莊曜宇 Chuang, Eric Y.
- 國立台灣大學電機工程學系 專任教授
-
財團法人工業技術研究院 副總暨生醫與醫材研究所所長
- 國立臺灣大學與中央研究院合辦-生物資訊學國際研究生博士學位學程 教授
- 國立臺灣大學生醫電子與資訊學研究所 教授
- 國立臺灣大學生命科學系 教授
- 國立臺灣大學流行病學與預防醫學研究所 教授
- 國立臺灣大學生命科學院與中央研究院合辦-基因體與系統生物學學位學程 教授
- 國立臺灣大學腫瘤醫學研究所 教授
- 國立臺灣大學醫療器材研發中心 副主任
- 國立臺灣大學基因體暨精準醫學研究中心-生物資訊暨生物統計核心實驗室 主持人
- Ph.D. Harvard University, 1997
- M.S. Illinois Institute of Technology, 1991
- B.S. Tunghai University, 1986
主要研究領域
研究領域摘要
*食道癌：
因應現今全球食道癌的發生機率持續攀升，然而食道癌患者卻因常在晚期才診斷出病症，而此時已不再適合做切除手術，因此導致治療效果普遍不佳。為增加療效，近幾年來，醫界發展出多種複合式療法，例如: 合併化學放射治療(concurrent chemoradiation therapy, CCRT)後再進行手術已用來增長食道癌病患的壽命，但此法僅有10%~40%食道癌患者有機會被完全治癒。本實驗室與台大外科部合作利用基因型微陣列晶片來檢視食道癌患者在施行CCRT反應與單核苷酸多型性(single-nucleotide polymorphism, SNP)的關連性。結果顯示兩種SNP(rs16863886及rs4954256)與CCRT的反應有密切的相關性，這結果已發表於頂尖的放射腫瘤國際期刊，並且通過美國與台灣的專利。
*肺癌：
肺癌是世界上持續高踞癌症死亡主因的前幾位。在癌細胞的發生過程中，癌症細胞內的目前治療肺癌的方式主要是透過化學療法和放射療法，但是這些治療方式皆會產生嚴重的副作用。我們團隊為了研究台灣非吸煙女性肺癌患者的新型分子靶點，從60名非吸煙肺癌患者中收集了成對的正常和腫瘤組織進行微陣列分析。從微陣列結果可以看出，SEMA3B，SEMA3G，SEMA5A，SEMA6A和SEMA6D在腫瘤組織中均顯著下調。我們團隊在semaphorin基因中，選擇SEMA6A進行進一步研究。第一、藉大量表現SEMA6A基因於肺癌細胞株中來探討這些基因於肺癌生成上的作用； 第二、利用微陣列來探討SEMA6A基因於肺癌生成的分子機轉； 第三、利用裸鼠實驗模型來進一步探討SEMA6A基因於體內功能上所扮演的角色。
除此之外，我們團隊以CL系列之肺癌細胞株結合生物資訊方式研究肺癌中micro-RNA及化療藥物對癌症可能之影響。結果顯示，在肺癌中miR-499a對Jagged 1的調控會促進放射線敏感性，因此可能可以做為肺癌醫療上的目標。此外，經過使用化療藥物Mitomycin C處理CL細胞實驗後，我們團隊提出直接證據證明，若未正確使用抗癌藥物可能反而會使癌細胞轉移，造成更嚴重的病況。此一系列肺癌相關研究也都已發表於相關的頂尖國際期刊中。
*台灣帝雉基因定序：
台灣帝雉，又稱帝雉和黑長尾雉，是台灣特有的長尾雉屬鳥類，棲息在海拔2500公尺以上中高海拔，地理分布於台灣的中、高海拔山區，是台灣的雉科鳥類中棲息於最高海拔者。過去台灣帝雉近年來因為溫室氣體效應，造成全球氣候急遽變化，逐漸減少成為瀕危物種，近年台灣對保育鳥類有較好的保護，許多地方 (含台灣中部山區的幾個國家公園)的野生帝雉族群有增加的現象，所以世界自然保護聯盟（IUCN）的紅皮書從1994年版將其定為近危物種。由於牠在鳥類種的分化與演化的特殊地位尚未被界定，牠的遺傳資源彌足珍貴，需要對其基因體有更詳盡的分析，以確立其在演化分類上的意義與價值。我們團隊利用既有之次世代定序平台進行帝雉全基因定序並達成下列五項目標：1.建立非模式物種定序演算平台；2.定序帝雉基因組序列；3.定序轉錄體協助基因組序列組裝；4.藉由轉錄體定序結果分析帝雉演化過程與親源；5.藉由比對其他雉科鳥類基因體以提供保育與繁殖參考。
我所指導的研究團隊長期致力於應用研究，尤其是生物晶片的開發與癌症、心臟疾病等基因體研究，利用高通量分析與資料分析方法，除了探討癌症內基因調控機制外，我們團隊亦提出了能夠準確預測各癌症預後的生物標記，這些應用研究之成果對於人類的健康與醫療具有極大貢獻，相關成果已發表在逾百篇之國際期刊論文中。以下分別說明：
*急性骨髓性白血病：
急性骨髓性白血病為台灣血癌中發生率最高的一種類型，在最近的研究中顯示，這種病人的白血病細胞中有許多基因的突變，與血癌的發生可能有重要關聯。在這項跨領域研究中，我們團隊利用高通量生物晶片技術，分析台大醫院約三百名血癌病患之基因表現圖譜，取得全基因表現之巨量資料，並使用生物資訊之分析方法，在數百個微小核糖核酸與幾萬個基因中，發現了在血癌中相當重要的三個微小核糖核酸（miR-9-5p、miR-155-5p與miR-203），以及另外十一個基因的表現可以預測病人的預後。該研究團隊並將這些微小核糖核酸及基因分別建構了兩套預測分數系統，未來病患在確診時，只需要測量這些微小核糖核酸及基因的表現情形並計算分數，即可快速的預測病患未來對治療的反應。此外，該研究團隊鎖定約四分之一帶有NPM1基因突變的血癌患者。此研究首度提出，該基因突變具有破壞血癌細胞中正常的「基因調控網路」之能力，更可能因此影響病患的預後，研究團隊並利用分子生物實驗與國際的血癌病患資料驗證了這個發現。這些成果不僅有助於了解血癌細胞內錯綜複雜的突變基因與基因網路，更提供未來抗血癌研究及開發新治療之可能標的。此研究的發現為未來血癌治療提供突破性的進展，更呼應了美國總統歐巴馬所提出的「精準醫學計畫（Precision Medicine Initiative）」，未來透過偵測這些分子標記，醫師得以了解每個患者的腫瘤細胞特性，安排個人化的治療方式，提高治癒率，同時有效地減低醫療資源的支出。上述研究成果已發表於國際腫瘤類期刊中排名前5%之白血病期刊（Leukemia）與前10%之腫瘤標靶（Oncotarget）等頂尖期刊，可見其研究品質深獲肯定，且經記者會發表後，受到眾多媒體報導，並刊載於本校校訊頭版，學術成果表現優異。
*心臟疾病：
心房顫動是最常見的一種心律不整，心房顫動患者發生中風的風險是一般人的五到七倍，我們與台大醫院心臟內科等多位醫師共同研究，利用新穎之全基因體掃描技術，發現引起心房顫動心律不整台灣特有之基因KCNIP1：第一型鈣調控鉀離子通道結合蛋白基因(Kv-channel interacting protein 1; KCNIP1)，並針對此基因進行功能性以及機轉的探討，第一個證實KCNIP1在心臟電生理的角色，帶有此基因拷貝數變異之個體，發生心房顫動風險為未帶有此基因拷貝數變異之個體的2倍多，未來將可應用在健康成人或病人檢驗，若檢驗出有上述基因拷貝數變異，可提早注意心律不整的症狀，並改善生活習慣，以減緩心房顫動及心律不整的發生，早期診斷、早期治療，進而減少台灣中風的發生率，減少社會的經濟與醫療成本。這項研究已刊載於國際知名的NATURE系列期刊NATURE COMMUNICATIONS上。
*華人乳癌基因資料庫：
我們與永齡健康基金會產學合作計畫「華人乳癌基因資料庫及個人化雲端諮詢平台」(執行期間：2015年5月至2017年5月) 針對東方人族群的乳癌進行研究，計畫建立華人女性的乳癌次世代定序基因資料庫及個人化雲端諮詢平台，用以協助醫師及患者進行個人化的乳癌療程將會有非常高的臨床醫療價值。此華人乳癌醫療諮詢平台可輸出提供醫護人員及病患、家屬友善的使用介面與基因檢測報告資訊，協助醫生提高乳癌個人化醫療的成功率。這項研究受到許多關注，台大研發處更因此專刊採訪我們，全文於106年1月刊登於刊物Landscope並公布於台大研發處英文版網站，供全球各界收看。
*建置生物資訊資料庫：
本人的研究主軸在生物醫學上，隨著研究問題拓展，不僅能以其他領域之方法解決遭逢之困難，並能輔以真實之實驗數據加速生物資訊演算法與生物統計方法之開發。現今而言，此二者結合之方向已成為當前研究之主流，以此方法尋找出的生物標記不僅只能發表於學術期刊上，且亦有其臨床醫學上的應用價值。我們與國際知名企業IBM及美國國家衛生總署NIH合作開發台灣第一套線上基因晶片分析系統(National Taiwan University Microarray Analysis Platforms)，此系統整合了多個基因資料庫與生物路徑資訊，讓使用者能在容易操作的圖型化介面下進行複雜的微陣列晶片之分析。此外，我們之研究團隊亦於2012年發表了一套微型核糖核酸線上分析工具(miRsystem)，使用者僅需輸入待研究之微型核糖核酸列表，系統即可自動進行分析統計分析，並輸出其下游之預測調控基因以及參與之生物路徑，此系統大幅簡化了生醫學者在研究微型核糖核酸上的困難，系統上線5年來已有來自82個國家、近54,000人次使用，該論文亦獲得超過149篇論文的引用，可見此系統已成為該研究領域之重要線上工具，並對於相關生醫研究帶來實質貢獻。
除了miRsystem之外，在 Biocondutor上的iGC and anamiR也有相當優秀的表現。
iGC: This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.
自2015年9月上線以來，截至2017年9月15日，已累積了3087筆使用量。
anamiR: This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.
2016年10月上線，截至2017年9月15日用量為1360筆。
Eric Y Chuang (莊曜宇), ScD, EMBA
Eric Y Chuang received his doctorate in cancer biology with toxicology and molecular genetics as two sub-specialties from Harvard University in 1997 and his doctoral thesis was to study radiation-induced mutagenesis in human cells. After graduation, he stayed at Harvard as a postdoctoral fellow for one year. He then joined the Radiation Biology Branch of National Cancer Institute (NCI), National Institutes of Health (NIH) as an IRTA fellow to study radiogenomics in Bethesda, MD, USA. Next, he became the Head of Microarray Laboratory for Radiation Oncology Sciences Program at NCI; his lab was to develop new initiatives that utilized state-of-the-art microarray technologies for studying radiation oncology related research projects. After working at the NIH for several years, he took a faculty position at National Taiwan University (NTU). In 2009, he joined the Radiation Research Program of Division of Cancer Treatment and Diagnosis at NCI as a Program Director to oversee a portfolio of NIH grants that included radiation-induced signaling pathways, molecular mechanisms and normal tissue injuries as well as radiation related genomic studies. In 2011, he returned to NTU and was serving as the Director of Graduate Institute of Biomedical Electronics and Bioinformatics (BEBI) in 2012-2018. Dr. Chuang received his Executive MBA degree in International Business Management from NTU in June 2017. Currently, he is a Professor of BEBI at NTU and serving as the VP & General Director, Biomedical Technology and Device Research Laboratories(BDL), Industrial Technology Research Institute(ITRI), Hsinchu, Taiwan. Being an expert in genomic technologies, bioinformatics, cancer, radiation biology & oncology, biomedical engineering, and precision medicine, he has published more than 168 peer-reviewed papers in related fields. Moreover, Dr. Chuang has been serving as an editorial board member of Scientific Reports and the Editor-in-Chief of Translation Cancer Research.
Current Research Interests: Radiogenomics, Radiation-induced signaling pathways, Cancer genomics, Bioinformatics, Precision medicine, and Artificial intelligence(AI).
Journal articles & book chapters
1. Z.Q. Hu, Y.M. Hung, L.H. Chen, L.C. Lai, M.H. Pang, Eric Y. Chuang, M.H. Tsai, “NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition” , IEEE/ACM Transactions on Computational Biology and Bioinformatics , Vol. 21 , 254-264, Mar. 2024
2. Kevin C.Y. Huang, T.W. Ke, C.Y. Lai, W.Z. Hong, H.Y. Chang, C.Y. Lee, C.H. Wu, S.F. Chiang, J.A. Liang, J.Y. Chen, P.C. Yang, William T.L. Chen, Eric Y. Chuang, K.S. Clifford Chao, “Inhibition of DNMTs increases neoantigen-reactive T-cell toxicity against microsatellite-stable colorectal cancer in combination with radiotherapy” , Biomedicine & Pharmacotherapy , Vol. 177 , 116958-undefined, Aug. 2024
3. C.H. Sally Chen, T.H. Yuan, T.P. Lu, H.Y. Lee, Y.H. Chen, L.C. Lai, M.H. Tsai, Eric Y. Chuang*, C.C. Chan, “Exposure-associated DNA methylation among people exposed to multiple industrial pollutants” , Clinical Epigenetics , Vol. 16 , Aug. 2024
4. H.L. Chen, H.Y. Chiang, D. R. Chang, C.F. Cheng, C. C.N. Wang, T.P. Lu, C.Y. Lee, A. Chattopadhyay, Y.T. Lin, C.C. Lin, P.T. Yu, C.F. Huang, C.H. Lin, H.C. Yeh, I.W. Ting, H.K. Tsai, Eric Y. Chuang, A. Tin, F.J. Tsai, C.C. Kuo, “Discovery and prioritization of genetic determinants of kidney function in 297,355 individuals from Taiwan and Japan” , Nature Communications , Vol. 15 , Sep. 2024
5. P.S. Huang, J.F. Cheng, G.W. Li, Eric Y. Chuang, J.J. Chen, F.C. Chiu, C.K. Wu, Y.C. Wang, J.J. Hwang, C.T. Tsai, “Copy number variation of gasdermin D gene is associated with atrial fibrillation-related thromboembolic stroke” , Europace , Vol. 25 , May 2023
6. Chattopadhyay,Lee,Shen,Lu,Hsiao,Lin,Lai,Tsai,Lu,Chuang, “Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data” , Journal of Biomedical Informatics , Vol. 143 , 104423-undefined, Jul. 2023
7. Watson H.S. Tseng, A. Chattopadhyay, N.N. Phan, Eric Y. Chuang, Oscar K. Lee, “Utilizing multimodal approach to identify candidate pathways and biomarkers and predicting frailty syndrome in individuals from UK Biobank” , GeroScience , Vol. 46 , 1211-1228, Jul. 2023
8. W.N. Lyu, M.C. Lin, C.Y. Shen, L.H. Chen, Y.H. Lee, S.K. Chen, L.C. Lai, Eric Y. Chuang, P.J. Lou, M.H. Tsai, “An Oral Microbial Biomarker for Early Detection of Recurrence of Oral Squamous Cell Carcinoma” , ACS Infectious Diseases , Vol. 9 , 1783-1792, Aug. 2023
9. Y.C. Hsu, H.L. Chen, C.F. Cheng, A. Chattopadhyay, P.S. Chen, C.C. Lin, H.Y. Chiang, T.Y. Liu, C.H. Huang, C.C. Kuo, Eric Y. Chuang, T.P. Lu, F.J. Tsai, “The largest genome-wide association study for breast cancer in Taiwanese Han population” , Breast Cancer Research and Treatment , Vol. 203 , 291-306, Oct. 2023
10. Chattopadhyay,Lee,Lee,Liu,Chen,Li,Lai,Tsai,Ni,Chiu,Lu,Chuang, “Twnbiome: a public database of the healthy Taiwanese gut microbiome” , BMC Bioinformatics , Vol. 24 , Dec. 2023
11. C.Y. Lin, W.T. Tseng, Y.Y. Chang, M.H. Tsai, Eric Y. Chuang, T.P. Lu, L.C. Lai, “Lidocaine and Bupivacaine Downregulate MYB and DANCR lncRNA by Upregulating miR-187-5p in MCF-7 Cells” , Frontiers in Medicine , Vol. 8 , Jan. 2022
12. U.N. Wisesty, A. Purwarianti, A. Pancoro, A. Chattopadhyay, N.N. Phan, Eric Y. Chuang, T.R. Mengko, “Join Classifier of Type and Index Mutation on Lung Cancer DNA Using Sequential Labeling Model” , IEEE Access , Vol. 10 , 9004-9021, Jan. 2022
13. M.Z. Chen, L.Y. Su, P.H. Ko, M.H. Hsu, L.L. Chuang, L.H. Chen, T.P. Lu, Eric Y. Chuang, L.P. Chow, M.H. Tsai, H.H. Hsu, L.C. Lai, “Extracellular domain of semaphorin 5A serves a tumor‑suppressing role by activating interferon signaling pathways in lung adenocarcinoma cells” , International Journal of Oncology , Vol. 60 , Feb. 2022
14. P.S. Huang, Y.H. Tseng, C.F. Tsai, J.J. Chen, S.C. Yang, F.C. Chiu, Z.W. Chen, J.J. Hwang , Eric Y. Chuang*, Y.C. Wang, C.T. Tsai, “An Artificial Intelligence-Enabled ECG Algorithm for the Prediction and Localization of Angiography-Proven Coronary Artery Disease” , Biomedicines , Vol. 10 , 394-undefined, Feb. 2022
15. Chiu,Tsai,Huang,Shih,Tsai,Hwang,Wang,Chuang,Tsai,Chang, “The Gut Microbiome, Seleno-Compounds, and Acute Myocardial Infarction” , Journal of Clinical Medicine , Vol. 11 , 1462-undefined, Mar. 2022
16. S. Shivani, C.Y. Kao, A. Chattopadhyay, J.W. Chen, L.C. Lai, W.H. Lin, T.P. Lu I.H. Huang, M.H. Tsai, C.H. Teng, J.J. Wu, Y.H. Hsieh, M.C. Wang, Eric Y. Chuang, “Uremic Toxin-Producing Bacteroides Species Prevail in the Gut Microbiota of Taiwanese CKD Patients: An Analysis Using the New Taiwan Microbiome Baseline” , Frontiers in Cellular and Infection Microbiology , Vol. 12 , Apr. 2022
17. Y.M. Hung, W.N. Lyu, M.L. Tsai, C. Liu, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “To compare the performance of prokaryotic taxonomy classifiers using curated 16S full-length rRNA sequences” , Computers in Biology and Medicine , Vol. 145 , 105416-undefined, Jun. 2022
18. Daniel T.L Chen, S.W. Cheng, Tiffany Chen, Jane P.C. Chang, B.F. Hwang, H.H. Chang, Eric Y. Chuang, C.H. Chen, K.P. Su, “Identification of Genetic Variations in the NAD-Related Pathways for Patients with Major Depressive Disorder: A Case-Control Study in Taiwan” , Journal of Clinical Medicine , Vol. 11 , 3622-undefined, Jun. 2022
19. Y.P. Hsieh, Y.M. Hung, M.H. Tsai, L.C. Lai, Eric Y. Chuang, “16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences” , Frontiers in Bioinformatics , Vol. 2 , Aug. 2022
20. H.H. Chao, J.L. Luo, M.H. Hsu, L.H. Chen, T.P. Lu, M.H. Tsai, Eric Y. Chuang, L.L. Chuang, L.C. Lai, “Regulatory mechanisms and function of hypoxia-induced long noncoding RNA NDRG1-OT1 in breast cancer cells” , Cell Death & Disease , Vol. 13 , Sep. 2022
21. C.S. Huang, M.L. Tsai, T.P. Lu, C.C. Tu, C.Y. Liu, C.J. Huang, Y.S. Ho, S.H. Tu, Eric Y Chuang, L.M. Tseng, C.C. Huang, “The extended concurrent genes signature for disease-free survival in breast cancer” , Journal of the Formosan Medical Association , Vol. 121 , 1945-1955, Oct. 2022
22. A. Chattopadhyay, C.Y. Shih, Y.C. Hsu, J.M. Jimmy Juang, Eric Y. Chuang, T.P. Lu, “CLIN_SKAT: an R package to conduct association analysis using functionally relevant variants” , BMC Bioinformatics , Vol. 23 , Oct. 2022
23. P.W. Yang, M.C. Lin, P.M. Huang, C.P. Wang, T.C. Chen, C.N. Chen, M.H. Tsai, Jason C.H. Cheng, Eric Y. Chuang, M.S. Hsieh, P.J. Lou, J.M. Lee, “Risk Factors and Genetic Biomarkers of Multiple Primary Cancers in Esophageal Cancer Patients” , Frontiers in Oncology , Vol. 10 , Jan. 2021
24. H.C. Chan, A. Chattopadhyay, Eric Y. Chuang, T.P. Lu, “Development of a Gene-Based Prediction Model for Recurrence of Colorectal Cancer Using an Ensemble Learning Algorithm” , Frontiers in Oncology , Vol. 11 , Feb. 2021
25. S. Shivani, A. Chattopadhyay, Eric Y. Chuang, “Targeting the gut microbiome for non-communicable diseases: present and future” , Annals of Translational Medicine , Vol. 9 , 361-361, Mar. 2021
26. C.H. Wu, H.T. Yeh, C.S. Hsieh, C.C. Huang, A. Chattopadhyay, Y.C. Chung, S.H. Tu, Y.H. Li, T.P. Lu, L.C. Lai, M.F. Hou, K.J. Chang, M.H. Tsai, Eric Y. Chuang, “Evolutionary Trajectories and Genomic Divergence in Localized Breast Cancers after Ipsilateral Breast Tumor Recurrence” , Cancers , Vol. 13 , 1821-undefined, Apr. 2021
27. Y.W. Hsiao, C.L. Tao, Eric Y. Chuang, T.P. Lu, “A risk prediction model of gene signatures in ovarian cancer through bagging of GA-XGBoost models” , Journal of Advanced Research , Vol. 30 , 113-122, May 2021
28. J.M. Jimmy Juang, T.P. Lu, M.W. Su, C.W. Lin, J.H. Yang, H.W. Chu, C.H. Chen, Y.W. Hsiao, C.Y. Lee, L.M. Chiang, Q.Y. Yu, C.H. Kate Hsiao, C.Y. Julius Chen, P.E. Wu, C.H. Pai, Eric Y. Chuang*, C.Y. Shen, “Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine” , Journal of Advanced Research , Vol. 30 , 147-158, May 2021
29. C.H. Shih, L.L. Chuang, M.H. Tsai, L.H. Chen, Eric Y. Chuang, T.P. Lu, and L.C. Lai, “Hypoxia-Induced MALAT1 Promotes the Proliferation and Migration of Breast Cancer Cells by Sponging MiR-3064-5p” , Frontiers in Oncology , Vol. 11 , 147-158, May 2021
30. Y.M. Hung, M.H. Tsai, L.C. Lai, Eric Y. Chuang, “ATTRACTIVE – An Auto-Updating Database for Experimental Protocols in Regenerative Medicine” , IEEE Access , Vol. 9 , 75202-75210, May 2021
31. Y.C. Cheng, L.Y. Su, L.H. Chen, T.P. Lu, Eric Y. Chuang, M.H. Tsai, L.L. Chuang, L.C. Lai, “Regulatory Mechanisms and Functional Roles of Hypoxia-Induced Long Non-Coding RNA MTORT1 in Breast Cancer Cells” , Frontiers in Oncology , Vol. 11 , Jun. 2021
32. C. Goswami, A. Chattopadhyay, Eric Y. Chuang, “Rare variants: data types and analysis strategies” , Annals of Translational Medicine , Vol. 9 , 961-961, Jun. 2021
33. C.H. Lin, Ruby Y.J. Huang, T.P. Lu, K.T. Kuo, K.Y. Lo, C.H. Chen, IC. Chen, Y.S. Lu, Eric Y. Chuang, J. P. Thiery, C.S. Huang, A.L. Cheng, “High prevalence of APOA1/C3/A4/A5 alterations in luminal breast cancers among young women in East Asia” , npj Breast Cancer , Vol. 7 , Jul. 2021
34. A. Chattopadhyay, Z.H. Teoh, C.Y. Wu , J.M. J. Juang, L.C. Lai, M.H. Tsai, C.H. Wu, T.P. Lu, Eric Y. Chuang, “CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer” , Database , Vol. 2021 , Jul. 2021
35. Y.M. Hung, T.P. Lu, M.H. Tsai, L.C. Lai, Eric Y. Chuang, “EasyMAP: A user-friendly online platform for analyzing 16S ribosomal DNA sequencing data” , New Biotechnology , Vol. 63 , 37-44, Jul. 2021
36. C.H. Wu, C.S. Hsieh, Y.C. Chang, C.C. Huang, H.T. Yeh, M.F. Hou, Y.C. Chung, S.H. Tu, K.J. Chang, A. Chattopadhyay, L.C. Lai, T.P. Lu, Y.H. Li, M.H. Tsai, Eric Y. Chuang, “Differential whole-genome doubling and homologous recombination deficiencies across breast cancer subtypes from the Taiwanese population” , Communications Biology , Vol. 4 , Sep. 2021
37. N.N. Phan, C.Y. Hsu, C.C. Huang, L.M. Tseng, Eric Y. Chuang, “Prediction of Breast Cancer Recurrence Using a Deep Convolutional Neural Network Without Region-of-Interest Labeling” , Frontiers in Oncology , Vol. 11 , Oct. 2021
38. N.N. Phan, A. Chattopadhyay, T.T. Lee, H,I Yin, T.P. Lu, L.C. Lai, H.L. Hwa, M.H. Tsai, Eric Y Chuang, “High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data” , Briefings in Bioinformatics , Vol. 22 , Nov. 2021
39. W.T. Fang, C.H. Wu, Q.L. Sun, Z.T. Gu, L. Zhu, T. Mao, X.F. Zhang, N. Xu, T.P. Lu, M.H. Tsai, L.H. Chen, L.C. Lai, Eric Y. Chuang, “Novel Tumor-Specific Antigens for Immunotherapy Identified From Multi-omics Profiling in Thymic Carcinomas” , Frontiers in Immunology , Vol. 12 , Nov. 2021
40. C.Y. Lee, Y.F. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes” , New Biotechnology , Vol. 65 , 42-52, Nov. 2021
41. C.H. Lu, C.H. Wu, M.H. Tsai, L.C. Lai, Eric Y Chuang, “MutScape: an analytical toolkit for probing the mutational landscape in cancer genomics” , NAR Genomics and Bioinformatics , Vol. 3 , Dec. 2021
42. N.N. Phan, C.C. Huang, L.M. Tseng, Eric Y. Chuang, “Predicting Breast Cancer Gene Expression Signature by Applying Deep Convolutional Neural Networks From Unannotated Pathological Images” , Frontiers in Oncology , Vol. 11 , Dec. 2021
43. P.H. Ko, G. Lenka, Y.A. Chen, Eric Y. Chuang, M.H. Tsai, Y.P. Sher, L.C. Lai, “Semaphorin 5A suppresses the proliferation and migration of lung adenocarcinoma cells” , International Journal of Oncology , Vol. undefined , Jan. 2020
44. J.M. Jimmy Juang, A. Binda, S.J. Lee, J.J. Hwang, W.J. Chen, Y.B. Liu, L. Y. Lin, C. C. Yu, L. T. Ho, H. C. Huang, C. Y. Julius Chen, T. P. Lu, L. C. Lai, S. F. Sherri Yeh, L. P. Lai, Eric Y. Chuang, I. Rivolta, C. Antzelevitch, “GSTM3 variant is a novel genetic modifier in Brugada syndrome, a disease with risk of sudden cardiac death” , EBioMedicine , Vol. 57 , 102843-undefined, Jul. 2020
45. Jimmy Juang,Liu,Julius Chen,Yu,Chattopadhyay,Lin,Chen,Yu,Huang,Ho,Lai,Hwang,Lin,Liao,Chen,Sherri Yeh,Chuang,Yang,Lin,Lu,Chuang,Ackerman, “Validation and Disease Risk Assessment of Previously Reported Genome-Wide Genetic Variants Associated With Brugada Syndrome” , Circulation: Genomic and Precision Medicine , Vol. 13 , 102843-undefined, Aug. 2020
46. H.C. Lo, D.S. Yu, H.W. Gao, M.H. Tsai, Eric Y. Chuang, “IL-27/IL-27RA signaling may modulate inflammation and progression of benign prostatic hyperplasia via suppressing the LPS/TLR4 pathway” , Translational Cancer Research , Vol. 9 , 4618-4634, Aug. 2020
47. P. S. Huang, C. S. Hsieh, S. N. Chang, J. J. Chen, F. C. Chiu, C. K. Wu, J. J. Hwang, Eric Y Chuang, C. T. Tsai, “Prevalence of sudden arrhythmic death syndrome-related genetic mutations in an Asian cohort of whole genome sequence” , EP Europace , Vol. 22 , 1287-1297, Aug. 2020
48. H.C. Lo, J.H. Hsu, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “MicroRNA-107 enhances radiosensitivity by suppressing granulin in PC-3 prostate cancer cells” , Scientific Reports , Vol. 10 , 1287-1297, Sep. 2020
49. C.C. Chen, W.K. Wu, C.M. Chang, S. Panyod, T.P. Lu, J.M. Liou, Y.J. Fang, Eric Y. Chuang, M.S. Wu, “Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles” , Journal of the Formosan Medical Association , Vol. 119 , 1791-1798, Dec. 2020
50. C.S. Hsieh, P.S. Huang, S.N. Chang, C.K. Wu, J.J. Hwang, E.Y. Chuang*, C.T. Tsai, “Genome-Wide Copy Number Variation Association Study of Atrial Fibrillation Related Thromboembolic Stroke” , J. Clin. Med , Vol. 8(3) , 332-, Mar. 2019
51. P.H. Ko, C.W. Huang, H.H. Chang, Eric Y. Chuang, M.H. Tsai, L.C. Lai, “Identifying the functions and biomarkers of Codonopsis pilosula and Astragalus membranaceus aqueous extracts in hepatic cells” , Chinese Medicine , Vol. 14 , Mar. 2019
52. T.T. Wang, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “anamiR: integrated analysis of MicroRNA and gene expression profiling” , BMC Bioinformatics , Vol. 20 , May 2019
53. C.H. Lin, C.C. Chen, H.L. Chiang, J.M. Liou, C.M. Chang, T.P. Lu, Eric Y. Chuang, Y.C. Tai, C. Cheng, H.Y. Lin, M.S. Wu, “Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson’s disease” , Journal of Neuroinflammation , Vol. 16 , Jun. 2019
54. C.Y. Lee, A. Chattopadhyay, L.M. Chiang, J.M. Jimmy Juang, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases” , Database , Vol. 2019 , Jul. 2019
55. W.C. Lin, L.H. Chen, Y.C. Hsieh, P.W. Yang, L.C. Lai, Eric Y. Chuang, J.M. Lee, M.H. Tsai, “miR-338-5p inhibits cell proliferation, colony formation, migration and cisplatin resistance in esophageal squamous cancer cells by targeting FERMT2” , Carcinogenesis , Vol. 40 , 883-892, Jul. 2019
56. L.C. Lai, Q.L. Sun, Y.A. Chen, Y.W. Hsiao, T.P. Lu, M.H. Tsai, L. Zhu, Eric Y. Chuang*, W.T. Fang, “Using proteomic profiling to characterize protein signatures of different thymoma subtypes” , BMC Cancer , Vol. 19 , 883-892, Aug. 2019
57. L.H. Chen, C.Y. Liao, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “Semaphorin 6A Attenuates the Migration Capability of Lung Cancer Cells via the NRF2/HMOX1 Axis” , Scientific Reports , Vol. 9 , 883-892, Sep. 2019
58. J.M. Liou, C.C. Chen, C.M. Chang, Y.J. Fang, M.J. Bair, P.Y. Chen, C.Y. Chang, Y.C. Hsu, M.J. Chen, C.C. Chen, J.Y. Lee, T.H. Yang, J.C. Luo, C.Y. Chen, W.F. Hsu, Y.N. Chen, J.Y. Wu, J.T. Lin, TP Lu, Eric Y Chuang, Emad M El-Omar, MS. Wu, “Long-term changes of gut microbiota, antibiotic resistance, and metabolic parameters after Helicobacter pylori eradication: a multicentre, open-label, randomised trial” , The Lancet Infectious Diseases , Vol. 19 , 1109-1120, Oct. 2019
59. W.C. Lin, L.H. Chen, Y.C. Hsieh, P.W. Yang, L.C. Lai, E.Y. Chuang, J.M. Lee, M.H. Tsai, “miR-338-5p inhibits cell proliferation, colony formation, migration, and cisplatin resistance in esophageal squamous cancer cells by targeting FERMT2” , Carcinogenesis , Vol. bgy189 , Jul. 2019
60. P.H. Ko, Y.C. Shen, K. Murugan, C.W. Huang, G. Sivakumar, P. Pal, C.C. Liao, K.S. Luo, E.Y. Chuang, M.H. Tsai, L.C. Lai, “Macrophage Migration Inhibitory Factor Acts as the Potential Target of a Newly Synthesized Compound, 1-(9′-methyl-3′-carbazole)-3, 4-dihydro-β-carboline” , Scientific Reports , Feb. 2019
61. Y.F. Lee, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, E.Y. Chuang*, “CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system” , DATABASE-OXFORD , Jan. 2018
62. T.H. Hsiao, Y.H. Chen, H.I. Chen, Y.C. Chiu, E.Y. Chuang*, Y. Chen, “Utilizing Cancer–Functional Gene set–Compound Networks to Identify Putative Drugs for Breast Cancer” , Comb Chem High T Scr , Vol. 21(2) , 74-83, Feb. 2018
63. C.Y. Lee, P.H. Hsieh, L.M. Chiang, A. Chattopadhyay, K.Y. Li, Y.F. Lee, T.P. Lu, L.C. Lai, E.C. Lin, H. Lee, S.T. Ding, M.H. Tsai, C.Y. Chen, E.Y. Chuang*, “Whole-Genome De Novo Sequencing Reveals Unique Genes that Contributed to the Adaptive Evolution of the Mikado Pheasant” , Gigascience , Vol. 7(5) , May 2018
64. C.Y. Shen, Y.C. Chang, L.H. Chen, W.C. Lin, Y.H. Lee, S.T. Yeh, H.K. Chen, W. Fang, C.P. Hsu, J.M. Lee, T.P. Lu, P.W. Hsiao, L.C. Lai, M.H. Tsai, E.Y. Chuang*, “The extracellular SEMA domain attenuates intracellular apoptotic signaling of semaphorin 6A in lung cancer cells” , Oncogenesis , Dec. 2018
65. C.S. Hsieh, C.T. Tsai, Y.H. Chen, S.N. Chang, J.J. Hwang, E.Y. Chuang*, I.H. Wu, “Global Expression Profiling Identifies a Novel Hyaluronan Synthases 2 Gene in the Pathogenesis of Lower Extremity Varicose Veins” , J. Clin. Med , Vol. 7(12) , 537-, Dec. 2018
66. Y.P. Lai, L.B. Wang, W.A. Wang, L.C. Lai, M.H. Tsai, T.P. Lu, E.Y. Chuang*, “iGC—an integrated analysis package of gene expression and copy number alteration” , BMC Bioinformatics , Jan. 2017
67. G.L., M.H. Tsai, H.C. Lin, J.H. Hsiao, Y.C. Lee, T.P. Lu, J.M. Lee, C.P. Hsu, L.C. Lai, E.Y. Chuang*, “Identification of Methylation-Driven, Differentially Expressed STXBP6 as a Novel Biomarker in Lung Adenocarcinoma” , Scientific Reports , Feb. 2017
68. Y.C. Chiu, L.J. Wang, T.P. Lu, T.H. Hsiao, E.Y. Chuang*, Y. Chen, “Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival” , BMC Bioinformatics , Feb. 2017
69. K.L. Chiu, Y.S. Lin, T.T. Kuo, C.C. Lo, Y.K. Huang, H.F. Chang, E.Y. Chuang, C.C. Lin, W.C. Cheng, Y.N. Liu, L.C. Lai, Y.P. Sher, “ADAM9 enhances CDCP1 by inhibiting miR-1 through EGFR signaling activation in lung cancer metastasis” , Oncotarget , Jul. 2017
70. A.L. Woolston, P.C. Hsiao, P.H. Kuo, S.H. Wang, Y.J. Lien, C.M. Liu, H.G. Hwu, T.P. Lu, E.Y. Chuang, L.C. Chang, C.H. Chen, J.Y. Wu, M.T. Tsuang, W.J. Chen, “Genetic loci associated with an earlier age at onset in multiplex schizophrenia” , Scientific Reports , Jul. 2017
71. Y.C. Chiu, L.J. Wang, T.H. Hsiao, E.Y. Chuang*, Y. Chen, “Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer” , BMC Genomics , Oct. 2017
72. S.C. Wei, H.F. Yang-Yen, P.N. Tsao, M.T. Weng, C.C. Tung, L.C.H. Yu, L.C. Lai, J.H. Hsiao, Eric Y. Chuang, C.T. Shun, Y.H. Ni, R.J. Xavier, D.K. Podolsky, J.J.Y. Yen, J.M. Wong, “SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway” , Inflamm Bowel Dis , Oct. 2017
73. C.Y. Shen, L.H. Chen, Y.F. Lin, L.C. Lai, E.Y. Chuang, M.H. Tsai, “Mitomycin C treatment induces resistance and enhanced migration via phosphorylated Akt in aggressive lung cancer cells” , Oncotarget , Nov. 2016
74. Chiu YC, Tsai MH, Chou WC, Liu YC, Kuo YY, Hou HA, Lu TP, Lai LC, Chen Y, Tien HF, Chuang EY*, “Prognostic significance of NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia.” , Leukemia , Feb. 2016
75. E.Y. Li, W.Y. Huang, Y.C. Chang, M.H. Tsai, E.Y. Chuang, Q.Y. Kuok, S.T. Bai, L.Y. Chao, Y.P. Sher, and L.C. Lai, “Aryl Hydrocarbon Receptor Activates NDRG1 Transcription under Hypoxia in Breast Cancer Cells.” , Sci Rep , Feb. 2016
76. Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, E.Y. Chuang, “Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs” , Oncotarget , Mar. 2016
77. Chi-Yun Wu, E.Y. Chuang*, Tzu-Pin Lu, “Low correlation of lncRNA and target gene expression in microarray data” , Transl Cancer Res , Apr. 2016
78. Govinda Lenka, Mong-Hsun Tsai, Jen-Hao Hsiao, Liang-Chuan Lai, E.Y. Chuang, “Overexpression of methylation-driven DCC suppresses proliferation of lung cancer cells.” , Transl Cancer Res , Apr. 2016
79. Yi-Hsuan Chang, Yu-Chiao Chiu1, Yu-Ching Hsu, Hui-Mei Tsai, E.Y. Chuang*, Tzu-Hung Hsiao, “Applying gene set analysis to characterize the activities of immune cells in estrogen receptor positive breast cancer.” , Transl Cancer Res , Apr. 2016
80. Yu-Ching Hsu, Yu-Chiao Chiu, Wei-Yi Liu, Chia-Yang Cheng, Tzu-Hung Hsiao, Mong-Hsun Tsai, “A simple gene set-based analysis accurately predicts the synergy of drug pairs.” , BMC Systems Biology , Aug. 2016
81. C.T. Tsai, C.S. Hsieh, S.N. Chang, E.Y. Chuang, K.C. Ueng, C.F. Tsai, T.H. Lin, C.K. Wu, J.K. Lee, L.Y. Lin, Y.C. Wang, C.C. Yu, L.P. Lai, C.D. Tseng, J.J. Hwang, F.T. Chiang, J.L. Lin, “Genome-wide screening identifies a KCNIP1 copy number variant as a genetic predictor for atrial fibrillation” , Nature Communications , Feb. 2016
82. T.H. Hsiao, Y.C. Chiu, P.Y. Hsu, T.P. Lu, L.C. Lai, M.H. Tsai, T.H. Huang, E.Y. Chuang*, Y. Chen, “Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers” , Scientific Reports , Mar. 2016
83. W.A. Wang, L.C. Lai, M.H. Tsai, T.P. Lu, E.Y. Chuang*, “Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs” , Oncotarget , May 2016
84. H.L. Wu, T.H. Hsiao, P.J. Chen, S.H. Wong, J.H. Kao, D.S. Chen, J.Y. Lu, T.P. Lu, Y. Chen, E.Y. Chuang, H.C. Tu, C.J. Liu, “Liver Gene Expression Profiles Correlate with Virus Infection and Response to Interferon Therapy in Chronic Hepatitis B Patients” , SCIENTIFIC REPORTS , Aug. 2016
85. Tsai CT, Hsieh CS, Chang SN, Chuang EY, Juang JM, Lin LY, Lai LP, Hwang JJ, Chiang FT, Lin JL, “Next-generation sequencing of nine atrial fibrillation candidate genes identified novel de novo mutations in patients with extreme trait of atrial fibrillation.” , J Med Genet , Vol. 52(1) , 28-36, Jan. 2015
86. Chang YY, Kuo WH, Hung JH, Lee CY, Lee YH, Chang YC, Lin WC, Shen CY, Huang CS, Hsieh FJ, Lai LC, Tsai MH, Chang KJ, Chuang EY*, “Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing.” , Molecular Cancer , Vol. 14:36 , Feb. 2015
87. Chiu YC, Hsiao TH, Chen Y, Chuang EY*, “Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers.” , BMC Genomics , Vol. 16(Suppl 4) , S1-, Feb. 2015
88. Chiu Y.C., Wu C.T., T.H. Hsiao, Y.P. Lai, C.K. Hsiao, Y. Chen, E.Y. Chuang*, “Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes.” , BMC Genomics , Vol. 16(Suppl 7) , S19-, Jan. 2015
89. Lu TP, Hsiao CK, Lai LC, Tsai MH, Hsu CP, Lee JM, Chuang EY*, “Identification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma.” , BMC Res Notes , Vol. 8:92 , Mar. 2015
90. Woolston A, Sintupisut N, Lu TP, Lai LC, Tsai MH, Chuang EY, Yeang CH, “Putative effectors for prognosis in lung adenocarcinoma are ethnic and gender specific.” , Oncotarget , Jun. 2015
91. Hsu, FM, Cheng, JCH, Chang, YL, Lee, JM , Koong, AC, Chuang, EY*, “Circulating mRNA Profiling in Esophageal Squamous Cell Carcinoma Identifies FAM84B As A Biomarker In Predicting Pathological Response to Neoadjuvant Chemoradiation.” , Sci Rep , Vol. 5:10291 , May 2015
92. Hsu YC, Chiu YC, Chen Y, Hsiao TH, Chuang EY*, “A gene-set approach to analyze copy number alterations in breast cancer.” , Translational Cancer Research , Vol. 4(3) , 291-302, May 2015
93. Chuang MK, Chiu YC, Chou WC, Hou HA, Tseng MH, Kuo YY, Chen Y, Chuang EY*, Tien HF, “An mRNA Expression Signature for Prognostication in De Novo Acute Myeloid Leukemia Patients with Normal Karyotype.” , Oncotarget , Nov. 2015
94. Luo EC, Chang YC, Sher YP, Huang WY, Chuang LL, Chiu YC, Tsai MH, Chuang EY, Lai LC, “MicroRNA-769-3p down-regulates NDRG1 and enhances apoptosis in MCF-7 cells during reoxygenation.” , Sci Rep , Vol. 4:5908 , Aug. 2014
95. Huang CC, Tu SH, Lien HH, Huang CS, Huang CJ, Lai LC, Tsai MH, Chuang EY*, “Refinement of breast cancer risk prediction with concordant leading edge subsets from prognostic gene signatures.” , Breast Cancer Res Tr , Vol. 147(2) , 353-370, Sep. 2014
96. Liu, C.-C., Wang, Y.-H., Chuang, E. Y., Tsai, M.-H., Chuang, Y.-H., Lin, C.-L., Liu, C.-J., Hsiao, B.-Y., Lin, S.-M., Liu, L.-Y. and Yu, M.-W, “Identification of a liver cirrhosis signature in plasma for predicting hepatocellular carcinoma risk in a population-based cohort of hepatitis B carriers.” , Mol. Carcinog , Vol. 53 , 58-66, Aug. 2014
97. Lu TP, Hsu YY, Lai LC, Tsai MH, Chuang EY*, “Identification of gene expression biomarkers for predicting radiation exposure.” , Sci Rep , Vol. 4:6293 , Sep. 2014
98. Juang JM, Lu TP, Lai LC, Ho CC, Liu YB, Tsai CT, Lin LY, Yu CC, Chen WJ, Chiang FT, Yeh SF, Lai LP, Chuang EY, Lin JL, “Disease-targeted sequencing of ion channel genes identifies de novo mutations in patients with non-familial Brugada syndrome.” , Sci Rep , Vol. 4:6733 , Oct. 2014
99. Chuang M, Chiu Y, Chou W, Hou H, Chuang EY, Tien H, “A 3-microRNA scoring system for prognostication in de novo acute myeloid leukemia patients.” , Leukemia , Vol. 29 , 1051-1059, Dec. 2014
100. Juang JM, Lu TP, Lai LC, Hsueh CH, Liu YB, Tsai CT, Lin LY, Yu CC, Hwang JJ, Chiang FT, Yeh SS, Chen WP, Chuang EY*, Lai LP, Lin JL, “Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome” , Sci Rep , Vol. 4:3850 , Jan. 2014
101. Huang CC, Tu SH, Lien HH, Jeng JY, Liu JS, Huang CS, Lai LC, Chuang EY*, “Estrogen receptor status prediction by gene component regression: a comparative study.” , Int J Data Min Bioi , Vol. 9(2) , 149-171, Feb. 2014
102. Lai LC, Tsai MH, Chen PC, Chen LH, Hsiao JH, Chen SK, Lu TP, Lee JM, Hsu CP, Hsiao CK, Chuang EY*, “SNP rs10248565 in HDAC9 as a novel genomic aberration biomarker of lung adenocarcinoma in non-smoking women.” , J Biomed Sci , Vol. 21:24 , Mar. 2014
103. Lu TP, Chen KT, Tsai MH, Kuo KT, Hsiao CK, Lai LC, Chuang EY*, “Identification of genes with consistent methylation levels across different human tissues.” , Sci Rep , Vol. 4:4351 , Mar. 2014
104. Sher YP, Wang LJ, Chuang LL, Tsai MH, Kuo TT, Huang CC, Chuang EY, Lai LC, “ADAM9 Up-Regulates N-Cadherin via miR-218 Suppression in Lung Adenocarcinoma Cells.” , PLoS One , Vol. 9(4 , e94065-, Apr. 2014
105. Wei SC, Tan YY, Weng MT, Lai LC, Hsiao JH, Chuang EY, Shun CT, Wu DC, Kao AW, Chuang CS, Ni YH, Shieh MJ, Tung CC, Chen Y, Wang CY, Xavier RJ, Podolsky DK, Wong JM, “SLCO3A1, a Novel Crohn's Disease-Associated Gene, Regulates NF-κB Activity and Associates with Intestinal Perforation.” , PLoS One , Vol. 9(6) , e100515-, Jun. 2014
106. Rosenstein BS, West CM, Bentzen SM, Alsner J, Andreassen CN, Azria D, Barnett GC, Baumann M, Burnet N, Chang-Claude J, Chuang EY, Coles CE, Dekker A, De Ruyck K, De Ruysscher D, Drumea K, Dunning AM, Easton D, Eeles R, Fachal L, Gutiérrez-Enríq, “Radiogenomics: radiobiology enters the era of big data and team science.” , Int J Radiat Oncol , Vol. 89(4) , 709-713, Jul. 2014
107. Yang YC, Wang DY, Cheng HF, Chuang EY, Tsai MH, “A reliable multiplex genotyping assay for HCV using a suspension bead array.” , Microb Biotechnol , Vol. 8(1) , 93-102, Jul. 2014
108. Chi-Cheng Huang, Shin-Hsiu Tu, Eric Y. Chuang*, “Dissecting the Heterogeneity of Luminal Subtype Breast Cancer Using Gene Component Analysis.” , Journal of Medical Research and Development(JMRD) , Vol. Vol. 2 Iss. 1 , 21-27, Jan. 2013
109. Flores M, Hsiao TH, Chiu YC, Chuang EY, Huang Y, Chen Y, “Gene regulation, modulation, and their applications in gene expression data analysis.” , Adv Bioinformatics , Vol. 2013 , 360678-, Mar. 2013
110. Huang CC, Jeng JY, Tu SH, Lien HH, Huang CS, Lai LC, Chuang EY*, “A preliminary study of concurrent gains and losses across gene expression profiles and comparative genomic hybridization in Taiwanese breast cancer patients.” , Transl Cancer Res , Vol. 2(1) , 18-24, Feb. 2013
111. Liu YJ, Lin YF, Chen YF, Luo EC, Sher YP, Tsai MH, Chuang EY, Lai LC, “MicroRNA-449a enhances radiosensitivity in CL1-0 lung adenocarcinoma cells.” , PLoS One , Vol. 8(4) , e62383-, Apr. 2013
112. Wang IJ, Chen SL, Lu TP, Chuang EY, Chen PC, “Prenatal smoke exposure, DNA methylation, and childhood atopic dermatitis.” , Clin Exp Allergy , Vol. 43(5) , 535-543, May 2013
113. Chen PC, Lu TP, Chang JC, Lai LC, Tsai MH, Hsiao CK, Chuang EY*, “Concurrent analysis of copy number variation and gene expression: application in paired non- smoking female lung cancer patients.” , Int J Data Min Bioinform , Vol. 8(1) , 92-104, Jan. 2013
114. Lai TY, Wu SD, Tsai MH, Chuang EY, Chuang LL, Hsu LC, Lai LC, “Transcription of Tnfaip3 Is Regulated by NF-κB and p38 via C/EBPβ in Activated Macrophages.” , PLoS One , Vol. 8(9) , e73153-, Sep. 2013
115. Huang CC, Tu SH, Lien HH, Jeng JY, Huang CS, Huang CJ, Lai LC, Chuang EY*, “Concurrent gene signatures for han chinese breast cancers.” , PLoS One , Vol. 8(10) , e76421-, Oct. 2013
116. Lu TP, Chuang EY, Chen JJ, “Identification of reproducible gene expression signatures in lung adenocarcinoma.” , BMC Bioinformatic , Vol. 14:371 , Dec. 2013
117. Huang CC, Tu SH, Huang CS, Lien HH, Lai LC, Chuang EY*, “Multiclass prediction with partial least square regression for gene expression data: applications in breast cancer intrinsic taxonomy.” , Biomed Res Int , Vol. 2013:248648 , Dec. 2013
118. Lin, S.Y., S.C. Hsieh, Y.C. Lin, C.N. Lee, M.H. Tsai, L.C. Lai, E.Y. Chuang, P.C. Chen, C.C. Hung, L.Y. Chen, W.S. Hsieh, D.M. Niu, Y.N. Su, and H.N. Ho, “A whole genome methylation analysis of systemic lupus erythematosus: hypomethylation of the IL10 and IL1R2 promoters is associated with disease activity.” , Genes Immun , Vol. 13(3) , 214-220, Apr. 2012
119. Lu, T.P., C.Y. Lee, M.H. Tsai, Y.C. Chiu, C.K. Hsiao, L.C. Lai, and E.Y. Chuang*, “miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.” , PLoS One , Vol. 7(8) , e42390-, Aug. 2012
120. Huang CC, Tu SH, Lien HH, Jeng JY, Liu JS, Huang CS, Wu YY, Liu CY, Lai LC, Chuang EY*, “Prediction consistency and clinical presentations of breast cancer molecular subtypes for Han Chinese population.” , J Transl Med , Vol. 10 Suppl 1 , S10-, Sep. 2012
121. Kuo, W.H., Y.Y. Chang, L.C. Lai, M.H. Tsai, C.K. Hsiao, K.J. Chang, and E.Y. Chuang*, “Molecular characteristics and metastasis predictor genes of triple-negative breast cancer: a clinical study of triple-negative breast carcinomas.” , PLoS One , Vol. 7(9) , e45831-, Sep. 2012
122. Chen, P.C., Y.C. Chen, L.C. Lai, M.H. Tsai, S.K. Chen, P.W. Yang, Y.C. Lee, C.K. Hsiao, J.M. Lee, and E.Y. Chuang*, “The Use of Germline Polymorphisms in Predicting Concurrent Chemoradiotherapy Response in Esophageal Cancer.” , Int J Radiat Oncol Biol Phys , Vol. 82(5) , 1996-2003, May 2011
123. Kuo, H.C., P.Y. Lin, T.C. Chung, C.M. Chao, L.C. Lai, M.H. Tsai, and E.Y. Chuang*, “DBCAT: database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells.” , J Comput Biol , Vol. 18(8) , 1013-1017, Aug. 2011
124. Lai, L.C., Y.Y. Su, K.C. Chen, M.H. Tsai, Y.P. Sher, T.P. Lu, C.Y. Lee, and E.Y. Chuang*, “Down-Regulation of NDRG1 Promotes Migration of Cancer Cells during Reoxygenation.” , PLoS One , Vol. 6(8) , e24375-, Sep. 2011
125. Lu, T.P., L.C. Lai, M.H. Tsai, P.C. Chen, C.P. Hsu, J.M. Lee, C.K. Hsiao, and E.Y. Chuang*, “Integrated analyses of copy number variations and gene expression in lung adenocarcinoma.” , PLoS One , Vol. 6(9) , e24829-, Sep. 2011
126. Hsu, F.H., H.I. Chen, M.H. Tsai, L.C. Lai, C.C. Huang, S.H. Tu, E.Y. Chuang*, and Y. Chen, “A model-based circular binary segmentation algorithm for the analysis of array CGH data.” , BMC Res Notes , Vol. 4(1) , 394-, Oct. 2011
127. Chen, L.H., W.H. Kuo, M.H. Tsai, P.C. Chen, C.K. Hsiao, E.Y. Chuang, L.Y. Chang, F.J. Hsieh, L.C. Lai, and K.J. Chang, “Identification of prognostic genes for recurrent risk prediction in triple negative breast cancer patients in Taiwan.” , PLoS One , Vol. 6(11) , e28222-, Dec. 2011
128. Chen, H., T.H. Chen, T.F. Tseng, J.T. Lu, C.C. Kuo, S.C. Fu, W.J. Lee, Y.F. Tsai, Y.Y. Huang, E.Y. Chuang, Y.J. Hwang, and C.K. Sun, “High-sensitivity in vivo THz transmission imaging of early human breast cancer in a subcutaneous xenograft mouse model.” , Opt Express , Vol. 19(22) , 21552-21562, Oct. 2011
129. Lu, T.P., L.C. Lai, B.I. Lin, L.H. Chen, T.H. Hsiao, H.L. Liber, J.A. Cook, J.B. Mitchell, M.H. Tsai, and E.Y. Chuang*, “Distinct signaling pathways after higher or lower doses of radiation in three closely related human lymphoblast cell lines.” , Int J Radiat Oncol Biol Phys , Vol. 76(1) , 212-219, Jan. 2010
130. Hsiao, T.H., C.H. Lin, T.T. Lee, J.Y. Cheng, P.K. Wei, E.Y. Chuang*, and K. Peck, “Verifying expressed transcript variants by detecting and assembling stretches of consecutive exons.” , Nucleic Acids Res , Vol. 38(20) , e187-, Nov. 2010
131. Lu, T.P., M.H. Tsai, J.M. Lee, C.P. Hsu, P.C. Chen, C.W. Lin, J.Y. Shih, P.C. Yang, C.K. Hsiao, L.C. Lai, and E.Y. Chuang*, “Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women.” , Cancer Epidemiol Biomarkers Prev , Vol. 19(10) , 2590-2597, Oct. 2010
132. Kassis, J.N., V.M. Virador, E.A. Guancial, D. Kimm, A.S. Ho, M. Mishra, E.Y. Chuang, J. Cook, D. Gius, and E.C. Kohn, “Genomic and phenotypic analysis reveals a key role for CCN1 (CYR61) in BAG3-modulated adhesion and invasion.” , J Pathol , Vol. 218(4) , 495-504, Aug. 2009
133. Lin, Y.F., H. Nagasawa, Y. Peng, E.Y. Chuang, and J.S. Bedford, “Comparison of several radiation effects in human MCF10A mammary epithelial cells cultured as 2D monolayers or 3D acinar stuctures in matrigel.” , Radiat Res , Vol. 171(6) , 708-715, Jun. 2009
134. Guo, Z., M.H. Tsai, Y.H. Shiao, L.H. Chen, M.L. Wei, X. Lv, D. Gius, J.B. Little, J.B. Mitchell, and E.Y. Chuang*, “DNA (cytosine-5)-methyltransferase 1 as a mediator of mutant p53-determined p16(ink4A) down-regulation.” , J Biomed Sci , Vol. 15(2) , 163-168, Mar. 2008
135. Chen, H.I., F.H. Hsu, Y. Jiang, M.H. Tsai, P.C. Yang, P.S. Meltzer, E.Y. Chuang*, and Y. Chen, “A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.” , Bioinformatics , Vol. 24(16) , 1749-1756, Aug. 2008
136. Lin, Y.F., C.Y. Chen, M.H. Tsai, M.S. Wu, Y.C. Wang, E.Y. Chuang, J.T. Lin, P.C. Yang, and L.P. Chow, “Duodenal ulcer-related antigens from Helicobacter pylori: immunoproteome and protein microarray approaches.” , Mol Cell Proteomics , Vol. 6(6) , 1018-1026, Jun. 2007
137. Tsai, M.H., J.A. Cook, G.V. Chandramouli, W. DeGraff, H. Yan, S. Zhao, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Gene expression profiling of breast, prostate, and glioma cells following single versus fractionated doses of radiation.” , Cancer Res , Vol. 67(8) , 3845-3852, Apr. 2007
138. Gius, D., M.C. Funk, E.Y. Chuang, S. Feng, P.C. Huettner, L. Nguyen, C.M. Bradbury, M. Mishra, S. Gao, B.M. Buttin, D.E. Cohn, M.A. Powell, N.S. Horowitz, B.P. Whitcomb, and J.S. Rader, “Profiling microdissected epithelium and stroma to model genomic signatures for cervical carcinogenesis accommodating for covariates.” , Cancer Res , Vol. 67(15) , 7113-7123, Aug. 2007
139. Tsai, M.H., X. Chen, G.V. Chandramouli, Y. Chen, H. Yan, S. Zhao, P. Keng, H.L. Liber, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Transcriptional responses to ionizing radiation reveal that p53R2 protects against radiation-induced mutagenesis in human lymphoblastoid cells.” , Oncogene , Vol. 25(4) , 622-632, Jan. 2006
140. Chuang, E.Y., X. Chen, M.H. Tsai, H. Yan, C.Y. Li, J.B. Mitchell, H. Nagasawa, P.F. Wilson, Y. Peng, M.M. Fitzek, J.S. Bedford, and J.B. Little, “Abnormal gene expression profiles in unaffected parents of patients with hereditary-type retinoblastoma.” , Cancer Res , Vol. 66(7) , 3428-3433, Apr. 2006
141. Zhao, W., E.Y. Chuang, M. Mishra, R. Awwad, K. Bisht, L. Sun, P. Nguyen, J.D. Pennington, T.J. Wang, C.M. Bradbury, L. Huang, Z. Chen, G. Bar-Sela, M.E. Robbins, and D. Gius, “Distinct effects of ionizing radiation on in vivo murine kidney and brain normal tissue gene expression.” , Clin Cancer Res , Vol. 12(12) , 3823-3830, Jun. 2006
142. Cook, J.A., E.Y. Chuang, M.H. Tsai, D. Coffin, W. Degraff, A.L. Sowers, and J.B. Mitchell, “Radiation-induced changes in gene-expression profiles for the SCC VII tumor cells grown in vitro and in vivo.” , Antioxid Redox Signal , Vol. 8(7-8) , 1263-1272, Aug. 2006
143. Samuni, A.M., U. Kasid, E.Y. Chuang, S. Suy, W. Degraff, M.C. Krishna, A. Russo, and J.B. Mitchell, “Effects of hypoxia on radiation-responsive stress-activated protein kinase, p53, and caspase 3 signals in TK6 human lymphoblastoid cells.” , Cancer Res , Vol. 65(2) , 579-586, Jan. 2005
144. Tsai, M.H., H. Yan, X. Chen, G.V. Chandramouli, S. Zhao, D. Coffin, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays.” , Mol Biotechnol , Vol. 29(3) , 221-224, Mar. 2005
145. Tsai, K.K., E.Y. Chuang, J.B. Little, and Z.M. Yuan, “Cellular mechanisms for low-dose ionizing radiation-induced perturbation of the breast tissue microenvironment.” , Cancer Res , Vol. 65(15) , 6734-6744, Aug. 2005
146. Stuart, J.R., H. Kawai, K.K. Tsai, E.Y. Chuang, and Z.M. Yuan, “c-Abl regulates early growth response protein (EGR1) in response to oxidative stress.” , Oncogene , Vol. 24(55) , 8085-8092, Dec. 2005
147. Jazaeri, A.A., C.S. Awtrey, G.V. Chandramouli, Y.E. Chuang, J. Khan, C. Sotiriou, O. Aprelikova, C.J. Yee, K.K. Zorn, M.J. Birrer, J.C. Barrett, and J. Boyd, “Gene expression profiles associated with response to chemotherapy in epithelial ovarian cancers.” , Clin Cancer Res , Vol. 11(17) , 6300-6310, Sep. 2005
148. Ge, H., Y.Y. Chuang, S. Zhao, M. Tong, M.H. Tsai, J.J. Temenak, A.L. Richards, and W.M. Ching, “Comparative genomics of Rickettsia prowazekii Madrid E and Breinl strains.” , J Bacteriol , Vol. 186(2) , 556-565, Jan. 2004
149. Goley, E.M., S.J. Anderson, C. Menard, E. Chuang, X. Lu, P.J. Tofilon, and K. Camphausen, “Microarray analysis in clinical oncology: pre-clinical optimization using needle core biopsies from xenograft tumors.” , BMC Cancer , Vol. 4 , 20-, May 2004
150. Rosenwald, A., E.Y. Chuang, R.E. Davis, A. Wiestner, A.A. Alizadeh, D.C. Arthur, J.B. Mitchell, G.E. Marti, D.H. Fowler, W.H. Wilson, and L.M. Staudt, “Fludarabine treatment of patients with chronic lymphocytic leukemia induces a p53-dependent gene expression response.” , Blood , Vol. 104(5) , 1428-1434, Sep. 2004
151. Dodd, L.E., E.L. Korn, L.M. McShane, G.V. Chandramouli, and E.Y. Chuang, “Correcting log ratios for signal saturation in cDNA microarrays.” , Bioinformatics , Vol. 20(16) , 2685-2693, Nov. 2004
152. Lu, X., W.E. Burgan, M.A. Cerra, E.Y. Chuang, M.H. Tsai, P.J. Tofilon, and K. Camphausen, “ranscriptional signature of flavopiridol-induced tumor cell death.” , Mol Cancer Ther , Vol. 3(7) , 861-872, Jul. 2004
153. Loercher, A., T.L. Lee, J.L. Ricker, A. Howard, J. Geoghegen, Z. Chen, J.B. Sunwoo, R. Sitcheran, E.Y. Chuang, J.B. Mitchell, A.S. Baldwin, Jr., and C. Van Waes, “Nuclear factor-kappaB is an important modulator of the altered gene expression profile and malignant phenotype in squamous cell carcinoma.” , Cancer Res , Vol. 64(18) , 6511-6523, Sep. 2004
154. Gius, D., H. Cui, C.M. Bradbury, J. Cook, D.K. Smart, S. Zhao, L. Young, S.A. Brandenburg, Y. Hu, K.S. Bisht, A.S. Ho, D. Mattson, L. Sun, P.J. Munson, E.Y. Chuang, J.B. Mitchell, and A.P. Feinberg, “Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach.” , Cancer Cell , Vol. 6(4) , 361-371, Oct. 2004
155. Lu, M., J. Suen, C. Frias, R. Pfeiffer, M.H. Tsai, E. Chuang, and S.L. Zeichner, “Dissection of the Kaposi's sarcoma-associated herpesvirus gene expression program by using the viral DNA replication inhibitor cidofovir.” , Virol , Vol. 78(24) , 13637-13652, Dec. 2004
156. Samuni, A.M., E.Y. Chuang, M.C. Krishna, W. Stein, W. DeGraff, A. Russo, and J.B. Mitchell, “Semiquinone radical intermediate in catecholic estrogen-mediated cytotoxicity and mutagenesis: chemoprevention strategies with antioxidants.” , Proc Natl Acad Sci U S A , Vol. 100(9) , 5390-5395, Apr. 2003
157. Ge, H., Y.Y. Chuang, S. Zhao, J.J. Temenak, and W.M. Ching, “Genomic studies of Rickettsia prowazekii virulent and avirulent strains.” , Ann N Y Acad Sci , Vol. 990 , 671-677, Jun. 2003
158. Su, H., N. Hu, J. Shih, Y. Hu, Q.H. Wang, E.Y. Chuang, M.J. Roth, C. Wang, A.M. Goldstein, T. Ding, S.M. Dawsey, C. Giffen, M.R. Emmert-Buck, and P.R. Taylor, “Gene expression analysis of esophageal squamous cell carcinoma reveals consistent molecular profiles related to a family history of upper gastrointestinal cancer.” , Cancer Res , Vol. 63(14) , 3872-3876, Jul. 2003
159. Chuang, Y.Y., Y. Chen, Gadisetti, V.R. Chandramouli, J.A. Cook, D. Coffin, M.H. Tsai, W. DeGraff, H. Yan, S. Zhao, A. Russo, E.T. Liu, and J.B. Mitchell, “Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells.” , Cancer Res , Vol. 62(21) , 6246-6254, Nov. 2002
160. Chuang, Y.Y., Q. Chen, J.P. Brown, J.M. Sedivy, and H.L. Liber, “Radiation-induced mutations at the autosomal thymidine kinase locus are not elevated in p53-null cells.” , Cancer Res , Vol. 59(13) , 3073-3076, Jul. 1999
161. Y.Y. Chuang, Q.C.a.H.L.L., “The construction of a p53-null cell line from human lymphoblast cells for mutagenesis studies.” , Environ. Mol. Mutagen , Vol. 31(Suppl. 29) , 65-, Jan. 1998
162. Y.C. and H.L. Liber, “Mutational spectra at the thymidine kinase locus of spontaneously-arising and mitomycin C (MMC)-induced mutants in two closely related human lymphoblast cell lines.” , Environ. Mol. Mutagen , Vol. 29(Suppl. 28) , 9-, Jan. 1997
163. Y.Y. Chuang, W.C.C.a.H.L.L., “A DNA cross-linking agent (MMC) induces systematic differences in toxicity and mutagenicity in two closely related human lymphoblast cell lines.” , Environ. Mol. Mutagen , Vol. 27(Suppl. 27) , 13-, Jan. 1996
164. Chuang, Y.Y. and H.L. Liber, “Effects of cell cycle position on ionizing radiation mutagenesis. I. Quantitative assays of two genetic loci in a human lymphoblastoid cell line.” , Radiat Res , Vol. 146(5) , 494-500, Nov. 1996
165. Liu, S.C., B. Ogretmen, Y.Y. Chuang, and B.C. Stark, “Selection and characterization of alpha-amylase-overproducing recombinant Escherichia coli containing the bacterial hemoglobin gene.” , Appl Microbiol Biotechnol , Vol. 38(2) , 239-242, Nov. 1992
Conference & proceeding papers:
1. Wu CT, Tsai MH, Lu TP, Lai LC, Chuang EY, “Performances evaluation of algorithms for identifying differently expressed genes in RNA-seq data.” , 2015 AACR annual meeting , Philadelphia, PA, USA , Apr. 2015
2. Wang WA, Lai LC, Tsai MH, Lu TP, Chuang EY, “Survival prediction model with long non-coding RNA profile in lung adenocarcinoma cancer.” , 2015 AACR annual meeting , Philadeplhia, PA, USA , Apr. 2015
3. Tsai MH*, Chou WC, Chiu YC, Tien HF, Chuang EY, “Investigation of Dynamic Cross-talk between miRNA and mRNA in Acute Myeloid Leukemia.” , Human Genome Meeting 2014 , Geneva, Switzerland , Apr. 2014
4. Chuang MK, Chiu YC, Chou WC, Hou HA, Chuang EY, Tien HF, “A Simple, Powerful, and Widely Applicable Micro-RNA Scoring System in Prognostication of De Novo Myeloid Leukemia Patients.” , 56th ASH® Annual Meeting and Exposition , San Francisco, CA, USA , Dec. 2014
5. Lai LC, Sher YP, Wang LJ, Tsai MH, Kuo TT, Chuang EY, “ADAM9 up-regulates N-Cadherin via miR-218 suppression in lung adenocarcinoma cells.” , Human Genome Meeting 2014 , Geneva, Switzerland , Apr. 2014
6. Hsu YC, Chiu YC, Chen Y, Chuang EY, and Hsiao TH, “A gene set approach to analyze copy number alterations profiles of breast cancer.” , International Conference on Intelligent Biology and Medicine (ICIBM2014) , San Antonio, TX, USA , Dec. 2014
7. Chiu YC, Wu CT, Hsiao TH , Lai YP , Hsiao CK, Yidong Chen Y, Chuang EY, “Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes.” , International Conference on Intelligent Biology and Medicine (ICIBM2014) , San Antonio, TX, USA , Dec. 2014
8. Lu TP, Chuang EY, Chen JJ, “Identification of universal survival predictors in lung adenocarcinoma.” , 2013 AACR annual meeting , Washington D.C., USA , Apr. 2013
9. Chen YH, Hsiao TH, Chen HIH, Chen Y, Chuang EY, “An integrative analysis to identify putative drugs for acute myeloid leukemia.” , 2013 AACR annual meeting , Washington D.C., USA , Apr. 2013
10. Chiu YC, Hsiao TH, Gu F, Chen Y, Huang THM, Chuang EY*, “Identification of estrogen receptor modulated gene methylation network in breast cancer.” , 2013 AACR annual meeting , Washington D.C., USA , Apr. 2013
11. Lee CY, Wang LB, Tsai MH, Lai LC, Chuang EY, “Identification of novel miRNAs in breast data of the next generation sequencing using miRDeep2 and Galaxy.” , 2013 AACR annual meeting , Washington D.C., USA , Apr. 2013
12. Chiu YC, Chuang EY*, Hsiao TH, Chen Y, “Characterization of conditions for competing endogenous RNA regulation in GBM. ” Oral presentation at 2013 IEEE International Workshop on Genomic Signal Processing and Statistics.” , 2013 IEEE Internatioal Workshop on Genomic Signal Processing and Statistics , Houston, USA , Nov. 2013
13. Chiu YC, Chuang EY, Hsiao TH, Chen Y, “Modeling competing endogenous RNA regulatory networks in glioblastoma multiforme.” , 2013 IEEE International Conference on Bioinformatics and Biomedicine , Shanghai, China , Dec. 2013
14. Liu YJ, Lin YF, Chen YF, Luo EC, Sher YP, Tsai MH, Chuang EY, and Liang LC, “MicroRNA-449a enhances radiosensitivity in lung adenocarcinoma cells.” , AACR 104th Annual Meeting 2013 , Washington, DC, USA , Apr. 2013
15. Eric Y. Chuang, “Combination of Genomic Technologies and Bioinformatics for Exploring New Cancer Biomarkers” , Princeton, NJ, 2012” , EITA 2012-BIO , Princeton, NJ , Oct. 2012
16. Eric Y. Chuang, “Radiogenomics: An Emerging Field for Personalized Radiation Therapy.” , 2011 International Symposium on Radiation Medicine: The Future Research and Development of Radiation Medicine , Taipei, Taiwan , Jan. 2011
17. Shen CY, Li YH, Lu TP, Lai LC, Chuang EY, Tsai MH, “Semaphorin 6A inhibits the cell migration in lung adenocarcinoma cells.” , 2011 AACR annual meeting , Orlando, Florida, USA , Apr. 2011
18. Liu YC, Lu TP, Hsaio TH, Lu JY,Hsu FM, Cheng JCH, Yang PC, Lai LC, Chuang EY, Tsai MH, “Differential cytokine-related signaling pathways responded to ionizing radiation in two lung adenocarcinoma cell lines.” , 2010 AACR annual meeting , Washington D.C.,USA , Apr. 2010
19. Eric Y. Chuang, “Microarray Gene Expression Data Analysis in Cancer Research” , The 28th World Congress of Internal Medicine , Taipei, Taiwan , Jan. 2006
20. M.H. Tsai, X. Chen, G.V.R. Chandramouli, Y. Chen, H. Yan, S. Zhao, H.L. Liber, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang, “Gene Expression Profiles Following Radiation in Different p53 status Human Lymphoblast Cell Lines Revealed p53R2 Protein Plays a Role in Radiation-Induced Mutagenesis.” , 34th Annual Meeting of the European Environmental Mutagen Society , Maastricht, the Netherlands , Jan. 2004
Books:
1. 莊曜宇，王志軒, “別瞎忙了！健康的關鍵就在腸道菌” , AME publishing company , 978-988-77840-4-3 , 978-988-77840-4-3 , Hong Kong, 2017
2. Jie He, Rafael Rosell, Eric Y. Chuang, “Lung Cancer Precision Medicine” , AME Publishing Company , 978-988-14028-1-3 Hardback , 978-988-14028-1-3 Hardback , Hong Kong, 2016
3. Huang Giap, Eric Y Chuang, Gary Y Yang, “Particle Beam Therapy: contemporary trends and reviews” , AME Publishing Company , 978-988-12997-4-1 , 978-988-12997-4-1 , 291 , Hong Kong, 2014
4. 熊映美、莊曜宇, “金屬奈米微粒暴露與勞工過敏發炎指標分析研究” , 行政院勞委會勞工安全研究所 , 57 , 臺灣, Mar. 2008
5. 熊映美、莊曜宇、蔡孟勳, “極細微粒二氧化鈦之細胞毒性與基因毒性之探討” , 行政院勞委會勞工安全研究所 , 9789860048872 , 9789860048872 , 67 , 臺灣, Mar. 2006
Patents:
1. 蔡孟勳、莊曜宇、華筱玲、潘日南, “一種判別源自不同個體之基因的方法及其深度學習模型” , 中華民國I783699號, Nov. 2022
2. 劉韋驛、邱育賢、徐仁徽、謝嘉珊、蔡孟勳、盧子彬、賴亮全、莊曜宇、蕭暉議, “藥物組合療效預測篩選系統與方法” , 中華民國第I622012號, Apr. 2018
3. 鄭少樺、邱育賢、莊曜宇、盧子彬、董恆元, “次世代定序分析系統及其次世代定序分析方法” , 中華民國第I571763號, Feb. 2017
4. 鄭佳揚、徐仁徽、劉韋驛、蔡孟勳、盧子彬、賴亮全、莊曜宇, “用以分析細菌菌種之定序資料的系統及其方法” , 中華民國第I582631號, May 2017
5. 周文堅、田蕙芬、莊曜宇、邱鈺喬、莊名凱, “利用三個微小核糖核酸之評分系統以預測急性骨髓性白血病之預後” , 中華民國第I531655號, May 2016
6. 陳佩君、 程蘊菁、 賴亮全、 蔡孟勳、 陳星光、 楊珮雯、 李章銘、 莊曜宇、 蕭朱杏, “預測食道癌病患對於化學暨放射線療法之反應的方法及套組” , 中華民國第I380018號, Dec. 2012
7. Chen, Pei-Chun; Chen, Yen-Ching; Lai, Liang-Chuan; Tsai, Mong-Hsun; Chen, Shin-Kuang; Yang, Pei-Wen; Lee, Jang-Ming; Chuang, Eric Y; Hsiao, Chuhsing K, “Biomarkers for predicting response of esophageal cancer patient to chemoradio therapy” , USA US 8,268,562 B2, Sep. 2012