferation of lung cancer cells, TRANSL CANCER RES (impact factor: 0.496, journal ranking: 99%), APR 2016, 5(2):169-175, DOI: 10.21037/tcr.2016.04.08
C.Y. Wu, Eric Y. Chuang*, T.P. Lu, Low correlation of lncRNA and target gene expression in microarray data, TRANSL CANCER RES (impact factor: 0.496, journal ranking: 99%), APR 2016, 5(2):160-168, DOI: 10.21037/tcr.2016.04.07
T.H. Hsiao, Y.C. Chiu, P.Y. Hsu, T.P. Lu, L.C. Lai, M.H. Tsai, T.H. Huang, Eric Y. Chuang*, Y. Chen, Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), MAR 14 2016, 6:23035, DOI: 10.1038/srep23035
E.Y. Li, W.Y. Huang, Y.C. Chang, M.H. Tsai, Eric Y. Chuang, Q.Y. Kuok, S.T. Bai, L.Y. Chao, Y.P. Sher, L.C. Lai, Aryl Hydrocarbon Receptor Activates NDRG1 Transcription under Hypoxia in Breast Cancer Cells, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), FEB 08 2016, 6:20808, DOI: 10.1038/srep20808
C.T. Tsai, C.S. Hsieh, S.N. Chang, Eric 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, NAT COMMUN (impact factor: 17.694, journal ranking: 8%), FEB 02 2016, 7:1019, DOI: 10.1038/ncomms10190
Y.C. Chiu, M.H. Tsai, W.C. Chou, Y.C. Liu, Y.Y. Kuo, H.A. Hou, T.P. Lu, L.C. Lai, Y. Chen, H.F. Tien, Eric Y. Chuang*, Prognostic significance of NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia, LEUKEMIA (impact factor: 12.897, journal ranking: 9%), FEB 2016, 30(2):274-284, DOI: 10.1038/leu.2015.253, Epub: SEP 16 2015
Y.C. Chiu, K.W. Liang, T.H. Hsiao, Y. Chen, Eric Y. Chuang, Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme, IEEE Xplore, DEC 17 2015,15668334, DOI: 10.1109/TCBB.2016.2635646
M.K. Chuang, Y.C. Chiu, W.C. Chou, H.A. Hou, M.H Tseng, Y.Y. Kuo, Y. Chen, Eric Y. Chuang*, H.F. Tien, An mRNA Expression Signature for Prognostication in De Novo Acute Myeloid Leukemia Patients with Normal Karyotype, ONCOTARGET, NOV 17 2015, 6(36):39098-110, DOI: 10.18632/oncotarget.5390
A. Woolston, N. Sintupisut, T.P. Lu, L.C. Lai, M.H. Tsai, Eric Y. Chuang, C.H. Yeang, Putative effectors for prognosis in lung adenocarcinoma are ethnic and gender specific, ONCOTARGET, AUG 14 2015, 6(23):19483-19499, DOI: 10.18632/oncotarget.4287
Y.C. Chiu, C.T. Wu, T.H. Hsiao, Y.P. Lai, C.K. Hsiao, Y. Chen, Eric Y. Chuang*, Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes, BMC GENOMICS (impact factor: 4.560, journal ranking: 29%), JUN 11 2015, 16(Suppl 7):S19, DOI: 10.1186/1471-2164-16-S7-S19
Y.C. Hsu, Y.C. Chiu, Y. Chen, T.H. Hsiao, Eric Y. Chuang*, A gene-set approach to analyze copy number alterations in breast cancer, TRANSL CANCER RES (impact factor: 0.496, journal ranking: 99%), JUN 2015, 4(3):291-302, DOI: 10.3978/j.issn.2218-676X.2015.05.03
F.M. Hsu, J.C.H. Cheng, Y.L. Chang, J.M. Lee, A.C. Koong, Eric Y. Chuang*, Circulating mRNA Profiling in Esophageal Squamous Cell Carcinoma Identifies FAM8(4)B As A Biomarker In Predicting Pathological Response to Neoadjuvant Chemoradiation, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), MAY 18 2015, 5:10291, DOI: 10.1038/srep10291
M.K. Chuang, Y.C. Chiu, W.C. Chou, H.A. Hou, Eric Y. Chuang, H.F. Tien, A 3-microRNA scoring system for prognostication in de novo acute myeloid leukemia patients, LEUKEMIA (impact factor: 12.897, journal ranking: 9%), MAY 2015, 29(5):1051-1059, DOI: 10.1038/leu.2014.333
Y.C. Chiu, T.H. Hsiao, Y. Chen, Eric Y. Chuang*, Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers, BMC GENOMICS (impact factor: 4.560, journal ranking: 29%), APR 21 2015, 16(Suppl 4):S1, DOI: 10.1186/1471-2164-16-S4-S1
T.P. Lu, C.K. Hsiao, L.C. Lai, M.H. Tsai, C.P. Hsu, J.M. Lee, Eric Y. Chuang*, Identification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma, BMC Res Notes, MAR 24 2015, 8:92, DOI: 10.1186/s13104-015-1053 -8
Y.Y. Chang, W.H. Kuo, J.H. Hung, C.Y. Lee, Y.H. Lee, Y.C. Chang, W.C. Lin, C.Y. Shen, C.S. Huang, F.J. Hsieh, L.C. Lai, M.H. Tsai, K.J. Chang, Eric Y. Chuang*, Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing, MOL CANCER (impact factor: 41.444, journal ranking: 1%), FEB 10 2015, 14:36, DOI: 10.1186/s12943-015-0301-9
Y.C. Yang, D.Y. Wang, H.F. Cheng, Eric Y. Chuang, M.H. Tsai, A reliable multiplex genotyping assay for HCV using a suspension bead array, MICROB BIOTECHNOL (impact factor: 6.575, journal ranking: 15%), JAN 2015, 8(1):93-102, DOI: 10.1111/1751-7915. 12140
C.T. Tsai, C.S. Hsieh, S.N. Chang, Eric Y. Chuang, J.M. Juang, L.Y. Lin, L.P. Lai, J.J. Hwang, F.T. Chiang, J.L. Lin, 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 (impact factor: 5.954, journal ranking: 16%), JAN 2015, 52(1):28-36, DOI: 10.1136/jmedgenet-2014-102618
M.K. Chuang, Y.C. Chiu, W.C Chou, H.A. Hou, Eric Y. Chuang, H.F. Tien, A Simple, Powerful, and Widely Applicable Micro-RNA Scoring System in Prognostication of De Novo Myeloid Leukemia Patients, BLOOD (impact factor: 25.476, journal ranking: 3%), DEC 06 2014, 124(21), DOI: 10.1182/blood.V124.21.71.71
J.M. Juang, T.P. Lu, L.C. Lai, C.C. Ho, Y.B. Liu, C.T. Tsai, L.Y. Lin, C.C. Yu, W.J. Chen, F.T. Chiang, S.F. Yeh, L.P. Lai, Eric Y. Chuang, J.L. Lin, Disease-targeted sequencing of ion channel genes identifies de novo mutations in patients with non-familial Brugada syndrome, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), OCT 23 2014, 4:6733, DOI: 10.1038/srep06733
T.P. Lu, Y.Y. Hsu, L.C. Lai, M.H. Tsai, Eric Y. Chuang*, Identification of gene expression biomarkers for predicting radiation exposure, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), SEP 05 2014, 4:6293, DOI: 10.1038/srep06293
C.C. Huang, S.H. Tu, H.H. Lien, C.S. Huang, C.J. Huang, L.C. Lai, M.H. Tsai, Eric Y. Chuang*, Refinement of breast cancer risk prediction with concordant leading edge subsets from prognostic gene signatures, BREAST CANCER RES TR (impact factor: 4.624, journal ranking: 45%), SEP 2014, 147(2):353-370, DOI: 10.1007/s10549-014-3104-6
E.C. Luo, Y.C. Chang, Y.P. Sher, W.Y. Huang, L.L. Chuang, Y.C. Chiu, M.H. Tsai, Eric Y. Chuang, L.C. Lai, MicroRNA-769-3p down-regulates NDRG1 and enhances apoptosis in MCF-7 cells during reoxygenation, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), AUG 01 2014, 4:5908, DOI: 10.1038/srep05908
B.S. Rosenstein, C.M. West, S.M. Bentzen, J. Alsner, C.N. Andreassen, D. Azria, G.C. Barnett, M. Baumann, N. Burnet, J. Chang-Claude, Eric Y. Chuang, C.E. Coles, A. Dekker, D.R. Kim, D.D. Ruysscher, K. Drumea, A.M. Dunning, D. Easton, R. Eeles, L. Fachal, S. Gutiérrez-Enríquez, K. Haustermans, L.A. Henríquez-Hernández, T. Imai, G.D.D. Jones, S.L. Kerns, Z. Liao, K. Onel, H. Ostrer, M. Parliament, P.D.P. Pharoah, T.R. Rebbeck, C.J. Talbot, H. Thierens, A. Vega, J.S. Witte, P. Wong, F. Zenhausern, Radiogenomics: Radiobiology Enters the Era of Big Data and Team Science, INT J RADIAT ONCOL (impact factor: 8.013, journal ranking: 10%), JUL 15 2014, 89(4):709-713, DOI: 10.1016/j.ijrobp.2014.03.009
S.C. Wei, Y.Y. Tan, M.T. Weng, L.C. Lai, J.H. Hsiao, Eric Y. Chuang, C.T. Shun, D.C. Wu, A.W. Kao, C.S. Chuang, Y.H. Ni, M.J. Shieh, C.C. Tung, Y. Chen, C.Y. Wang, R.J. Xavier, D.K. Podolsky, J.M. Wong,SLCO3A1, a Novel Crohn's Disease-Associated Gene, Regulates NF-κB Activity and Associates with Intestinal Perforation, PLOS ONE (impact factor: 3.752, journal ranking: 40%), JUN 19 2014, 9(6):e100515, DOI: 10.1371/journal.pone.0100515
Y.P. Sher, L.J. Wang, L.L. Chuang, M.H. Tsai, T.T. Kuo, C.C. Huang, Eric Y. Chuang, L.C. Lai, ADAM9 Up-Regulates N-Cadherin via miR-218 Suppression in Lung Adenocarcinoma Cells, PLOS ONE (impact factor: 3.752, journal ranking: 40%), APR 04 2014, 9(4):e94065, DOI: 10.1371/ journal.pone.0094065
L.C. Lai, M.H. Tsai, P.C. Chen, L.H. Chen, J.H. Hsiao, S.K. Chen, T.P. Lu, J.M. Lee, C.P. Hsu, C.K. Hsiao, Eric Y. Chuang*, SNP rs10248565 in HDAC9 as a novel genomic aberration biomarker of lung adenocarcinoma in non-smoking women, J BIOMED SCI (impact factor: 12.771, journal ranking: 8%), MAR 21 2014, 21:24, DOI: 10.1186/1423-0127-21-24
T.P. Lu, K.T. Chen, M.H. Tsai, K.T. Kuo, C.K. Hsiao, L.C. Lai, Eric Y. Chuang*, Identification of genes with consistent methylation levels across different human tissues, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), MAR 12 2014, 4:4351, DOI: 10.1038/srep04351
C.C. Huang, S.H. Tu, H.H. Lien, J.Y. Jeng, J.S. Liu, C.S. Huang, L.C. Lai, Eric Y. Chuang*, Estrogen receptor status prediction by gene component regression: a comparative study, INT J DATA MIN BIOIN (impact factor: 0.339, journal ranking: 100%), FEB 04 2014, 9(2):149-171, DOI: 10.1504/IJDMB.2014.059065
J.M. Juang, T.P. Lu, L.C. Lai, C.H. Hsueh, Y.B. Liu, C.T. Tsai, L.Y. Lin, C.C. Yu, J.J. Hwang, F.T. Chiang, S.S. Yeh, W.P. Chen, Eric Y. Chuang*, L.P. Lai,, J.L. Lin, Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome, SCI REP-UK (impact factor: 4.996, journal ranking: 26%), JAN 27 2014, 4:3850, DOI: 10.1038/srep03850
C.C. Liu, Y.H. Wang, Eric Y. Chuang, M.H. Tsai, Y.H. Chuang, C.J. Lin, C.J Liu, B.Y. Hsiao, S.M. Lin, L.Y. Liu, M.W. Yu, Identification of a liver cirrhosis signature in plasma for predicting hepatocellular carcinoma risk in a population-based cohort of hepatitis B carriers, MOL CARCINOGEN (impact factor: 5.139, journal ranking: 35%), JAN 2014, 53(1):58-66, DOI: 10.1002/mc.21952, Epub: 2012 AUG 21.
C.C. Huang, S.H. Tu, C.S. Huang, H.H. Lien, L.C. Lai, Eric Y. Chuang*, Multiclass prediction with partial least square regression for gene expression data: applications in breast cancer intrinsic taxonomy, BIOMED RES INT (impact factor: 3.246, journal ranking: 57%), DEC 30 2013,248648, DOI: 10.1155/2013/248648
T.P. Lu, Eric Y. Chuang, J.J. Chen, Identification of reproducible gene expression signatures in lung adenocarcinoma, BMC BIOINFORMATICS (impact factor: 3.328, journal ranking: 35%), DEC 26 2013, 14:371, DOI: 10.1186/1471-2105-14-371
C.C. Huang, S.H. Tu, H.H. Lien, J.Y. Jeng, C.S. Huang, C.J. Huang, L.C. Lai, Eric Y. Chuang*, Concurrent gene signatures for Han Chinese breast cancers, PLOS ONE (impact factor: 3.752, journal ranking: 40%), OCT 03 2013, 8(10):e76421, DOI: 10.1371/journal.pone.0076421
T.Y. Lai, S.D. Wu, M.H. Tsai, Eric Y. Chuang, L.L. Chuang, L.C. Hsu, L.C. Lai, Transcription of Tnfaip3 Is Regulated by NF-κB and p38 via C/EBPβ in Activated Macrophages, PLOS ONE (impact factor: 3.752, journal ranking: 40%), SEP 02 2013, 8(9):e73153, DOI: 10.1371/journal.pone.0073153
P.C. Chen, T.P. Lu, J.C. Chang, L.C. Lai, M.H. Tsai, C.K. Hsiao, Eric Y. Chuang*, Concurrent analysis of copy number variation and gene expression: application in paired non-smoking female lung cancer patients, INT J DATA MIN BIOIN (impact factor: 0.339, journal ranking: 100%), 2013, 8(1):92-104, DOI: 10.1504/IJDMB.2013.054699
I.J. Wang, S.L. Chen, T.P. Lu, Eric Y. Chuang, P.C. Chen, Prenatal smoke exposure, DNA methylation, and childhood atopic dermatitis, CLIN EXP ALLERGY (impact factor: 5.401, journal ranking: 41%), MAY 2013, 43(5):535-543, DOI: 10.1111/cea.12108
Y.J. Liu, Y.F. Lin, Y.F. Chen, E.C. Luo, Y.P. Sher, M.H. Tsai, Eric Y. Chuang, L.C. Lai. , MicroRNA-449a enhances radiosensitivity in CL1-0 lung adenocarcinoma cells, PLOS ONE (impact factor: 3.752, journal ranking: 40%), APR 17 2013, 8(4):e62383, DOI: 10.1371/journal.pone.0062383
M. Flores, T.H. Hsiao, Y.C. Chiu, Eric Y. Chuang, Y. Huang, Y. Chen, Gene regulation, modulation, and their applications in gene expression data analysis, Adv in Bioinformatics, MAR 13 2013, 2013:360678, DOI: 10.1155/2013/360678
C.Y. Lee, Y.C. Chiu, L.B. Wang, Y.L. Kuo, Eric Y. Chuang, L.C. Lai, M.H. Tsai, Common applications of next-generation sequencing technologies in genomic research, TRANSL CANCER RES (impact factor: 0.496, journal ranking: 99%), FEB 2013, 2(1):33-45, DOI: 10.3978/j.issn.2218-676X.2013.02.09
C.C. Huang, J.Y. Jeng, S.H. Tu, H.H. Lien, C.S. Huang, L.C. Lai, Eric Y. Chuang*, A preliminary study of concurrent gains and losses across gene expression profiles and comparative genomic hybridization in Taiwanese breast cancer patients, TRANSL CANCER RES (impact factor: 0.496, journal ranking: 99%), FEB 2013, 2(1):18-24, DOI: 10.3978/j. issn.2218-676X.2013.02.07
C.C. Huang, S.H. Tu, Eric Y. Chuang*, Dissecting the Heterogeneity of Luminal Subtype Breast Cancer Using Gene Component Analysis, Journal of Medical Research and Development (JMRD),, JAN 2013, 2(1):21-27
W.H. Kuo, Y.Y. Chang, L.C. Lai, M.H. Tsai, C.K. Hsiao, K.J. Chang, Eric Y. Chuang*, Molecular characteristics and metastasis predictor genes of triple-negative breast cancer: a clinical study of triple-negative breast carcinomas, PLOS ONE (impact factor: 3.752, journal ranking: 40%), SEP 25 2012, 7(9):e45831, DOI: 10.1371/journal.pone.0045831
C.C. Huang, S.H. Tu, H.H. Lien, J.Y. Jeng, J.S. Liu, C.S. Huang, Y.Y. Wu, C.Y. Liu, L.C. Lai, Eric Y. Chuang*, Prediction consistency and clinical presentations of breast cancer molecular subtypes for Han Chinese population, J TRANSL MED (impact factor: 8.459, journal ranking: 18%), SEP 19 2012, 10(Suppl 1):S10, DOI: 10.1186/1479-5876-10- S1–S10
T.P. Lu, C.Y. Lee, M.H. Tsai, Y.C. Chiu, C.K. Hsiao, L.C. Lai, Eric Y. Chuang*, miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets, PLOS ONE (impact factor: 3.752, journal ranking: 40%), AUG 01 2012, 7(8):e42390, DOI: 10.1371/journal.pone.0042390
S.Y. Lin, S.C. Hsieh, Y.C. Lin, C.N. Lee, M.H. Tsai, L.C. Lai, Eric Y. Chuang, P.C. Chen, C.C. Hung, L.Y. Chen, W.S. Hsieh, D.M. Niu, Y.N. Su, 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 (impact factor: 4.248, journal ranking: 37%), APR 2012, 13(3):214-220, DOI: 10.1038/gene.2011.74, Epub: NOV 03 2011
P.C. Chen, Y.C. Chen, L.C. Lai, M.H. Tsai, S.K. Chen, P.W. Yang, Y.C. Lee, C.K. Hsiao, J.M. Lee, Eric Y. Chuang*, Use of Germline Polymorphisms in Predicting Concurrent Chemoradiotherapy Response in Esophageal Cancer, INT J RADIAT ONCOL (impact factor: 8.013, journal ranking: 10%), APR 01 2012, 82(5):1996-2003, DOI: 10.1016/j.ijrobp.2011.02.036, Epub: MAY 17 2011
L.H. Chen, W.H. Kuo, M.H. Tsai, P.C. Chen, C.K. Hsiao, Eric Y. Chuang, L.Y. Chang, F.J. Hsieh, L.C. Lai, K.J. Chang, Identification of prognostic genes for recurrent risk prediction in triple negative breast cancer patients in Taiwan, PLOS ONE (impact factor: 3.752, journal ranking: 40%), NOV 29 2011, 6(11):e28222, DOI: 10.1371/journal. pone.0028222
H. Chen, T.H. Chen, T.F. Tseng, J.T. Lu, C.C. Kuo, S.C. Fu, W.J. Lee, Y.F. Tsai, Y.Y. Huang, Eric Y. Chuang, Y.J. Hwang, C.K. Sun, High-sensitivity in vivo THz transmission imaging of early human breast cancer in a subcutaneous xenograft mouse model, OPT EXPRESS (impact factor: 3.833, journal ranking: 28%), OCT 24 2011, 19(22):21552-21562, DOI: 10.1364/OE.19.021552
F.H. Hsu, H.I. Chen, M.H. Tsai, L.C. Lai, C.C. Huang, S.H. Tu, Eric Y. Chuang*, Y. Chen, A model-based circular binary segmentation algorithm for the analysis of array CGH data, BMC Res Notes, OCT 10 2011, 4(1):394, DOI: 10.1186/1756-0500-4-394
T.P. Lu, L.C. Lai, M.H. Tsai, P.C. Chen, C.P. Hsu, J.M. Lee, C.K. Hsiao, Eric Y. Chuang*, Integrated analyses of copy number variations and gene expression in lung adenocarcinoma, PLOS ONE (impact factor: 3.752, journal ranking: 40%), SEP 14 2011, 6(9):e24829, DOI: 10.1371/journal.pone.0024829
L.C. Lai, Y.Y. Su, K.C. Chen, M.H. Tsai, Y.P. Sher, T.P. Lu, C.Y. Lee, Eric Y. Chuang*, Down-Regulation of NDRG1 Promotes Migration of Cancer Cells during Reoxygenation, PLOS ONE (impact factor: 3.752, journal ranking: 40%), AUG 30 2011, 6(8):e24375, DOI: 10.1371/journal.pone.0024375
H.C. Kuo, P.Y. Lin, T.C. Chung, C.M. Chao, L.C. Lai, M.H. Tsai, Eric Y. Chuang*, DBCAT: database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells, J COMPUT BIOL (impact factor: 1.549, journal ranking: 51%), AUG 2011, 18(8):1013-1017, DOI: 10.1089/cmb.2010.0038, Epub: JAN 08 2011
T.H. Hsiao, C.H. Lin, T.T. Lee, J.Y. Cheng, P.K. Wei, Eric Y. Chuang*, K. Peck, Verifying expressed transcript variants by detecting and assembling stretches of consecutive exons, NUCLEIC ACIDS RES (impact factor: 19.160, journal ranking: 3%), NOV 2010, 38(20):e187, DOI: 10.1093/nar/gkq754, Epub: AUG 26 2010
T.P. Lu, 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, Eric Y. Chuang*, Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women, CANCER EPIDEM BIOMAR (impact factor: 4.090, journal ranking: 40%), OCT 2010, 19(10):2590-2597, DOI: 10.1158/1055-9965.EPI-10-0332, Epub: AUG 27 2010
T.P. Lu, L.C. Lai, B.I. Lin, L.H. Chen, T.H. Hsiao, H.L. Liber, J.A. Cook, J.B. Mitchell, M.H. Tsai, Eric Y. Chuang*, Distinct signaling pathways after higher or lower doses of radiation in three closely related human lymphoblast cell lines, INT J RADIAT ONCOL (impact factor: 8.013, journal ranking: 10%), JAN 01 2010, 76(1):212-219, DOI: 10.1016/j.ijrobp.2009.08.015
Y.F. Lin, H. Nagasawa, Y. Peng, Eric Y. Chuang, 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 (impact factor: 3.372, journal ranking: 38%), JUN 2009, 171(6):708-715, DOI: 10.1667/RR1554.1
J.N. Kassis, V.M. Virador, E.A. Guancial, D. Kimm, A.S. Ho, M. Mishra, Eric Y. Chuang, J. Cook, D. Gius, E.C. Kohn, Genomic and phenotypic analysis reveals a key role for CCN1 (CYR61) in BAG3-modulated adhesion and invasion, J PATHOL (impact factor: 9.883, journal ranking: 5%), AUG 2009, 218(4):495-504, DOI: 10.1002/path.2557
H.I. Chen, F.H. Hsu, Y. Jiang, M.H. Tsai, P.C. Yang, P.S. Meltzer, Eric Y. Chuang*, A probe-density-based analysis method for array CGH data: simulation, normalization and centralization, BIOINFORMATICS (impact factor: 6.931, journal ranking: 9%), AUG 15 2008, 24(16):1749-1756, DOI: 10.1093/bioinformatics/btn321, Epub: JUL 04 2008
Z. Guo, M.H. Tsai, Y.H. Shiao, L.H. Chen, M.L. Wei, X. Lv, D. Gius, J.B. Little, J.B. Mitchell, Eric Y. Chuang*, DNA (cytosine-5)-methyltransferase 1 as a mediator of mutant p53-determined p16(ink4A) down-regulation, J BIOMED SCI (impact factor: 12.771, journal ranking: 8%), MAR 2008, 15(2):163-168, DOI: 10.1007/s11373-007-9222-y, Epub: NOV 24 2007
D. Gius, M.C. Funk, Eric 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, J.S. Rader, Profiling microdissected epithelium and stroma to model genomic signatures for cervical carcinogenesis accommodating for covariates, CANCER RES (impact factor: 13.312, journal ranking: 8%), AUG 01 2007, 67(15):7113-7123, DOI: 10.1158/0008-5472.CAN-07-0260
Y.F. Lin, C.Y. Chen, M.H. Tsai, M.S. Wu, Y.C. Wang, Eric Y. Chuang, J.T. Lin, P.C. Yang, L.P. Chow, Duodenal ulcer-related antigens from Helicobacter pylori: immunoproteome and protein microarray approaches, MOL CELL PROTEOMICS (impact factor: 7.381, journal ranking: 9%), JUL 2007, 6(6):1018-1026, DOI: 10.1074/mcp.M700009-MCP200, Epub: FEB 21 2007
M.H. Tsai, J.A. Cook, G.V. Chandramouli, W. DeGraff, H. Yan, S. Zhao, C.N. Coleman, J.B. Mitchell, Eric Y. Chuang*, Gene expression profiling of breast, prostate, and glioma cells following single versus fractionated doses of radiation, CANCER RES (impact factor: 13.312, journal ranking: 8%), APR 15 2007, 67(8):3845-3852, DOI: 10.1158/0008-54 72.CAN-06-4250
J.A. Cook, Eric Y. Chuang, M.H. Tsai, D. Coffin, W. Degraff, A.L. Sowers, J.B. Mitchell, Radiation-induced changes in gene-expression profiles for the SCC VII tumor cells grown in vitro and in vivo, ANTIOXID REDOX SIGN (impact factor: 7.468, journal ranking: 16%), JUL-AUG 2006, 8(7-8):1263-1272, DOI: 10.1089/ars.2006.8.1263
W. Zhao, Eric 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, D. Gius, Distinct effects of ionizing radiation on in vivo murine kidney and brain normal tissue gene expression, CLIN CANCER RES (impact factor: 13.801, journal ranking: 7%), JUN 15 2006, 12(12):3823-3830, DOI: 10.1158/1078-0432.CCR-05-2418
Eric Y. Chuang, 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, J.B. Little, Abnormal gene expression profiles in unaffected parents of patients with hereditary-type retinoblastoma, CANCER RES (impact factor: 13.312, journal ranking: 8%), APR 01 2006, 66(7):3428-3433, DOI: 10.1158/0008-5472.CAN-05-2847
M.H. Tsai, X. Chen, G.V. Chandramouli, Y. Chen, H. Yan, S. Zhao, P. Keng, H.L. Liber, C.N. Coleman, J.B. Mitchell, Eric Y. Chuang*, Transcriptional responses to ionizing radiation reveal that p53R2 protects against radiation-induced mutagenesis in human lymphoblastoid cells, ONCOGENE (impact factor: 8.756, journal ranking: 9%), JAN 26 2006, 25(4):622-632, DOI: 10.1038/sj.onc.1209082,Epub: OCT 10 2005
J.R. Stuart, H. Kawai, K.K. Tsai, Eric Y. Chuang, c-Abl regulates early growth response protein (EGR1) in response to oxidative stress, ONCOGENE (impact factor: 8.756, journal ranking: 9%), DEC 08 2005, 24(55):8085-8092, DOI: 10.1038/sj.onc. 1208953,Epub: AUG 01 2005
A.A. Jazaeri, 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, J. Boyd, Gene expression profiles associated with response to chemotherapy in epithelial ovarian cancers, CLIN CANCER RES (impact factor: 13.801, journal ranking: 7%), SEP 01 2005, 11(17): 6300-6310, DOI: 10.1158/1078-0432.CCR-04-2682
K.K. Tsai, Eric Y. Chuang, J.B. Little, Z.M. Yuan, Cellular mechanisms for low-dose ionizing radiation-induced perturbation of the breast tissue microenvironment, CANCER RES (impact factor: 13.312, journal ranking: 8%), AUG 01 2005, 65(15):6734-6744, DOI: 10.1158/0008-5472.CAN-05-0703
M.H. Tsai, H. Yan, X. Chen, G.V. Chandramouli, S. Zhao, D. Coffin, C.N. Coleman, J.B. Mitchell, Eric Y. Chuang*, Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays, MOL BIOTECHNOL (impact factor: 2.860, journal ranking: 67%), MAR 2005, 29(3):221-224, DOI: 10.1385/MB:29:3:221
A.M. Samuni, U. Kasid, Eric Y. Chuang, S. Suy, W. Degraff, M.C. Krishna, A. Russo, 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 (impact factor: 13.312, journal ranking: 8%), JAN 15 2005, 65(2):579-586
M. Lu, J. Suen, C. Frias, R. Pfeiffer, M.H. Tsai, E. Chuang, S.L. Zeichner, Dissection of the Kaposi's sarcoma-associated herpesvirus gene expression program by using the viral DNA replication inhibitor cidofovir, J VIROL (impact factor: 6.549, journal ranking: 30%), DEC 2004, 78(24):13637-13652, DOI: 10.1128/JVI.78.24.13637-13652.2004
L.E. Dodd, E.L. Korn, L.M. McShane, G.V. Chandramouli, Eric Y. Chuang, Correcting log ratios for signal saturation in cDNA microarrays, BIOINFORMATICS (impact factor: 6.931, journal ranking: 9%), NOV 01 2004, 20(16):2685-2693, DOI: 10.1093/bioinformatics/bth309, Epub: MAY 18 2004
D. Gius, 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, Eric Y. Chuang, J.B. Mitchell, A.P. Feinberg, Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach, CANCER CELL (impact factor: 38.585, journal ranking: 3%), OCT 2004, 6(4):361-371, DOI: 10.1016/j.ccr.2004.08.029
A. Loercher, T.L. Lee, J.L. Ricker, A. Howard, J. Geoghegen, Z. Chen, J.B. Sunwoo, R. Sitcheran, Eric Y. Chuang, J.B. Mitchell, A.S. Baldwin Jr., Nuclear factor-kappaB is an important modulator of the altered gene expression profile and malignant phenotype in squamous cell carcinoma, CANCER RES (impact factor: 13.312, journal ranking: 8%), SEP 15 2004, 64(18):6511-6523, DOI: 10.1158/0008-5472.CAN -04-0852
A. Rosenwald, Eric 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, L.M. Staudt, Fludarabine treatment of patients with chronic lymphocytic leukemia induces a p53-dependent gene expression response, BLOOD (impact factor: 25.476, journal ranking: 3%), SEP 01 2004, 104(5):1428-1434, DOI: 10.1182/blood-2003-09-3236, Epub: MAY 11 2004
X. Lu, W.E. Burgan, M.A. Cerra, Eric Y. Chuang, M.H. Tsai, P.J. Tofilon, K. Camphausen, Transcriptional signature of flavopiridol-induced tumor cell death, MOL CANCER THER (impact factor: 6.009, journal ranking: 28%), JUL 2004, 3(7):861-872
E.M. Goley, S.J. Anderson, C. Menard, E. Chuang, X. Lu, P.J. Tofilon, K. Camphausen, Microarray analysis in clinical oncology: pre-clinical optimization using needle core biopsies from xenograft tumors, BMC Cancer (impact factor: 4.638, journal ranking: 44%), MAY 19 2004, 4:20, DOI: 10.1186/1471-2407-4-20
H. Ge, Y.Y.E. Chuang, S. Zhao, M. Tong, Comparative genomics of Rickettsia prowazekii Madrid E and Breinl strains, J BACTERIOL (impact factor: 3.476, journal ranking: 58%), JAN 2004, 186(2):556-565, DOI: 10.1128/JB.186.2.556-565.2004
H. Su, N. Hu, J. Shih, Y. Hu, Q.H. Wang, Eric Y. Chuang, M.J. Roth, C. Wang, A.M. Goldstein, T. Ding, S.M. Dawsey, C. Giffen, M.R. Emmert-Buck, 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 (impact factor: 13.312, journal ranking: 8%), JUL 15 2003, 63(14):3872-3876
H. Ge, Y.E. Chuang, S. Zhao, J.J. Temenak, W.M. Ching, Genomic studies of Rickettsia prowazekii virulent and avirulent strains, ANN NY ACAD SCI (impact factor: 6.499, journal ranking: 19%), JUN 2003, 990:671-677, DOI: 10.1111/j.1749-6632.2003.tb 07442.x
A.M. Samuni, Eric Y. Chuang, M.C. Krishna, W. Stein, W. DeGraff, A. Russo, J.B. Mitchell, Semiquinone radical intermediate in catecholic estrogen-mediated cytotoxicity and mutagenesis: chemoprevention strategies with antioxidants, P NATL ACAD SCI USA (impact factor: 12.779, journal ranking: 12%), APR 29 2003, 100(9):5390-5395, DOI: 10.1073/pnas.0930078100
Y.Y. Chuang, 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, J.B. Mitchell, Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells, CANCER RES (impact factor: 13.312, journal ranking: 8%), NOV 01 2002, 62(21):6246-6254
Y.Y. Chuang, Q. Chen, J.P. Brown, J.M. Sedivy, H.L. Liber, Radiation-induced mutations at the autosomal thymidine kinase locus are not elevated in p53-null cells, CANCER RES (impact factor: 13.312, journal ranking: 8%), JUL 01 1999, 59(13):3073-3076
Y.Y. Chuang, Q. Chen, H.L. Liber, The construction of a p53-null cell line from human lymphoblast cells for mutagenesis studies, ENVIRON MOL MUTAGEN (impact factor: 3.579, journal ranking: 48%),1998, 31(Suppl 29):65
Y.Y. Chuang, 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 (impact factor: 3.579, journal ranking: 48%),1997, 29(Suppl 28):9
Y.Y. Chuang, 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 (impact factor: 3.372, journal ranking: 38%), NOV 1996, 146(5):494-500, DOI: 10.2307/3579549
Y.Y. Chuang, W.C. Chen, H.L. Liber, A DNA cross-linking agent (MMC) induces systematic differences in toxicity and mutagenicity in two closely related human lymphoblast cell lines, ENVIRON MOL MUTAGEN (impact factor: 3.579, journal ranking: 48%),1996, 27(Suppl 27):13
S.C. Liu, B. Ogretmen, Y.Y. Chuang, B.C. Stark, Selection and characterization of alpha-amylase-overproducing recombinant Escherichia coli containing the bacterial hemoglobin gene, APPL MICROBIOL BIOT (impact factor: 5.560, journal ranking: 23%), NOV 1992, 38(2):239-242
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Opportunity and Challenge of Bioinformatics, UCI-NTU joint symposium, January 3, 2019, Taipei
Advanced Biotechnologies in Translational Research, 2018 The 23rd Taiwan Joint Cancer Conference, May 5-6, 2018, Taipei
Genomics and Bioinformatics Approaches to Characterize non-coding RNAs for Radiosensitivity, the 63rd Annual Meeting of the Radiation Research Society, October 15-18, 2017, Cancun, Mexico.
Using Genomics and Bioinformatics Approaches to Explore Cancer Biomarkers, Radiation Oncology, MD Anderson Cancer Center, April 20-21, 2016, Houston, USA
Integration of Genomics and Bioinformatics for Exploring Cancer Biomarkers, 1st Chinese Precision Medicine Forum on Lung Cancer & 4th National Cancer Institute Annual Symposium, Beijing, China, 2016
Prognostication and Molecular Regulation of Acute Myeloid Leukemia: an Integration of Bioinformatics and Clinical Medicine, ICICIBME 2015, November 13, 2015, Indonesia
Combination of Genomic Technologies and Bioinformatics for Exploring New Cancer Biomarkers, EITA2012-BIO, Princeton, NJ, 2012.
Radiogenomics: An Emerging Field for Personalized Radiation Therapy, the 2011 International Symposium on Radiation Medicine: The Future Research and Development of Radiation Medicine, Taipei, Taiwan, 2011.
Potential Funding Mechanism for the Radiogenomics Consortium from NIH/NCI, 2nd International Radiogenomics Consortium Conference, New York City, NY, USA, 2010.
Use of Microarray Analysis for Radiogenomics, 1st International Radiogenomics Consortium Conference, Manchester, UK, 2009.
Microarray Gene Expression Data Analysis in Cancer Research, The 28th World Congress of Internal Medicine, Taipei, Taiwan, 2006.
Transcriptional Responses to Ionizing Radiation Reveal that p53R2 Protects Against Radiation-induced Mutagenesis in Human Lymphoblastoid Cells, 1st Asian Congress of Radiation Research, Hiroshima, Japan, 2005.
Gene expression profiles revealed p53R2 play a role in radiation-induced mutagenesis, 34th Annual Meeting of the European Environmental Mutagen Society, Maastricht, the Netherlands, 2004.
DNA Microarray Technology for functional genomics, 2002 Summer Institute on Bioinformatics, Taipei, Taiwan, 2002.
Microarray Technologies at the US National Cancer Institute, 2001 International Forum on Shanghai Biopharm Industry Development, Shanghai, China, 2001.
Patterns of gene expression following ionizing radiation in vivo, 2001 International Symposium of Radiation Research, Taipei, Taiwan, 2001.
Overview of gene array platforms, Gene Expression Profiling Technologies Workshop, The Jackson Laboratory, Bar Harbor, Maine, 2001.
Microarray, the technology, 92nd Annual Meeting of the American Association for Cancer Research, New Orleans, Louisiana, 2001.
Profiling oxidative stress-induced gene expression using cDNA microarrays, 2nd Annual Symposium of the John B. Little Center for Radiation Sciences & Environmental Health, Harvard University, 1999.
Cell cycle effects on X-ray mutagenesis at the thymidine kinase locus in a human lymphoblastoid cell line, 43rd Annual Meeting of the Radiation Research Society, San Jose, California, 1995.