Mass spectrometry-based quantitative proteomic analysis in biological systems.
Methodology development for separation and site-specific identification of post-translational modifications (especially for glycosylation, cysteine-based PTMs, etc.) by mass spectrometry analysis, and application in diseases.
Sample preparation for clinical samples and large-scale quantitative proteomic analysis.

1. Chen, Yi-Ju; Roumeliotis, T. I.; Chang, Y.-H.; Chen, C.-T.; Han, C.-L.; Lin, M.-H.; Chen, H.-W.; Chang, G.-C.; Chang, Y.-L.; Wu, C.-T.; Lin, M.-W.; Hsieh, M.-S.; Wang, Y.-T.; Chen, Y.-R.; Jonassen, I.; Ghavidel, F. Z.; Lin, Z.-S.; Lin, K.-T.; Chen, C.-W.; Sheu, P.-Y.; Hung, C.-T.; Huang, K.-C.; Yang, H.-C.; Lin, P.-Y.; Yen, T.-C.; Lin, Y.-W.; Wang, J.-H.; Raghav, L.; Lin, C.-Y.; Chen, Y.-S.; Wu, P.-S.; Lai, C.-T.; Weng, S.-H.; Su, K.-Y.; Chang, W.-H.; Tsai, P.-Y.; Robles, A. I.; Rodriguez, H.; Hsiao, Y.-J.; Chang, W.-H.; Sung, T.-Y.; Chen, J.-S.; Yu, S.-L.; Choudhary, J. S.; Chen, H.-Y.; Yang, P.-C.; Chen, Y.-J. Proteogenomic Landscape of Early Stage Non-smoking Lung Adenocarcinoma in East Asia. Cell, 2020 182, 226-244. (Cover Story) (First author)
2. Waniwan, J. T.; Chen, Yi-Ju; Capangpangan, R.; Weng, S.-H.; Chen, Y.-J. Glycoproteomic Alterations in Drug-Resistant Nonsmall Cell Lung Cancer Cells Revealed by Lectin Magnetic Nanoprobe-Based Mass Spectrometry. J. Proteome Res. 2018, 17, 3761-3773.
3. Chang, L.;Chen, Yi-Ju; Fan, C.-Y.; Tang, C.-J.; Chen, Y.-H.; Low, P.-Y.; Ventura, A.; Lin, C.-C.; Chen, Y.-J.; Angata, T. Identification of Siglec Ligands Using a Proximity Labeling Method. J. Proteome Res. 2017, 16, 3929–3941. (Co-first author)
4. Rosa, M. A. C. dela; Chen, W.-C.; Chen, Yi-Ju; Obena, R. P.; Chang, C.-H.; Capangpangan, R. Y.; Su, T.-H.; Chen, C.-L.; Chen, P.-J.; Chen, Y.-J. Uncovering Single Protein-omic Biosignatures using a One-pot Dual Nanoprobe Assay. Anal. Chem. 2017 89, 3973-3980.
5. Liu, K.-M.; Chen, Yi-Ju; Shen, L.-F.; Haddad, A. N S; Song, I-W.; Chen, L.-Y.; Chen,Y.-J.; Wu, J.-Y.; Yen, J. J Y; Chen, Y.-T. Cyclic Alopecia and Abnormal Epidermal Cornification in Zdhhc13-Deficient Mice Reveal the Importance of Palmitoylation in Hair and Skin Differentiation. J. Invest. Dermatol. 2015. 135, 2603-2610.
6. Chen, Yi-Ju ; Lu, C.-T.; Huang, K.-Y.; Wu, H.-Y.; Chen, Y.-J.; Lee, T.-Y. GSHSite: exploiting an iteratively statistical method to identify S-glutathionylation sites with substrate specificity. PLoS One. 2015, 10, e0118752. *First author
7. Chen, Yi-Ju; Lu, C.-T.; Su, M.-G.; Huang, K.-Y.; Ching, W.-C.; Yang, H.-H.; Liao, Y.-C.; Chen, Y.-J.; Lee, T.-Y. dbSNO 2.0: a resource for exploring structural environment, functional and disease association, and regulatory network of protein S-nitrosylation. Nucleic Acids Res. 2015, 43(Database issue): D503-D511. (Special Issue) *First author
8. Chen, Y.-J.; Ching, W.-C.; Chen, J.-S.; Lee, T.-Y.; Lu, C.-T.; Chou, H.-C.; Lin, P.-Y.; Khoo, K.-H.; Chen, J.-H.; Chen, Y.-J. Decoding the S-Nitrosoproteomic Atlas in Individualized Human Colorectal Cancer Tissues Using a Label-Free Quantitation Strategy. J Proteome Res. 2014, 13, 4942-4958. (Special Issue) *First author
9. Chen, Y.-J.; Lu, C.-T.; Lee, T.-Y.; Chen, Y.-J. dbGSH: a database of S-glutathionylation. Bioinformatics 2014, 30, 2386-2388. *First author
10. Lu, C.-T.; Lee, T.-Y.; Chen, Y.-J.; Chen,Yi-J. An intelligent system for identifying acetylated lysine on histones and nonhistone proteins. Biomed Res Int. 2014, 2014:528650. (Special Issue) *Corresponding author
11. Chen, Yi-Ju; Ching, W.-C.; Lin, Y.-P.; Chen. Y.-J. Methods for detection and characterization of protein S-nitrosylation. Methods. 2013, 62, 138-150. (Special Issue, Invited Review) *First author
12. Lee, T.-Y.; Chen, Yi-Ju; Lu, C.-T.; Ching, W.-C.; Teng, Y.-C.; Huang, H.-D.; Chen, Y.-J. dbSNO: a database of cysteine S-nitrosylation. Bioinformatics. 2012, 28, 2293-2295.
13. Lee, T.-Y.; Chen, Yi-Ju; Lu, T.-C.; Huang, H.-D.; Chen, Y.-J. SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. PLoS ONE. 2011, 6, e21849.
14. Chen, Y.-J. ; Ku, W.-C.; Lin, P.-Y.; Chou, H.-C.; Khoo, K.-H.; Chen, Y.-J. S-alkylating labeling strategy for site-specific identification of the S-nitrosoproteome.
    J. Proteome. Res. 2010, 9, 6417-6439. *First author
15. Chen, Yi-Ju; Ku, W.-C.; Feng, L.-T.; Tsai, M.-L.; Hsieh, C.-H.; Hsu, W.-H.; Liaw, W.-F.; Hung, C.-H.; Chen, Y.-J. Nitric Oxide Physiological Responses and Delivery Mechanisms Probed by Water-soluble Roussin’s Red Ester and {Fe(NO)2}10 DNIC. J. Am. Chem. Soc. 2008, 130, 10929-10938. *First author

Update： 2021-05-31

1. Chi-Ya Shen, Wen-Hsin Chang, Yi-Ju Chen, Chia-Wei Weng, Prabha Regmi, Mickiela K. K. Kier, Kang-Yi Su, Gee-Chen Chang, Jin-Shing Chen, Yu-Ju Chen, and Sung-Liang Yu* Tissue Proteogenomic Landscape Reveals the Role of Uncharacterized SEL1L3 in Progression and Immunotherapy Response in Lung Adenocarcinoma. Journal of Proteome Research 2022-11-09, 0, 0.
2. Yi-Ju Chen, Ta-Chi Yen, Yu-Hsien Lin, Yan-Lin Chen, Kay-Hooi Khoo, Yu-Ju Chen* ZIC-cHILIC-Based StageTip for Simultaneous Glycopeptide Enrichment and Fractionation toward Large-Scale N-Sialoglycoproteomics. ANALYTICAL CHEMISTRY 2021-11-15, 93(48), 15931-15940.
3. Tiara Pradita, Yi-Ju Chen, Elias Gizaw Mernie, Sharine Noelle Bendulo, Yu-Ju Chen* ZIC-cHILIC Functionalized Magnetic Nanoparticle for Rapid and Sensitive Glycopeptide Enrichment from < 1 µL Serum. Nanomaterials 2021-08-24, 11, 9-2159.
4. Yi-Jing Hsiao, Wen-Hsin Chang, Hsuan-Yu Chen, Yin-Chen Hsu, Su-Chin Chiu, Ching-Cheng Chiang, Gee-Chen Chang, Yi-Ju Chen, Chia-Yu Wang, Yan-Ming Chen, Chien-Yu Lin, Yu-Ju Chen, Pan-Chyr Yang, Jeremy Chen*, Sung-Liang Yu* MITF Functions as a Tumor Suppressor in Non-Small Cell Lung Cancer beyond the Canonically Oncogenic Role. Aging (Albany NY) 2021-01-15, 13(1), 646.
5. Yi-Ju Chen, Theodoros I Roumeliotis, Ya-Hsuan Chang, Ching-Tai Chen, Chia-Li Han*, Miao-Hsia Lin, Huei-Wen Chen, Gee-Chen Chang, Yih-Leong Chang, Chen-Tu Wu, Mong-Wei Lin, Min-Shu Hsieh, Yu-Tai Wang, Yet-Ran Chen, Inge Jonassen, Fatemeh Zamanzad Ghavidel, Ze-Shiang Lin, Kuen-Tyng Lin, Ching-Wen Chen, Pei-Yuan Sheu, Chen-Ting Hung, Ke-Chieh Huang, Hao-Chin Yang, Pei-Yi Lin, Ta-Chi Yen, Yi-Wei Lin, Jen-Hung Wang, Lovely Raghav, Chien-Yu Lin, Yan-Si Chen, Pei-Shan Wu, Chi-Ting Lai, Shao-Hsing Weng, Kang-Yi Su, Wei-Hung Chang, Pang-Yan Tsai, Ana I Robles, Henry Rodriguez, Yi-Jing Hsiao, Wen-Hsin Chang, Ting-Yi Sung*, Jin-Shing Chen*, Sung-Liang Yu*, Jyoti S Choudhary*, Hsuan-Yu Chen*, Pan-Chyr Yang*, Yu-Ju Chen* Proteogenomics of non-smoking lung cancer in East Asia delineates molecular signatures of pathogenesis and progression. CELL 2020-07-09, 182(1), 226-244.
6. Li-Ying Chen, Kuo-Ray Lin, Yi-Ju Chen, Yun-Jung Chiang, Kun-Chin Ho, Li-Fen Shen, I-Wen Song, Kai-Ming Liu, Hsin-Fang Yang-Yen, Yu-Ju Chen, Yuan-Tsong Chen, Fu-Tong Liu, Jeffrey JY Yen* Palmitoyl acyltransferase activity of ZDHHC13 regulates skin barrier development partly by controlling PADi3 and TGM1 protein stability. JOURNAL OF INVESTIGATIVE DERMATOLOGY 2020-05-01, 140(5), 959-970.e3.
7. Chun-Mei Hu*, Sui-Chih Tien, Ping-Kun Hsieh, Yung-Ming Jeng, Ming-Chu Chang, Yu-Ting Chang, Yi-Ju Chen, Yu-Ju Chen, Y-HP Lee Eva, Wen-Hwa Lee* High glucose triggers nucleotide imbalance through O-GlcNAcylation of key enzymes and induces KRAS mutation in pancreatic cells. CELL METABOLISM 2019-06-04, 29(6), 1334-1349.e10.
8. Juanilita T Waniwan, Yi-Ju Chen, Rey Capangpangan, Shao-Hsing Weng, Yu-Ju Chen* Glycoproteomic alterations in drug-resistant nonsmall cell lung cancer cells revealed by lectin magnetic nanoprobe-based mass spectrometry. JOURNAL OF PROTEOME RESEARCH 2018-09-28, 17(11), 3761-3773.
9. Chia-Ying Hsu, Gee-Chen Chang, Yi-Ju Chen, Yi-Chiung Hsu, Yi-Jing Hsiao, Kang-Yi Su, Hsuan-Yu Chen, Chien-Yu Lin, Jin-Shing Chen, Yu-Ju Chen, Qi-Sheng Hong, Wen-Hui Ku, Chih-Ying Wu, Bing-Ching Ho, Ching-Cheng Chiang, Pan-Chyr Yang, Sung-Liang Yu* FAM198B is associated with prolonged survival and inhibits metastasis in lung adenocarcinoma via blockage of ERK-mediated MMP-1 expression. CLINICAL CANCER RESEARCH 2018-02-15, 24(4), 916-926.
10. Hui-Yin Chang, Ching-Tai Chen, Chu-Ling Ko, Yi-Ju Chen, Yu-Ju Chen, Wen-Lian Hsu, Chiun-Gung Juo, Ting-Yi Sung* ITop-Q: an intelligent tool for top-down proteomics quantitation using DYAMOND algorithm. ANALYTICAL CHEMISTRY 2017-12-19, 89(24), 13128-13136.
11. Lanyi Chang, Yi-Ju Chen, Chan-Yo Fan, Chin-Ju Tang, Yi-Hsiu Chen, Penk-Yeir Low, Albert Ventura, Chun-Cheng Lin, Yu-Ju Chen, Takashi Angata* Identification of Siglec ligands using a proximity labeling method. JOURNAL OF PROTEOME RESEARCH 2017-10-06, 16(10), 3929-3941.
12. Li-Fen Shen, Yi-Ju Chen, Kai-Ming Liu, Amir N Saleem Haddad, I-Wen Song, Hsiao-Yuh Roan, Li-Ying Chen, Jeffrey JY Yen, Yu-Ju Chen, Jer-Yuarn Wu, Yuan-Tsong Chen* Role of S-palmitoylation by ZDHHC13 in mitochondrial function and metabolism in liver. SCIENTIFIC REPORTS 2017-05-19, 7(1), 1-14.
13. Mira Anne C. dela Rosa, Wei-Chun Chen, Yi-Ju Chen, Rofeamor P. Obena, Chih-Hsiang Chang, Rey Y. Capangpangan, Tung-Hung Su, Chi-Ling Chen, Pei-Jer Chen, Yu-Ju Chen* One-Pot Two-Nanoprobe Assay Uncovers Targeted Glycoprotein Biosignature. ANALYTICAL CHEMISTRY 2017-03-21, 89(7), 3973-3980.
14. Han-Tsang Wu, Yi-Chih Kuo, Jung-Jyh Hung, Chi-Hung Huang, Wei-Yi Chen, Teh-Ying Chou, Yeh Chen, Yi-Ju Chen, Yu-Ju Chen, Wei-Chung Cheng, Shu-Chun Teng, Kou-Juey Wu* K63-polyubiquitinated HAUSP deubiquitinates HIF-1α and dictates H3K56 acetylation promoting hypoxia-induced tumour progression. NATURE COMMUNICATIONS 2016-12-09, 7(1), 1-17.
15. Jung-Lin Wu, Hsin-Yi Wu, Dong-Yan Tsai, Ming-Feng Chiang, Yi-Ju Chen, Shijay Gao, Chun-Cheng Lin, Chun-Hung Lin, Kay-Hooi Khoo, Yu-Ju Chen*, Kuo-I Lin* Temporal regulation of Lsp1 O-GlcNAcylation and phosphorylation during apoptosis of activated B cells. NATURE COMMUNICATIONS 2016-08-24, 7(1), 1-11.
16. Tsung-Che Chang, Avijit K Adak, Ting-Wei Lin, Pei-Jhen Li, Yi-Ju Chen, Chain-Hui Lai, Chien-Fu Liang, Yu-Ju Chen, Chun-Cheng Lin* A photo-cleavable biotin affinity tag for the facile release of a photo-crosslinked carbohydrate-binding protein. BIOORGANIC & MEDICINAL CHEMISTRY 2016-03-15, 24(6), 1216-1224.
17. Kai-Ming Liu, Yi-Ju Chen, Li-Fen Shen, Amir NS Haddad, I-Wen Song, Li-Ying Chen, Yu-Ju Chen, Jer-Yuarn Wu, Jeffrey JY Yen, Yuan-Tsong Chen* Cyclic alopecia and abnormal epidermal cornification in Zdhhc13-deficient mice reveal the importance of palmitoylation in hair and skin differentiation. Journal of Investigative Dermatology 2015-11-01, 135(11), 2603-2610.
18. Reta Birhanu Kitata, Baby Rorielyn T Dimayacyac-Esleta, Wai-Kok Choong, Chia-Feng Tsai, Tai-Du Lin, Chih-Chiang Tsou, Shao-Hsing Weng, Yi-Ju Chen, Pan-Chyr Yang, Susan D Arco, Alexey I Nesvizhskii, Ting-Yi Sung, Yu-Ju Chen* Mining missing membrane proteins by high-pH reverse-phase StageTip fractionation and multiple reaction monitoring mass spectrometry. JOURNAL OF PROTEOME RESEARCH 2015-09-04, 14(9), 3658-3669.
19. Yi-Ju Chen, Cheng-Tsung Lu, Kai-Yao Huang, Hsin-Yi Wu, Yu-Ju Chen*, Tzong-Yi Lee* GSHSite: exploiting an iteratively statistical method to identify s-glutathionylation sites with substrate specificity. PLOS ONE 2015-04-07, 10(4), e0118752.
20. Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Kai-Yao Huang, Wei-Chieh Ching, Hsiao-Hsiang Yang, Yen-Chen Liao, Yu-Ju Chen, Tzong-Yi Lee* dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. NUCLEIC ACIDS RESEARCH 2015-01-28, 43(D1), D503-D511.
21. Jason Ching-Yao Lin, Bing-Yu Chiang, Chi-Chi Chou, Tzu-Chieh Chen, Yi-Ju Chen, Yu-Ju Chen, Chun-Hung Lin* Glutathionylspermidine in the modification of protein SH groups: the enzymology and its application to study protein glutathionylation. MOLECULES 2015-01-15, 20(1), 1452-1474.
22. Hsin-Yi Wu, Cheng-Tsung Lu, Hui-Ju Kao, Yi-Ju Chen, Yu-Ju Chen*, Tzong-Yi Lee* Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. BMC BIOINFORMATICS 2014-12-08, 15(16), 1-12.
23. Yi-Ju Chen, Wei-Chieh Ching, Jinn-Shiun Chen, Tzong-Yi Lee, Cheng-Tsung Lu, Hsiao-Chiao Chou, Pei-Yi Lin, Kay-Hooi Khoo, Jenn-Han Chen, Yu-Ju Chen Decoding the s-nitrosoproteomic atlas in individualized human colorectal cancer tissues using a label-free quantitation strategy. JOURNAL OF PROTEOME RESEARCH 2014-11-07, 13(11), 4942-4958.
24. Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee*, Yu-Ju Chen* dbGSH: a database of S-glutathionylation. BIOINFORMATICS 2014-08-15, 30(16), 2386-2388.
25. Cheng-Tsung Lu, Tzong-Yi Lee, Yu-Ju Chen*, Yi-Ju Chen* An intelligent system for identifying acetylated lysine on histones and nonhistone proteins. BIOMED RESEARCH INTERNATIONAL 2014-07-24, 2014, 528650.
26. Sakdithep Chaiyarit, Nilubon Singhto, Yi-Ju Chen, Chia-Ying Cheng, Wararat Chiangjong, Rattiyaporn Kanlaya, Henry HN Lam, Paleerath Peerapen, Ting-Yi Sung, Phornpimon Tipthara, Akhilesh Pandey, Terence CW Poon, Yu-Ju Chen, Ravi Sirdeshmukh, Maxey CM Chung, Visith Thongboonkerd* Chromosome-centric human proteome project (C-HPP): Chromosome 12. JOURNAL OF PROTEOME RESEARCH 2014-05-15, 13(7), 3160-3165.
27. Kai-Yao Huang, Hsin-Yi Wu, Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Yun-Chung Hsieh, Chih-Ming Tsai, Kuo-I Lin, Hsien-Da Huang, Tzong-Yi Lee*, Yu-Ju Chen* RegPhos 2.0: an updated resource to explore protein kinase–substrate phosphorylation networks in mammals. DATABASE 2014-04-25, 2014, bau034.
28. I-Wen Song, Wei-Ru Li, Li-Ying Chen, Li-Fen Shen, Kai-Ming Liu, Jeffrey JY Yen, Yi-Ju Chen, Yu-Ju Chen, Virginia Byers Kraus, Jer-Yuarn Wu, MT Michael Lee*, Yuan-Tsong Chen* Palmitoyl acyltransferase, Zdhhc13, facilitates bone mass acquisition by regulating postnatal epiphyseal development and endochondral ossification: a mouse model. PLOS ONE 2014-03-17, 9(3), e92194.
29. Yi-Ju Chen, Wei-Chieh Ching, Yu-Pei Lin, Yu-Ju Chen* Methods for detection and characterization of protein S-nitrosylation. METHODS 2013-08-01, 62(2), 138-150.
30. Cheng-Tsung Lu, Kai-Yao Huang, Min-Gang Su, Tzong-Yi Lee, Neil Arvin Bretana, Wen-Chi Chang, Yi-Ju Chen, Yu-Ju Chen, Hsien-Da Huang* DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. NUCLEIC ACIDS RESEARCH 2012-11-26, 41(D1), D295-D305.
31. Tzong-Yi Lee*, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang, Yu-Ju Chen* dbSNO: a database of cysteine S-nitrosylation. BIOINFORMATICS 2012-07-10, 18(17), 2293-2295.
32. Tzong-Yi Lee*, Yi-Ju Chen, Tsung-Cheng Lu, Hsien-Da Huang, Yu-Ju Chen* SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. PLOS ONE 2011-07-15, 6(7), e21849.
33. Yi-Ju Chen, Wei-Chi Ku, Pei-Yi Lin, Hsiao-Chiao Chou, Kay-Hooi Khoo, Yu-Ju Chen* S-Alkylating Labeling Strategy for Site-Specific Identification of the S-Nitrosoproteome. JOURNAL OF PROTEOME RESEARCH 2010-10-06, 9(12), 6417-6439.
34. Wei-Chi Ku, Sung-Kay Chiu, Yi-Ju Chen, Hsin-Hung Huang, Wen-Guey Wu, Yu-Ju Chen* Complementary quantitative proteomics reveals that transcription factor AP-4 mediates E-box-dependent complex formation for transcriptional repression of HDM2. MOLECULAR & CELLULAR PROTEOMICS 2009-09-01, 8(9), 2034-2050.
35. Chih-Chiang Tsou, Yin-Hao Tsui, Yi-Hwa Yian, Yi-Ju Chen, Han-Yin Yang, Chuan-Yih Yu, Ke-Shiuan Lynn, Yu-Ju Chen, Ting-Yi Sung*, Wen-Lian Hsu* MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC–MS. NUCLEIC ACIDS RESEARCH 2009-07-01, 37(suppl_2), W661-W669.
36. Yi-Ju Chen, Wei-Chi Ku, Li-Ting Feng, Ming-Li Tsai, Chung-Hung Hsieh, Wen-Hwei Hsu, Wen-Feng Liaw, Chen-Hsiung Hung, Yu-Ju Chen Nitric Oxide Physiological Responses and Delivery Mechanisms Probed by Water-Soluble Roussin’s Red Ester and {Fe(NO)2}10 DNIC. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2008-08-20, 130(33), 10929-10938.

1. Yi-Ju Chen, Kuen-Tyng Lin, Yi-Jing Hsiao, Gee-ChenChang, Jin-ShingChen, Sung-Liang Yu, Yu-Ju Chen, 2022, “Discovery of protein signature of early-stage recurrent lung adenocarcinoma by plasma proteome profiling”, paper presented at HUPO 2022 Congress, Cancun, Mexico: HUPO, 2022-12-04 ~ 2022-12-08.
2. Yi-Ju Chen, Ta-Chi Yen, Yu-Hsien Lin, Kai-Hooi Khoo, Yu-Ju Chen*, 2020, “Enhanced N-sialoglycoproteomic Profile by Using Zwitter-Ionic Hydrophilic Interaction Chromatography (ZIC-cHILIC)”, paper presented at 68th American Society for Mass Spectrometry (ASMS) (Live Webinars), Houston, America: 美國質譜學會, 2020-06-01 ~ 2020-06-12.
3. Yi-Ju Chen, Theodoros I. Roumeliotis, Ya-Hsuan Chang, Ching-Tai Chen, Chia-Li Han, Miao-Hsia Lin, Ze-Shiang Lin, Wei-Hung Chang, Ke-Chieh Huang, Hao-Chin Yang, Pei-Shan Wu, Pei-Yi Lin, Kuen-Tyng Lin, Jen-Hung Wang, Gee‐Chen Chang, Yet-Ran Chen, Ana I. Robles, Henry Rodriguez, Jin-Shing Chen*, Sung-Liang Yu*, Ting-Yi Sung*, Jyoti S. Choudhary*, Hsuan-Yu Chen*, Pan-Chyr Yang*, Yu-Ju Chen*, 2019, “Proteogenomics landscape of early lung adenocarcinoma patients identifies stratification hallmarks of early onset and progression”, paper presented at Taiwan Proteomics Society Annual Conference & 2019 Multiomics and precision medicine joint conference, 台灣，台南: 台灣蛋白體學會, 2019-12-07 ~ 2019-12-08.
4. Yi-Ju Chen, Theodoros I. Roumeliotis, Ya-Hsuan Chang, Ching-Tai Chen, Chia-Li Han, Miao-Hsia Lin, Ze-Shiang Lin, Wei-Hung Chang, Ke-Chieh Huang, Hao-Chin Yang, Pei-Shan Wu, Pei-Yi Lin, Kuen-Tyng Lin, Jen-Hung Wang, Gee‐Chen Chang, Yet-Ran Chen, Ana I. Robles, Henry Rodriguez, Jin-Shing Chen*, Sung-Liang Yu*, Ting-Yi Sung*, Jyoti S. Choudhary*, Hsuan-Yu Chen*, Pan-Chyr Yang*, Yu-Ju Chen*, 2019, “Proteogenomics landscape of early-stage lung adenocarcinoma patients identifies stratification hallmarks of early onset and progression”, paper presented at International Cancer Moonshot Joint Meeting and Human Proteome Organization World Congress (HUPO 2019), Adelaide, Australia: 世界人類蛋白體學會, 2019-09-13 ~ 2019-09-18.
5. Lee A Gethings, Christopher Hughes, Yi-Ju Chen, Yu-Ju Chen, Johannes PC Vissers*, 2018, “GLYCOPEPTIDE FRAGMENTATION OPTIMIZATION AND QUANTITATION BY MULTI COLLISION ENERGY RAMP SCANNING QUADRUPOLE DIA”, paper presented at 66th American Society for Mass Spectrometry (ASMS), San Diego, America: 美國質譜學會, 2018-06-03 ~ 2018-06-07.
6. Yi-Ju Chen, Yu-Hsien Lin, Kay-Hooi Khoo, Yu-Ju Chen*, 2017, “Decoding site-specific alteration of Sialo-glycoproteome in EGFR-subtype of non-small cell lung cancer towards precision medicine”, paper presented at 16th Human Proteome Organization World Congress, 愛爾蘭，都柏林: 世界人類蛋白體學會, 2017-09-17 ~ 2017-09-21.
7. Yi-Ju Chen, Yu-Hsien Lin, Ta-Chi Yen, Kai-Hooi Khoo, Yu-Ju Chen*, 2017, “Mass spectrometry-based quantitative analysis for decoding site-specific alteration of Sialo-glycoproteome in EGFR-subtypes of non-small cell lung cancers”, paper presented at 65th American Society for Mass Spectrometry, Indianapolis, America: 美國質譜學會, 2017-06-04 ~ 2017-06-08.
8. Yi-Ju Chen, Yu-Hsien Lin, Ta-Chi Yen, Kay-Hooi Khoo, Yu-Ju Chen*, 2017, “Decoding site-specific alteration of Sialo-glycoproteome in EGFR-subtype of non-small cell lung cancer”, paper presented at US HUPO, San Diego, America: 美國人類蛋白體學會, 2017-03-19 ~ 2017-03-22.
9. Yi-Ju Chen, Yu-Hsien Lin, Kay-Hooi Khoo, Yu-Ju Chen*, 2016, “Decoding site-specific alteration of Sialo-glycoproteome in EGFR-subtype of non-small cell lung cancers”, paper presented at The Human Proteomics (HUPO) 15th Annual World Congress, 2016, Taipei, Taiwan: 世界人類蛋白體學會, 2016-09-17 ~ 2016-09-21.
10. Yi-Ju Chen, Yu-Hsieh Lin, Kay-Hooi Khoo, Yu-Ju Chen*, 2016, “Decoding Site-Specific Alteration of Sialo-Glycoproteome in EGFR-Subtype of Non-Small Cell Lung Cancer”, paper presented at The 8th Asia Oceania Human Proteome Organization (AOHUPO) Congress, Sun Moon Lake, Taiwan: 世界人類蛋白體學會, 2016-09-22 ~ 2016-09-23.
11. Yi-Ju Chen, Yu-Hsien Lin, Kay-Hooi Khoo, Yu-Ju Chen*, 2016, “Decoding site-specific alteration of Sialo-glycoproteome in EGFR-subtype of non-small cell lung cancer”, paper presented at 13th Annual Conference of the TSMS, 台灣，高雄: 台灣質譜學會, 2016-06-27 ~ 2016-06-29.
12. Yi-Ju Chen, Yu-Hsien Lin, Yu-Ju Chen*, 2016, “Mass spectrometry-based quantitative analysis for decoding site-specific alteration of Sialo-glycoproteome in EGFR-subtype of non-small cell lung cancers”, paper presented at 64th American Society for Mass Spectrometry, San Antonio, America: 美國質譜學會, 2016-06-05 ~ 2016-06-09.
13. Yi-Ju Chen, Yu-Ching Su, Sheng-Huang Lin, Wen-Ying Shen, Chun-Hung Lin, Yu-Ju Chen*, 2015, “Characterizing the Dynamic Change of Global and Site-Specific S-nitrosoproteome and Glutathionylome”, paper presented at 14th Human Proteome Organization World Congress, 2015, 加拿大溫哥華: 世界人類蛋白體學會, 2015-09-26 ~ 2015-10-01.
14. Yi-Ju Chen, Yu-Ching Su, Sheng-Huang Lin, Wen-Ying Shen, Chun-Hung Lin, Yu-Ju Chen*, 2014, “Characterizing the Interplay and Dynamic Change of S-nitrosoproteome and Glutathionylome”, paper presented at 2014 Taiwan Proteomics Society Annual Conference & Translational and Systems Biology Symposium, 台灣，台北: 台灣蛋白體學會, 2014-11-11 ~ 2014-11-12.
15. Yi-Ju Chen, Yu-Ching Su, Sheng-Huang Lin, Wen-Ying Shen, Chun-Hung Lin*, Yu-Ju Chen*, 2014, “Characterizing the Dynamic Change of Global and Site-specific Quantitative S-nitrosoproteome and Glutathionylome”, paper presented at 11th TSMS Annual Conference, 2014, 台灣，台中: 台灣質譜學會, 2014-06-29 ~ 2014-07-01.
16. Yi-Ju Chen, Sheng-Huang Lin, Wen-Ying Shen, Yu-Ju Chen*, Chun-Hung Lin*, 2013, “Characterizing the Dynamic Change of S-nitrosoproteome and Glutathionylome by Site-specific Quantitation Strategy”, paper presented at 4th AOMSC and 10th TSMS Annual Conference, 台灣，台北: 台灣質譜學會, 2013-07-10 ~ 2013-07-12.
17. Yi-Ju Chen, Sheng-Huang Lin, Wen-Ying Shen, Yu-Ju Chen*, Chun-Hung Lin*, 2013, “Site-specific Quantitation strategy for characterizing the dynamic change of S-nitrosoproteome and glutathionylome”, paper presented at 61th American Society for Mass Spectrometry, Minneapolis, America: 美國質譜學會, 2013-06-08 ~ 2013-06-13.
18. Yi-Ju Chen, Sheng-Huang Lin, Wen-Ying Shen, Yu-Ju Chen*, Chun-Hung Lin*, 2013, “Characterizing the Dynamic Change of Global and Site-specific Quantitative S-nitrosoproteome and Glutathionylome”, paper presented at 2013 Taiwan Proteomics Society International Conference (TPSIC): Recent Advances in Translational Medicine, 台灣，台北: 台灣蛋白體學會, 2013-05-24 ~ 2013-05-25.
19. Yi-Ju Chen, Wei-Chieh Ching, Jinn-Shiun Chen, Hsiao-Chiao Chou, Pei-Yi Lin, Kay-Hooi Khoo, Jenn-Han Chen, Yu-Ju Chen*, 2012, “Site-specific quantitation of in-vivo S-nitrosoproteome in human colorectal cancer”, paper presented at The 4th World Chinese Mass spectrometry Conference (WCMSC) and 2012 Taiwan Society for Mass Spectrometry (TSMS) Annual Conference, 台灣，台南: 台灣質譜學會, 2012-06-28.
20. Yi-Ju Chen, Wei-Chieh Ching, Hsiao-Chiao Chou, Pei-Yi Lin, Jinn-Shiun Chen, Kay-Hooi Khoo, Jenn-Han Chen, Yu-Ju Chen*, 2011, “Exploring the S-nitrosoproteome of human colorectal cancer tissues by Site-specific Identification and Quantitation Strategy”, paper presented at 2011 International Conference on Functional Proteomics: Advances in Post-Translation Modification, 台灣，台北: 台灣蛋白體學會, 2011-11-14 ~ 2011-11-15.
21. Yi-Ju Chen, Wei-Chieh Ching, Hsiao-Chiao Chou, Jinn-Shiun Chen, Kay-Hooi Khoo, Jenn-Han Chen, Yu-Ju Chen*, 2011, “S-Alkylating Biotin Switch Method Combining Label-free Strategy for Site-specific Quantitation of the S-nitrosoproteome in Human Colorectal Cancer Tissues”, paper presented at 59th American Society for Mass Spectrometry (ASMS), Denver, America: 美國質譜學會, 2011-06-05 ~ 2011-06-09.
22. Yi-Ju Chen, Wei-Chieh Ching, Hsiao-Chiao Chou, Pei-Yi Lin, Jinn-Shiun Chen, Kay-Hooi Khoo, Jenn-Han Chen, Yu-Ju Chen*, 2011, “Site-specific Quantitation of the Personalized S-nitrosoproteome in Human Colorectal Cancer Tissues”, paper presented at Translational Medicine Conference and Taiwan Proteomics Society Annual Symposium, 台灣，台北: 台灣蛋白體學會, 2011-04-27 ~ 2011-04-28.
23. Yi-Ju Chen, Pei-Yi Lin, Kay-Hooi Khoo, Jenn-Han Chen, and Yu-Ju Chen*, 2010, “Assessing the Dynamic Change of S-nitrosoproteome in Human Colorectal Cancer by Label-free Quantitation”, paper presented at 9th Human Proteome Organization World Congress (HUPO 2010), 澳洲、雪梨: 世界人類蛋白體學會, 2010-09-19 ~ 2010-09-23.
24. Yi-Ju Chen, Pei-Yi Lin, Kay-Hooi Khoo, Jenn-Han Chen, and Yu-Ju Chen*, 2010, “Label-free Quantitation for Assessing the Potential Targets and Dynamic Change of S-nitrosoproteome in Human Colorectal Cancer”, paper presented at 2010第七屆台灣質譜年會暨學術研討會, 台灣，高雄: 台灣質譜學會, 2010-06-28 ~ 2010-06-29.
25. Yi-Ju Chen, Hsiao-Chiao Chou, Wei-Chi Ku, Pei-Yi Lin, Kao-Yu Chou, Kay-Hooi Khoo, Jenn-Han Chen, Yu-Ju Chen*, 2010, “Assessing the Dynamic Change of S-nitrosoproteome in Human Colorectal Cancer by Label-free Quantitation”, paper presented at 2010 Disease Biomarker and TPS International Conference, 台灣，桃園: 台灣蛋白體學會, 2010-04-23 ~ 2010-04-24.
26. Yi-Ju Chen, Wei-Chi Ku, Pei-Yi Lin, Hsiao-Chiao Chou, Kao-Yu Chou, Kay-Hooi Khoo, Yu-Ju Chen*, 2009, “SIDSNOMS, A Proteome-wide Approach towards Comprehensive Site-specific Identification of S-Nitrosylome”, paper presented at The 3rd International Symposium on Bio-Inspired Engineering (ISBIE), 台灣，台北: 中央研究院, 2009-10-21 ~ 2009-10-23.
27. Yi-Ju Chen, Wei-Chi Ku, Hsiao-Chiao Chou, Kao-Yu Chou, Pei-Yi Lin, Kay-Hooi Khoo, Yu-Ju Chen*, 2009, “SIDSNOMS, A Proteome-wide Approach towards Comprehensive Site-specific Identification of S-Nitrosylome”, paper presented at 2009 TPS International Proteomics Conference and 5th AOHUPO Membrane Proteomics Initiative Workshop, Taipei, Taiwan: 台灣蛋白體學會, 2009-06-19 ~ 2009-06-20.
28. Yi-Ju Chen, Hsiao-Chiao Chou, Wei-Chi Ku, Kay-Hooi Khoo, Yu-Ju Chen*, 2009, “Mass spectrometry-based site-specific identification of S-nitrosylome in cardiovascular system”, paper presented at 57th American Society for Mass Spectrometry, 美國、費城: 美國質譜學會, 2009-05-31 ~ 2009-06-04.
29. Yi-Ju Chen, Hsiao-Chiao Chou, Wei-Chi Ku, Kay-Hooi Khoo, Yu-Ju Chen*, 2008, “Assessing Dynamic Change of Protein S-nitrosylation by Label-free Quantitative Proteomics”, paper presented at 56th American Society for Mass Spectrometry (ASMS), Denver, USA: 美國質譜學會, 2008-06-01 ~ 2008-06-05.
30. Yi-Ju Chen, Wei-Chi Ku, Ming-Li Tsai, Wen-Feng Liaw, Yu-Ju Chen*, 2007, “Exploring the Acting Mechanism of Nitric Oxide by Proteomic Study Using in-vitro Cell Cultures as a Model System”, paper presented at Taiwan Proteomics Society International Conference 2007 (TPSIC 2007), 台灣，台南: 台灣蛋白體學會, 2007-12-04 ~ 2007-12-05.
31. Yi-Ju Chen, Wei-Chi Ku, Ming-Li Tsai, Wen-Feng Liaw, Yu-Ju Chen*, 2007, “Exploring the Acting Mechanism of Nitric Oxide by Proteomic Study Using in-vitro Cell Cultures as a Model System”, paper presented at HUPO 6th Annual World Congress (HUPO 2007), 韓國，首爾: 世界人類蛋白體學會, 2007-10-06 ~ 2007-10-10.