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Yu-Ju Chen (陳玉如)

Proteomics and Mass Spectrometry

Yu-Ju Chen (陳玉如)

Director(2013~);Deputy Director(2011-2013);Research Fellow (2010-);Associate Research Fellow (2005-2010);Adjunt Professor, National Taiwan University (2007-);Adjunt Professor, National Chia- Yi University (2007-);Adjunct Research Fellow, Genomic Research Center (2004-Present);Assistant Research Fellow (1999-2005);Postdoctoral Fellow, National Tsing Hua University (1998-1999);Postdoctoral Fellow, Ames Laboratory, U.S.A(1999);Ph.D., Iowa State University (1997);BS, National Taiwan University (1992);President, Taiwan Proteomics Society (2008-2011);Editorial Board Member, European Journal of Mass Spectrometry (2012-2015);Wu Ta-you Memorial Award, National Science Council, Taiwan (2008);Junior Researcher Award Research Investigators, Academia Sinica (2008);Distinguished Young Chemists Award, Federation of Asian Chemical Societies (2007);Outstanding Young Investigator Award, the Chinese Chemical Society (2006);Outstanding Scholar Award, Taiwan Society for Mass Spectrometry(2011);Award for Outstanding Young Scholar, Shui-Mu Foundation of Chemistry(2012);Outstanding Research Award from the National Science Council.(2012);
Research Interests

Advanced bioinformatics-assisted mass spectrometry methods for comprehensive signatures of membrane sub-proteome and its downstream phosphoproteome and nitrosylproteome associated with disease.
Surface functionalized nanoprobe-based affinity mass spectrometry for multiplexed quantitation of disease-associated protein markers, discovery of post-translational modification in disease and epitope mapping for drug-interacting protein.



Selected Publications
  1. Tsai, C.-F.; Wang, Y.-T.; Yen, H.-Y.; Tsou, C.-C.; Ku, W.-C.; Lin, P.-Y.; Chen, H.-Y.; Nesvizhskii, A.; Ishihama, Y.; Chen, Y.-J. Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics. Nat. Commun. 2015, 6, 6622.
  2. Wang, W.-L.; Huang, H.-C.; Kao, S.-H.; Hsu, Y.-C.; Wang, Y.-T.; Li, K.-C.; Chen, Y.-J.; Yu, S.-L.; Wang, S.-P.; Hsiao, T.-H.; Yang, P.-C.; Hong, T.-M. Slug is temporally regulated by cyclin E in cell cycle and controls genome stability. Oncogene 2014, 1-10. Oncogene advance online publication, doi: 10.1038/onc.2014.58, 1–10
  3. Kao, S.-H.; Wang, W.-L.; Chen, C.-Y.; Chang, Y.-L.; Wu, Y.-Y.; Wang, Y.-T.; Wang, S.-P.; Nesvizhskii, AI; Chen, Y.-J.; Hong, T.-M.; Yang, P.-C. GSK3β controls epithelial–mesenchymal transition and tumor metastasis by CHIP-mediated degradation of Slug. Oncogene 2013, 1-11, doi:10.1038/onc.2013.279
  4. Huang, T.-K.; Han, C.-L.; Lin, S.-I; Chen, Y.-J.; Tsai, Y.-C.; Chen, Y.-R.; Chen, J.-W.; Lin, W.-Y.; Chen, P.-M.; Liu, T.-Y.; Chen, Y.-S.; Sun, C.-M.; Chiou, T.-J. Identification of Downstream Components of Ubiquitin-Conjugating Enzyme PHOSPHATE2 by Quantitative Membrane Proteomics in Arabidopsis Roots. The Plant Cell 2013, 25, 4044.
  5. Chang, Y.-W.; Chang, Y.-T.; Wang, Q.; Lin, J. J.-C.; Chen, Y.-J.; Chen, C.-C. Quantitative Phosphoproteomic Study of Pressure-Overloaded Mouse Heart Reveals Dynamin-Related Protein 1 as A Modulator of Cardiac Hypertrophy. Mol Cell Proteomics 2013, 12, 3094.
  6. Lu, Y.-W.; Chien, C.-W.; Lin, P.-C.; Huang, L.-D.; Chen, C.-Y.; Wu, S.-W.; Han, C.-L.; Khoo, K.-H.; Lin, C.-C.; Chen, Y.-J. BAD-Lectins: Boronic Acid-Decorated Lectins with Enhanced Binding Affinity for the Selective Enrichment of Glycoproteins. Anal. Chem. 2013, 85, 8268.
  7. Lin, P.-C.; Yu, C.-C.; Wu, H.-T.; Lu, Y.-W.; Han, C.-L.; Su, A.-K.; Chen, Y.-J.; Lin, C.-C. A Chemically Functionalized Magnetic Nanoplatform for Rapid and Specific Biomolecular Recognition and Separation. Biomacromolecules 2013, 14, 160.
  8. Chen, L.-C.; Liu, M.-Y.; Hsiao, Y.-C.; Choong, W.-K.; Wu, H.-Y.; Hsu, W.-L.; Liao, P.-C.; Sung, T.-Y.; Tsai, S.-F.; Yu, J.-S.; Chen, Y.-J. Decoding the Disease-Associated Proteins Encoded In the Human Chromosome 4. J. Proteome Res. 2012, 12, 33.
  9. Lee, T.-Y.; Chen, Y.-J.; 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.
  10. Han, C.-L.; Chen, J.-S.; Chan, E.-C.; Wu, C.-P.; Yu, K.-H.; Chen, K.-T.; Tsou, C.-C.; Tsai, C.-F.; Chien,C.-W.; Kuo, Y.-B.; Lin, P.-Y.; Yu, J.-S.; Hsueh, C.; Chen, M.-C.; Chan, C.-C.; Chang, Y.-S.; Chen, Y.-J. An Informatics-assisted Label-free Approach for Personalized Tissue Membrane Proteomics: Case Study on Colorectal Cancer.Mol. Cell. Proteomics 2011, 10, 1. (Selected as top 2% of published articles in biology and medicine by Faculty of 1000).
  11. Wu, H.-T.; Hsu, C.-C.; Tsai, C.-F.; Lin, P.-C.; Lin, C.-C.; Chen, Y.-J. Nanoprobe-based Immobilized Metal Affinity Chromatography for Sensitive and Complementary Enrichment of Multiply Phosphorylated Peptides. Proteomics 2011, 11, 2639.
  12. Tsou, C.-C.; Tasi, C.-F.; Tsui, Y.-H.; Sudhir, P.-R.; Wang, Y.-T.; Chen, Y.-J.; Chen, J.-Y.; Sung, T.-Y.; Hsu, W.-L. IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation. Mol. Cell. Proteomics 2010, 9, 131..
  13. Wang, Y.-T.; Tsai, C.-F.; Hong, T.-C.; Tsou, C.-C.; Lin, P.-Y.; Pan, S.-H.; Hong, T.-M.; Yang, P.-C.; Sung, T.-Y.; Hsu, W.-L.; Chen, Y.-J. An informatics-assisted label-free quantitation strategy that depicts phosphoproteomic profiles in lung cancer cell invasion. J. Proteome Res. 2010, 9, 5882.
  14. Lin, P.-C.; Chen, S.-H.; Wang, K.-Y.; Chen, M.-L.; Adak, A. K.; Hwu, J.-R. R.; Chen, Y.-J.; Lin, C.-C. Fabrication of Oriented Antibody-Conjugated Magnetic Nanoprobes and Their Immunoaffinity Application. Anal. Chem. 2009, 81, 8774.
  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, Yu-Ju 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.
  16. Han, C.-L.; Chien, C.-W.; Chen, W.-C.; Chen,Y.-R.; Wu, C.-P.; Li, H.; Chen, Y.-J. A Multiplexed Quantitative Strategy for Membrane Proteomics: Opportunities for Mining Therapeutic Targets for Autosomal-Dominant Polycystic Kidney Disease. Mol. Cell. Proteomics. 2008, 7, 1983. (Selected by “Faculty of 1000 Biology” in 2009)

Update: 2016-01-06

Journal Paper
  1. 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 2017-11-2289(24), 13128-13136.
  2. Wei-Sheng Tien, Pei-Mien Chen, Ching-Yu Chuang, Shook-Mun Lui, Hung-Chih Kuo, Yu-Ju Chen, Kun-Pin Wu* Combining membrane proteomics and computational three-way pathway analysis revealed signalling pathways preferentially regulated in human iPSCs and human ESCs. Scientific Reports 2017-11-087(1), 15055-1-15055-14.
  3. Wai-Kok Choong, Tung-Shing Mamie Lih, Yu-Ju Chen, Ting-Yi Sung* Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome. Journal of Proteome Research 2017-09-2016(12), 4415-4424.
  4. 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 2017-09-1316(10), 3929-3941.
  5. Faezeh Shekari, Hossein Nezari, Yu-Ju Chen*, Hossein Baharvand*, Ghasem Hosseini Salekdeh* Data for Whole and Mitochondrial Proteome of Human Embryonic Stem Cells. Data in Brief 2017-06-1213, 371-376.
  6. Deng-Chyang Wu*, Kai-Yi Wang*, Sophie S.W. Wang, Ching-Min Huang, Yi-Wei Lee, Michael Isaac Chen, Szu-An Chuang, Shu-Hua Chen, Ying-Wei Lu, Chun-Cheng Lin, Ka-Wo Lee, Wen-Hung Hsu, Wu Kun-Pin*, Yu-Ju Chen Exploring the expression bar code of SAA variants for gastric cancer detection. PROTEOMICS 2017-0617(11), 1600356.
  7. Li-Fen Shen, Yi-Ju Chen, Kai-Ming Liu, Amir N. Saleem Haddad, I-Wen Song, Hsiao-Yuh Roan, Li-Ying Chen, Jeffrey J. Y. 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 2017-05-197(1), 2128-1-2128-14.
  8. Faezeh Shekari, Hossein Nezari, Mehran Rezaei Larijani, Chia-Li Han, Hossein Baharvand*, Yu-Ju Chen*, Ghasem Hosseini Salekdeh* Proteome analysis of human embryonic stem cells organelles. Journal of Proteomics 2017-04-20162, 108-118.
  9. Mira Anne dela Rosa, Wei-Chun Chen, Yi-Ju Chen, Rofeamor Obena, Chih-Hsiang Chang, Rey Capangpangan, Tung-Hung Su, Chi-Ling Chen, Pei-Jer Chen, Yu-Ju Chen* One-Pot Two-Nanoprobe Assay Uncovers Targeted Glycoprotein Biosignature. ANALYTICAL CHEMISTRY 2017-03-2189 (7), 3973-3980.
  10. Meng-Tsz Tsai, Yu-Jen Chen, Ching-Yi Chen, Mong-Hsun Tsai, Chia-Li Han, Yu-Ju Chen, Harry J Mersmann, Shih-Torng Ding* Identification of Potential Plasma Biomarkers for Nonalcoholic Fatty Liver Disease by Integrating Transcriptomics and Proteomics in Laying Hens. The Journal of Nutrition 2017-03147(3), 293-303.
  11. Yi-Ting Wang, Szu-Hua Pan, Chia-Feng Tsai, Ting-Chun Kuo, Hsin-Yung Yen, Wai-Kok Choong, Hsin-Yi Wu, Yuan-Ling Hsu, Tse-Ming Hong, Ting-Yi Sung, Pan-Chyr Yang, Yu-Ju Chen* Phosphoproteomics Reveals HMGA1, a CK2 Substrate, as a Drug-Resistant Target in Non-Small Cell Lung Cancer. SCIENTIFIC REPORTS 2017-01-25,.
  12. Nai-Wen Chang*, Hong-Jie Dai*, Yung-Yu Shih, Chi-Yang Wu, Mira Anne C. Dela Rosa, Rofeamor P. Obena, Yu-Ju Chen, Wen-Lian Hsu*, Yen-Jen Oyang* Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017-01-04(2017), 1-13.
  13. 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 2016-12-097(13644 ), doi:10.1038/ncomms13644.
  14. Yi-Hsuan Chen, Hua-Yi Hsu, Ming-Tyng Yeh, Chen-Cheng Chen, Chang-Yu Huang, Ying-Hsuan Chung, Zee-Fen Chang, Wei-Chen Kuo, Nei-Li Chan, Jui-Hsia Weng, Bon-chu Chung, Yu-Ju Chen, Cheng-Bang Jian, Ching-Chieh Shen, Hwan-Ching Tai, Sheh-Yi Sheu*, Jim-Min Fa Chemical Inhibition of Human Thymidylate Kinase and Structural Insights into the Phosphate Binding Loop and Ligand-Induced Degradation. JOURNAL OF MEDICINAL CHEMISTRY 2016-10-1759 (21), 9906-9918.
  15. Chih-Wei Chen, Ning Tsao, Lin-Yi Huang, Yun Yen, Xiyong Liu, Christine Lehman, Yuh-Hwa Wang, Mei-Chun Tseng, Yu-Ju Chen, Yi-Chi Ho, Chian-Feng Chen, Zee-Fen Chang* Download: The Impact of Dupase on Ribonucleotide Reductase-Induced Genome Instability in Cancer Cells.. CELL REPORTS 2016-08-0216(5), 1287-1299.
  16. Indah Primadona, Yin-Hung Lai, Rey Y. Capangpangan, Rofeamor P. Obena, Mei-Chun Tseng, Ming-Feng Huang, Huan-Tsung Chang, Shiou-Ting Li, Chung-Yi Wu, Wei-Ting Chien, Chun-Cheng Lin, Yi-Sheng Wang*, Yu-Ju Chen* Functionalized HgTe Nanoparticles Promote Laser-Induced Solid Phase Ionization/Dissociation for Comprehensive Glycan Sequencing . ANALYST 2016-08141, 6093-6103.
  17. Chih-Chiang Tsou,Chia-Feng Tsai,Guoci Teo, Yu-Ju Chen, Alexey I. Nesvizhskii* Untargeted, Spectral Library-Free Analysis of Data Independent Acquisition Proteomics Data Generated Using Orbitrap Mass Spectrometers. PROTEOMICS 2016-0816, (15-16).
  18. 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 2016-087:12526, doi: 10.1038/ncomms12526.
  19. 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 2016-03-1524(6), 1216-1224.
  20. Sui-Chih Tien, Hsiao-Hui Lee, Ya-Chi Yang, Miao-Hsia Lin, Yu-Ju Chen, Zee-Fen Chang* The Shp2-Induced Epithelial Disorganization Defect is Reversed by HDAC6 Inhibition Independent of Cdc42. NATURE COMMUNICATIONS 2016-01, 7:10420.
  21. Kai-Ming Liu, Yi-Ju Chen, Li-Fen Shen, Amir N.S. Haddad, I-Wen Song, Li-Ying Chen, Yu-Ju Chen, Jer-Yuarn Wu, Jeffrey J.Y. 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 2015-11135 (11), 2603-10.
  22. Wai-Kok Choong, Hui-Yin Chang, Ching-Tai Chen, Chia-Feng Tsai, Wen-Lian Hsu, Yu-Ju Chen, Ting-Yi Sung Informatics View on the Challenges of Identifying Missing Proteins From Shotgun Proteomics. JOURNAL OF PROTEOME RESEARCH 2015-1114, 5396−5407.
  23. Baby Rorielyn Dimayacyac-Esleta, Chia-Feng Tsai, Reta Birhanu Kitata, Pei-Yi Lin, Wai Kok Choong, Tai-Du Lin, Yi-Ting Wang, Shao-Hsing Weng, Pan-Chyr Yang, Susan Arco, Ting-Yi Sung, Yu-Ju Chen* Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling. ANALYTICAL CHEMISTRY 2015-1187 (24), 12016–12023.
  24. Rey Y. Capangpangan, Mira Anne C. dela Rosa, Rofeamor P. Obena,Yu-Jen Chou, Der-Lii Tzou, Shao-Ju Shih, Ming-Hsi Chiang, Chun-Cheng Lin*, Yu-Ju Chen* Monodispersity of Magnetic Immuno-Nanoprobes Enhances the Detection Sensitivity of Low Abundance Biomarkers in One Drop of Serum. ANALYST 2015-09140, 7678–7686.
  25. Hsin-Yi Wu, Yih-Gang Goan, Ying-Hua Chang, Yi-Fang Yang, Hsiao-Jen Chang, Pin-Nan Cheng, Chih-Chieh Wu, Victor Zgoda, Yu-Ju Chen*, Pao-Chi Liao Qualification and Verification of Serological Biomarker Candidates for Lung Adenocarcinoma by Targeted Mass Spectrometry. JOURNAL OF PROTEOME RESEARCH 2015-0814(8), 3039-3050.
  26. Horvatovich Péter, Lundberg Emma, Yu-Ju Chen, Ting-Yi Sung, Fuchu He, Edouard Nice, Robert Goode, Simon Yu, Shoba Ranganathan, Mark Baker, Gilberto Domont, Erika Velasquez, Dong Li, Siqi Liu, Quanhui Wang, Qing-Yu He, Rajasree Menon, Yuanfang Guan, Fern A Quest for Missing Proteins: Update 2015 on Chromosome-Centric 2 Human Proteome Project. JOURNAL OF PROTEOME RESEARCH 2015-07, DOI: 10.1021/pr5013009.
  27. Horvatovich Péter, Lundberg Emma, Yu-Ju Chen, Ting-Yi Sung, Fuchu He, Edouard Nice, Robert Goode, Simon Yu, Shoba Ranganathan, Mark Baker, Gilberto Domont, Erika Velasquez, Dong Li, Siqi Liu, Quanhui Wang, Qing-Yu He, Rajasree Menon, Yuanfang Guan, Fern Quest for Missing Proteins: Update 2015 on Chromosome-Centric 2 Human Proteome Project. JOURNAL OF PROTEOME RESEARCH 2015-0714(9), 3415-31.
  28. Kitata Reta Birhanu, Dimayacyac-Esleta Baby Rorielyn, Choong Wai-Kok, Chia-Feng Tsai, Tai-Du Lin, Chih-Chiang Tsou, Shao-Hsing Weng, Yi-Ju Chen, Pan-Chyr Yang, Arco Susan, Nesvizhskii Alexey, 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 2015-07, DOI: 10.1021/acs.jproteome.5b00477.
  29. Rofeamor P. Obena, Mei-Chun Tseng, Indah Primadona, Jun Hsiao, I.-Che Li, Rey Y. Capangpangan, Hsiu-Fong Lu, Wan-Sheung Li, Ito Chao, Chun-Cheng Lin, Yu-Ju Chen* UV-Activated Multi-Layer Nanomatrix Provides Onestep Tunable Carbohydrate Structural Characterization in MALDI-MS. CHEMICAL SCIENCE 2015-056, 4790-4800.
  30. Einav Amit, Rofeamor Palarca Obena, Yi-Ting Wang, Roman Zhuravel, Aaron Reyes, Shir Elbaz, Dvir Rotem, Danny Porath, Assaf Friedler, Yu-Ju Chen, Shlomo Yitzchaik Integrating Proteomics with Electrochemistry for Identifying Kinase Biomarkers. CHEMICAL SCIENCE 2015-056, 4756-4766.
  31. 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, 10(4):e0118752. doi: 10.1371/journal.pone.0118752.
  32. Hsin-Yung Yen, Ying-Chih Liu, Nai-Yu Chen, Chia-Feng Tsai, Yi-Ting Wang, Yu-Ju Chen, Tsui-Ling Hsu, Pan-Chyr Yang, Chi-Huey Wong*  Effect of Sialylation on EGFR Phosphorylation and Resistance to Tyrosine Kinase Inhibition. PNAS 2015-04112 (22), 6955-6960.
  33. Chia-Feng Tsai, Yi-Ting Wang, Hsin-Yung Yen, Chih-Chiang Tsou, Wei-Chi Ku, Pei-Yi Lin, Hsuan-Yu Chen, Alexey Nesvizhskii, Yasushi Ishihama*, Yu-Ju Chen* Large-Scale Determination of Absolute Phosphorylation Stoichiometries in Human Cells by Motif-Targeting Quantitative Proteomics. NATURE COMMUNICATIONS 2015-03, 6:6622 | DOI: 10.1038/ncomms7622.
  34. Ke-Shiuan Lynn, Chen-Chun Chen, T. Mamie Lih, Cheng-Wei Cheng, Wan-Chih Su, Chun-Hao Chang, Chia-Ying Cheng, Wen-Lian Hsu, Yu-Ju Chen*, Ting-Yi Sung* MAGIC: An Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach. ANALYTICAL CHEMISTRY 2015-01-1687 (4), 2466-2473.
  35. 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 2014-1215, S1.
  36. 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 Associations, and Regulatory Networks of Protein S-Nitrosylation. NUCLEIC ACIDS RESEARCH 2014-1143, Database issue D503–D511 doi: 10.1093/nar/gku1.
  37. Ching-Wen Chang, Yu-Syuan Chen, Shiu-Huey Chou, Chia-Li Han, Yu-Ju Chen, Cheng-Chieh Yang, Chih-Yang Huang*, Jeng-Fan Lo* Distinct Subpopulations of Head and Neck Cancer Cells with Different Levels of Intracellular Reactive Oxygen Species Exhibit Diverse Stemness, Proliferation, and Chemosensitivity. CANCER RESEARCH 2014-09, DOI: 10.1158/0008-5472.CAN-14-0626.
  38. Min-Gang Su, Chien-Hsun Huang, Tzong-Yi Lee, Yu-Ju Chen*, Hsin-Yi Wu* Incorporating Amino Acids Composition and Functional Domains for Identifying Bacterial Toxin Proteins. BioMed Research International 2014-072014, 972692.
  39. 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, 528650.
  40. Wei-Ting Chien, Chien-Fu Liang, Ching-Ching Yu, Chien-Hung Lin, Si-Peng Li, Indah Primadona, Yu-Ju Chen, Kwok Kong T. Mong, Chun-Cheng Lin* Sequential One-Pot Enzymatic Synthesis of Oligo-N-Acetyllactosamine and Its Multi-Sialylated Extensions. CHEMICAL COMMUNICATIONS 2014-0650, 5786-5789.
  41. S-H Kao, W-L Wang, C-Y Chen, Y-L Chang, Y-Y Wu, Y-T Wang, S-P Wang, AI Nesvizhskii, Y-J Chen, T-M Hong*, P-C Yang* GSK3β Controls Epithelial-Mesenchymal Transition and Tumor Metastasis by CHIP-Mediated Degradation of Slug. ONCOGENE 2014-06, doi:10.1038/onc.2013.279.
  42. Chih-Ming Tsai, Hsin-Yi Wu, Tseng-Hsiung Su, Chu-Wei Kuo, Han-Wen Huang, Cheng-Han Chung, Chien-Sin Chen, Kay-Hooi Khoo, Yu-Ju Chen*, Kuo-I Lin* Phosphoproteomic Analyses Reveal that Galectin-1 Augments the Dynamics of B-Cell Receptor Signaling. JOURNAL OF PROTEOMICS 2014-05103, 241-253.
  43. Yi-Ju Chen, Cheng-Tsung Lu,Tzong-Yi Lee*, Yu-Ju Chen* DbGSH: A Database of S-Glutathionylation. BIOINFORMATICS 2014-0430(16):2386-2388, 10.1093/bioinformatics/btu301.
  44. 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. JOURNAL OF PROTEOMICS 2014-03,  2014(0):bau034. doi: 10.1093/database/bau034.
  45. Wan-Jiun Chen, Chao-Chi Ho, Yih-Leong Chang, Hsuan-Yu Chen, Chih-An Lin, Thai-Yen Ling, Sung-Liang Yu, Shin-Sheng Yuan, Yu-Ju Louisa Chen, Chien-Yu Lin, Szu-Hua Pan, Han-Yi Elizabeth Chou,Yu-Ju Chen,Gee-Chen Chang, Wen-Cheng Chu, Yee-Ming Lee, Jen-Yi Le Cancer-Associated Fibroblasts Regulate the Plasticity of Lung Cancer Stemness via Paracrine Signalling. Nature Communications 2014-035:3472, DOI: 10.1038/ncomms4472.
  46. Wen-Lung Wang, Hsiao-Chun Huang, Shih-Han Kao, Yi-Chiung Hsu, Yi-Ting Wang ,Ker- Chau Li , Yu-Ju Chen, Sung-Liang Yu, Shu-Ping Wang, Tzu-Hung Hsiao, Pan-Chyr Yang and Tse-Ming Hong* Slug is Temporally Regulated by Cyclin E in Cell Cycle and Controls Genome Stability. ONCOGENE 2014-03doi: 10.1038/onc. 2014. 58, 1–10.
  47. 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 2 Colorectal Cancer Tissues Using a Label-Free Quantitation Strategy. JOURNAL OF PROTEOME RESEARCH 2014-0313(11), 4942–4958.
  48. I-Wen Song, Wei-Ru Li, Li-Ying Chen, Li-Fen Shen, Kai-Ming Liu, Jeffrey J. Y. Yen, Yi-Ju Chen, Yu-Ju Chen, Virginia Byers Kraus, Jer-Yuarn Wu, M. T. 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 2014-039 (3),e92194.
  49. Yi-Ju Chen, Wei-Chieh Ching, Yu-Pei Linc, Yu-Ju Chen* Methods for Detection and Characterization of Protein S-nitrosylation. METHODS 2014-0262 (2), 138-150.
  50. Li Kao, Yi-Ting Wang, Yu-Chen Chen, Shun-Fu Tseng, Jia-Cin Jhang, Yu-Ju Chen*, Shu-Chun Teng Global Analysis of Cdc14 Dephosphorylation Sites Reveals Essential Regulatory Role in Mitosis and Cytokinesis. MOLECULAR & CELLULAR PROTEOMICS 2014-0213(2), 594-605.
  51. Chia-Feng Tsai, Chuan-Chih Hsu, Jo-Nan Hung, Yi-Ting Wang, Wai-Kok Choong, Ming-Yao Zeng, Pei-Yi Lin, Ruo-Wei Hong, Ting-Yi Sung, Yu-Ju Chen* Sequential Phosphoproteomic Enrichment through Complementary Metal-directed Immobilized Metal Ion Affinity Chromatography. ANALYTICAL CHEMISTRY 2014-0186 (1), pp 685–693.
  52. Su-Chien Chiang, Chia-Li Han, Kun-Hsing Yu, Yu-Ju Chen, Kun-Pin Wu* Prioritization of Cancer Marker Candidates Based on The Immunohistochemistry Staining Images Deposited in The Human Protein Atlas. PLoS One 2013-11, 8(11): e81079.
  53. Yu-Wang Chang, Ya-Ting Chang, Qinchuan Wang, Jim Jung-Ching Lin, Yu-Ju Chen, Chien-Chang Chen* Quantitative Phosphoproteomic Study of Pressure-Overloaded Mouse Heart Reveals Dynamin-Related Protein 1 as a Modulator of Cardiac Hypertrophy. MOLECULAR & CELLULAR PROTEOMICS 2013-1112(11), 3094-3107.
  54. Chen-Chun Chen, Wan-Chih Su, Bao-Yu Huang, Yu-Ju Chen, Hwan-Ching Tai*, Rofeamor Palarca Obena* Interaction Modes and Approaches to Glycopeptide and Glycoprotein Enrichment. ANALYST 2013-11139 (4), 688-704.
  55. Tsung-Che Chang, Chian-Hui Lai, Chih-Wei Chien, Chien-Fu Liang, Avijit Kumar Adak, Yung-Jen Chuang, Yu-Ju Chen, Chun-Cheng Lin* Synthesis and Evaluation of a Photoactive Probe with a Multivalent Carbohydrate for Capturing Carbohydrate−Lectin Interactions. BIOCONJUGATE CHEMISTRY 2013-1024 (11),1895-1906.
  56. Teng-Kuei Huang, Chia-Li Han, Shu-I Lin, Yu-Ju Chen, Yi-Chuan Tsai, Yet-Ran Chen, June-Wei Chen,Wei-Yi Lin, Pei-Mien Chen, Tzu-Yin Liu, Ying-Shin Chen, Ching-Mei Sun, Tzyy-Jen Chiou* Identification of Downstream Components of Ubiquitin-Conjugating Enzyme PHOSPHATE2 by Quantitative Membrane Proteomics in Arabidopsis Roots. THE PLANT CELL 2013-10, tpc.113.115998.
  57. Yi-Hsuan Wu, Chia-Wei Hu, Chih-Wei Chien, Yu-Ju Chen,Hsuan-Cheng Huang*, Hsueh-Fen Juan* Quantitative Proteomic Analysis of Human Lung Tumor Xenografts Treated with the EctopicATP Synthase Inhibitor Citreoviridin. PLoS One 2013-08, 8(8): e70642. doi:10.1371/journal.pone.0070642.
  58. Chia-Wei Hu, Chien-Wei Tseng, Chih-Wei Chien, Hsuan-Cheng Huang, Wei-Chi Ku, Shyh-Jye Lee, Yu-Ju Chen*, Hsueh-Fen Juan* Quantitative Proteomics Reveals Diverse Roles of miR-148a from Gastric Cancer Progression to Neurological Development. JOURNAL OF PROTEOME RESEARCH 2013-0712(9), pp 3993–4004.
  59. Ying-Wei Lu, Chih-Wei Chien, Po-Chiao Lin, Li-De Huang, Chang-Yang Chen, Sz-Wei Wu,Chia-Li Han, Kay-Hooi Khoo, Chun-Cheng Lin*, Yu-Ju Chen* BAD-Lectins: Boronic Acid-Decorated Lectins with Enhanced Binding Affinity for the Selective Enrichment of Glycoproteins. ANALYTICAL CHEMISTRY 2013-0785 (17), 8268–8276.
  60. Chia-Ying Cheng, Chia-Feng Tsai, Yu-Ju Chen, Ting-Yi Sung*, Wen-Lian Hsu Spectrum-based Method to Generate Good Decoy Libraries for Spectral Library Searching in Peptide Identifications. JOURNAL OF PROTEOME RESEARCH 2013-0512 (5), 2305-2310.
  61. Cheng-An Wang, Wei-Ta Chen, Ho-Shun Cheng, Cheng-Chih Chung, Yu-Ju Chen, Ming-Hsiung Hsieh* Thyroid Storm and Incidental Anterior Mediastinal Teratoma: Coincidence or Correlation?. Acta Cardiological Sinica 2013-04, 29:467470.
  62. Cheng-Chih Chung, Yu-Hsun Kao, Yu-Ju Chen, Yi-Jen Chen* Androgen Modulates Cardiac Fibrosis Contributing to Gender Differences on Heart Failure. AGING MALE 2013-0316 (1), 22-27.
  63. Po-Chiao Lin*, Ching-Ching Yu, Huan-Ting Wu,Ying-Wei Lu, Chia-Li Han, An-Kai Su, Yu-Ju Chen*, Chun-Cheng Lin* A Chemically Functionalized Magnetic Nanoplatform for Rapid and Specific Biomolecular Recognition and Separation. BIOMACROMOLECULES 2013-0114 (1), pp 160–168.
  64. Lien-Chin Chen, Mei-Ying Liu, Yung-Chin Hsiao, Wai-Kok Choong, Hsin-Yi Wu, Wen-Lian Hsu, Pao-Chi Liao*, Ting-Yi Sung*, Shih-Feng Tsai*, Jau-Song Yu*, Yu-Ju Chen* Decoding the Disease-Associated Proteins Encoded in The Human Chromosome 4. JOURNAL OF PROTEOME RESEARCH 2013-0112 (1), 33–44.
  65. 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 2013-01,  41(D1): D295-D305.
  66. Jennifer Ho*, Oscar Lee, Yun-Ju Fu, Hung-Ta Shih, Chien-Yu Tseng, Cheng-Chih Chung, Chia-Li Han, Yu-Ju Chen* An iTRAQ Proteomic Study Reveals an Association between Diet-induced Enhanced Fatty-acid Metabolism and the Development of Glucose Intolerance in Prediabetic Mice. JOURNAL OF PROTEOME RESEARCH 2013-0112 (3), pp1120-1133.
  67. Chen-Chun Chen, Wan-Chih Su, Bao-Yu Huang, Yu-Ju Chen, Hwan-Ching Tai, Rofeamor Palarca Obena Interaction Modes and Approaches to Glycopeptide and Glycoprotein Enrichment. ANALYST 2013139 (4), 688-704.
  68. 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 2012-0928, 2293-2295.
  69. Alan Chuan-Ying Lai, Chia-Feng Tsai, Chuan-Chih Hsu, Yu-Ni Sun, Yu-Ju Chen* Complementary Fe3+- and Ti4+-Immobilized Metal Ion Affinity Chromatography for Purification of Acidic and Basic Phosphopeptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY 2012-0926, 2186-2194.
  70. Chun-Mei Hu, Ming-Tyng Yeh, Chih-Wei Chen, Ning Tsao, Quan-Ze Gao, Chia-Yun Chang, Ming-Hsiang Lee, Jim-Min Fang, Sheh-Yi Sheu, Chow-Jaw Lin, Mei-Chun Tseng, Yu-Ju Chen, Zee-Fen Chang* Tumor cells require thymidylate kinase to prevent dUTP incorporation during DNA repair. CANCER CELL 2012-0722 (1) ,36-50.
  71. Ting Lo, Chia-Feng Tsai, Yu-Ru V. Shih, Yi-Ting Wang, Sheng-Chieh Lu, Ting-Yi Sung, Wen-Lian Hsu, Yu-Ju Chen*, and Oscar K. Lee Phosphoproteomic Analysis of Human Mesenchymal Stromal Cells during Osteogenic Differentiation. JOURNAL OF PROTEOME RESEARCH 2012-0210,1021.
  72. Obena Rofeamor, Lin Po-Chiao, Lu Ying-Wei, Li I-Che, del Mundo Florian, Arco Susan, Nuesca Guillermo, Lin Chun-Cheng, Chen Yu-Ju* Iron Oxide Nanomatrix Facilitates Metal Ionization in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. ANALYTICAL CHEMISTRY 2011-1183(24), 9337-9343.
  73. Tzu-Chi Chou, Wei Hsu, Ching-Ho Wang, Yu-Ju Chen*, Jim-Min Fang* Rapid and Specific Influenza Virus Detection by Functionalized Magnetic Nanoparticles and Mass Spectrometry. JOURNAL OF NANOBIOTECHNOLOGY 2011-119(52),1477-3155.
  74. Young-Eun Cho, Thoudam S.K. Singh, Hyun-Chul Lee, Pyong-Gon Moon, Jeong-Eun Lee, Myung-Hoon Lee, Eung-Chil Choi, Yu-Ju Chen, Sang-Hyun Kim, Moon-Chang Baek* In-Depth Identification of Pathways Related to Cisplatin-Induced Hepatotoxicity Through an Integrative Method Based on An Informatics-Assisted Label-Free Protein Quantitation and Microarray Gene Expression Approach. MOLECULAR & CELLULAR PROTEOMICS 2011-1010, 1074.
  75. Hsin-Fu Chen, Ching-Yu Chuang, Wen-Chih Lee, Hsiang-Po Huang, Han-Chung Wu, Hong-Nerng Ho, Yu-Ju Chen and Hung-Chih Kuo* Surface Marker Epithelial Cell Adhesion Molecule and E-Cadherin Facilitate the Identification and Selection of Induced Pluripotent Stem Cells. Stem Cell Reviews and Reports 2011-097, 722-735.
  76. Tzong-Yi Lee*, Yi-Ju Chen, Tsung-Cheng Lu, Hsien-Da Huang and Yu-Ju Chen* SNOSite: Exploiting Maximal Dependence Decomposition to Identify Cysteine S-Nitrosylation with Substrate Site Specificity. PLoS One 2011-076(7),1-11.
  77. Huan-Ting Wu, Chuan-Chih Hsu, Chia-Feng Tsai, Po-Chiao Lin, Chun-Cheng Lin*, and Yu-Ju Chen* Nanoprobe-Based Immobilized Metal Affinity Chromatography for Sensitive and Complementary Enrichment of Multiply Phosphorylated Peptides. PROTEOMICS 2011-0713,11.
  78. Pei-Yi Cheng, Yu-Ping Lin, Ya-Ling Chen, Yi-Ching Lee, Chia-Chen Tai, Yi-Ting Wang, Yu-Ju Chen, Cheng-Fu Kao*, John Yu* Interplay Between SIN3A and STAT3 Mediates Chromatin Conformational Changes and GFAP Expression During Cellular Differentiation. PLoS One 2011-076, 1-15.
  79. Putty-Reddy Sudhir, Chia-Lang Hsu, Mei-Jung Wang, Yi-Ting Wang, Yu-Ju Chen, Ting-Yi Sung, Wen-Lian Hsu, Ueng-Cheng Yang, Jeou-Yuan Chen Phosphoproteomics Identifies Oncogenic Ras Signaling Targets and Their Involvement in Lung Adenocarcinomas. PLoS One 2011-056, 1-10.
  80. Chung-Wei Fan,Chung-Chuan Chan,Kuei-Tien Chen,Jen Twu,Ya-Shu Huang,Chia-Li Han,Yu-Ju Chen,Jau-Song Yu,Yu-Sun Chang,Yung-Bin Kuo,Err-Cheng Chan* Identification of SEC61 Beta and Its Autoantibody As Biomarkers for Colorectal Cancer. CLINICA CHIMICA ACTA 2011-05412 (11-12), 887–893.
  81. Yi-Chi Ho, Mei-Chun Tseng, Ying-Wei Lu, Chun-Cheng Lin, Yu-Ju Chen*, Ming-Ren Fuh* Nanoparticle-assisted MALDI-TOF MS combined with Seed-Layer Surface Preparation for Quantification of Small Molecules. ANALYTICA CHIMICA ACTA 2011-04697, 1-7.
  82. Chia-Li Han, Jinn-Shiun Chen, Err-Cheng Chan, Chien-Peng Wu, Kun-Hsing Yu, Kuei-Tien Chen, Chih-Chiang Tsou, Chia-Feng Tsai, Chih-Wei Chien, Yung-Bin Kuo, Pei-Yi Lin, Jau-Song Yu, Chuen Hsueh, Min-Chi Chen, Chung-Chuan Chan, Yu-Sun Chang, Yu-Ju Chen* An Informatics-assisted Label-free Approach for Personalized Tissue Membrane Proteomics: Case Study on Colorectal Cancer. MOLECULAR & CELLULAR PROTEOMICS 2011-0410,1-15.
  83. Yi-Ju Chen, Wei-Chi Ku, Pei-Yi Lin, Hsiao-Chiao Chou, Kay-Hooi Khoo, and Yu-Ju Chen* S-Alkylating Labeling Strategy for Site-Specific Identification of The S-Nitrosoproteome. JOURNAL OF PROTEOME RESEARCH 2010-129, 6417–6439.
  84. Lifeng Peng, Eugene A. Kapp, David Fenyö, Min-Seok Kwon, Pu Jiang, Songfeng Wu, Ying Jiang, Marie-Isabel Aguilar, Nikhat Ahmed, Mark S. Baker, Zongwei Cai, Yu-Ju Chen, Phan Van Chi, Maxey C. M. Chung, Fuchu He, Alice C. L. Len, Pao-Chi Liao, Kazuyuki Naka The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate-washed membrane standard. PROTEOMICS 2010-1110, 4142–4148.
  85. Mei-Chun Tseng, Rofeamor Obena, Ying-Wei Lu, Po-Chiao Lin, Ping-Yu Lin, Yung-Sheng Yen, Jiann-Tsuen Lin, Li-De Huang, Kuang-Lieh Lu, Long-Li Lai, Chun-Cheng Lin, Yu-Ju Chen* Dihydrobenzoic Acid Modified Nanoparticle as a MALDI-TOF MS Matrix for Soft Ionization and Structure Determination of Small Molecules with Diverse Structures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010-1121, 1930–1939.
  86. Wang, Yi-Ting,Tsai, Chia-Feng, Hong Tzu-Chan, Tsou, Chih-Chiang, Lin, Pei-Yi, Pan, Szu-Hua, Hong, Tse-Ming, Yang, Pan-Chyr, Sung, Ting-Yi, Hsu Wen-Lian, Chen, Yu-Ju An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion. JOURNAL OF PROTEOME RESEARCH 2010-099, 5582–5597.
  87. Jinn-Shiun Chen, Kuei-Tien Chen, Chung-Wei Fan, Chia-Li Han, Yu-Ju Chen, Jao-Song Yu, Yu-Sun Chang, Chih-Wei Chien, Chien-Peng Wu, Ray-Ping Hung, Err-Cheng Chan* Comparison of Membrane Fraction Proteomic Profiles of Normal and Cancerous Human Colorectal Tissues with Gel-assisted Digestion and iTRAQ Labeling Mass Spectrometry. FEBS JOURNAL 2010-07277, 3028–3038.
  88. Shyh-Horng Chiou, Chun-Hao Huang, I-Liang Lee, Yi-Ting Wang, Nai-Yu Liu, Yeou-Guang Tsay, and Yu-Ju Chen Identification of In Vivo Phosphorylation Sites of Lens Proteins From Porcine Eye Lenses By A Gel-Free Phosphoproteomics Approach. MOLECULAR VISION 2010-0216, 294–302.
  89. Shu-Ling Lin, Chih-Wei Chien, Chia-Li Han, Eric S.-W. Chen, Shao-Hsuan Kao, Yu-Ju Chen and Fang Liao Temporal Proteomics Profiling of Lipid Rafts in CCR6-Activated T Cells Reveals the Integration of Actin Cytoskeleton Dynamics. JOURNAL OF PROTEOME RESEARCH 2010-019 (1), 283–297.
  90. Chih-Chiang Tsou, Chia-Feng Tsai, Ying-Hao Tsui, Putty-Reddy Sudhir, Yi-Ting Wang, Yu-Ju Chen, Jeou-Yuan Chen, Ting-Yi Sung, and Wen-Lian Hsu IDEAL-Q, an Automated Tool for Label-free Quantitation Analysis Using an Efficient Peptide Alignment Approach and Spectral Data Validation. MOLECULAR & CELLULAR PROTEOMICS 2010-019, 131 - 144..
  91. Po-Chiao Lin, Shu-Hua Chen, Kai-Yi Wang, Mu-Lin Chen, Avijit Kumar Adak, Jih-Ru R. Hwu, Yu-Ju Chen,*| and Chun-Cheng Lin* Fabrication of Oriented Antibody-Conjugated Magnetic Nanoprobes and Their Immunoaffinity Application. ANALYTICAL CHEMISTRY 2009-1081 (21), 8774–8782.
  92. Ta-Wei Liu, Ching-Wen Ho, Hsing-Hung Huang, Sue-Ming Chang, Shide S. Popat, Yi-Ting Wang, Ming-Shiang Wu, Yu-Ju Chen*, and Chun-Hung Lin Role for L-Fucosidase in the Contro; of Helicobacter pylori-infected Gastric Cancer Cells. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2009-08106, 14581-14586.
  93. 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,* and 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 2009-0637(2), 661-669.
  94. Wei-Chi Ku, Sung-Kay Chiu, Yi-Ju Chen, Hsin-Hung Huang, Wen-Guey Wu, and 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 20098, 2034-2050.
  95. Chia-Li Han, Chih-Wei Chien, Wen-Cheng Chen, Yet-Ran Chen, Chien-Peng Wu, Hung Li, and Yu-Ju Chen* A Multiplexed Quantitative Strategy for Membrane Proteomics: Opportunities for Mining Therapeutic Targets for Autosomal-Dominant Polycystic Kidney Disease. MOLECULAR & CELLULAR PROTEOMICS 20087, 1983–1997.
  96. Chia-Feng Tsai, Yi-Ting Wang, Yet-Ran Chen, Chen-Yu Lai, Pei-Yi Lin, Kuan-Ting Pan, Jeou-Yuan Chen, Kay-Hooi Khoo, and Yu-Ju Chen* Immobilized Metal Affinity Chromatography Revisited: pH/acid Control toward High Selectivity in Phosphoproteomics. JOURNAL OF PROTEOME RESEARCH 20087, 4058-4069.
  97. Yen-Ta Lu, Chia-Li Han, Chien-Liang Wu, Tien-Min Yu, Chih-Wei Chien, Ching-Lung Liu and Yu-Ju Chen* Proteomic Profiles of Bronchoalveolar Lavage Fluid from Patients with Ventilator- associated Pneumonia by Gel-assisted Digestion and 2DLC/MS/MS. PROTEOMICS 20082, 1208-1212.
  98. Kai-Yi Wang, Szu-An Chuang, Po-Chiao Lin, Li-Shing Huang, Shu-Hua Chen, Saib Ouarda, Wen-Harn Pan, Ping-Ying Lee, Chun-Cheng Lin*, and Yu-Ju Chen* Multiplexed Immunoassay: Quantitation and Profiling of Serum Biomarkers Using Magnetic Nanoprobes and MALDI-TOF MS. ANALYTICAL CHEMISTRY 200880, 6159-6167.
  99. Yuh-Yih Chien, Mi-Dan Jan, Avijit Kumar Adak, Hsiao-Chien Tzeng, Yen-Ping Lin, Yu-Ju Chen, Ken-Tseng Wang, Chien-Tien Chen, Chia-Chun Chen*, and Chun-Cheng Lin* Globotriose-Functionalized Gold Nanoparticles as Multivalent Probes for Shiga-like Toxin. CHEMBIOCHEM 20089, 1100-1109.
  100. Yi-Ju Chen, Wei-Chi Ku, Li-Ting Feng, Ming-Li Tsai, Chung-Hung Hsieh, Wen-Hwei Hsu, Wen-Feng Liaw, Chen-Hsiung Hung*, and 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 2008130,10929-10938.
  101. Shu-Hua Chen, Hsin-Kai Liao, Chih-Yang Chang, Chiun-Gung Juo, Jenn-Han Chen, Sunney I. Chan, and Yu-Ju Chen* Targeted Protein Quantitation and Profiling Using PVDF Affinity Probe and MALDI-TOF MS. PROTEOMICS 20077, 3038–3050.
  102. Po-Chiao Lin, Mei-Chun Tseng, An-Kai Su, Chun-Cheng Lin* and Yu-Ju Chen* Functionalized Magnetic Nanoparticles for Small Molecule Isolation, Identification and Quantification. ANALYTICAL CHEMISTRY 200779, 3401-3408.
  103. Tai-Chia Chiu, Li-Shing Huang, Po-Chiao Lin, Yu-Chie Chen*, Yu-Ju Chen*, Chun-Cheng Lin, and Huan-Tsung Chang* Nanomaterial Based Affinity Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Biomolecules and Pathogenic Bacteria. Recent Patents on Nanotechnology 20071, 99-111.
  104. De-Chuan Chan*, Cheng-Jueng Chen, Heng-Cheng Chu, Wei-Kuo Chang, Jyh-Cherng Yu, Yu-Ju Chen, Li-Li Wen, Su-Ching Huang, Chih-Hung Ku, Yao-Chi Liu and Jenn-Han Chen* Evaluation of Serum Amyloid A as a Biomarker for Gastric Cancer. ANNALS OF SURGICAL ONCOLOGY 200714, 84-93.
  105. Hung-Yi Kao, Yi-Ning Su, Hsin-Kai Liao, Ming S. Liu, and Yu-Ju Chen* Determination of SMN1/SMN2 Gene Dosage by a Quantitative Genotyping Platform Combining Capillary Electrophoresis and MALDI-TOF Mass Spectrometry. CLINICAL CHEMISTRY 200652, 361-369.
  106. Po-Chiao Lin, Shau-Hua Ueng, Mei-Chun Tseng, Jia-Ling Ko, Kuo-Ting Huang, Sheng- Chieh Yu, Avijit Kumar Adak, Yu-Ju Chen, and Chun-Cheng Lin* Site-specific Protein Modification through Cu-I-catalyzed 1,2,3-Triazole Formation and Its Implementation in Protein Microarray Fabrication. Angewandte Chemie (International Edition in English) 200645(26), 4286-4290.
  107. Po-Chiao Lin, Po-Hung Chou, Shu-Hua Chen, Hsin Kai Liao, Kai-Yi Wang, Yu-Ju Chen*, and Chun-Cheng Lin* Ethylene Glycol-Protected Magnetic Nanoparticles for Multiplexed Immunoassay in Human Plasma. SMALL 20062(4), 485-489.
  108. Chih-Yang Chang, Hsin-Kai Liao, Chiun-Gung Juo, Shu-Hua Chen, and Yu-Ju Chen* Improved Analysis of Membrane Protein by PVDF-Aided, Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. ANALYTICA CHIMICA ACTA 2006556,237-246.
  109. Yet-Ran Chen, Hsueh-Fen Juan, Hsuan-Cheng Huang , Hsin-Hung Huang, Ya-Jung Lee, Mei-Yueh Liao, Chien-Wei Tseng, Li-Ling Lin, Jeou-Yuan Chen, Mei-Jung Wang, Jenn-Han Chen,and Yu-Ju Chen* Quantitative Proteomic and Genomic Profiling Reveals Metastasis-Related Protein Expression Patterns in Gastric Cancer Cells. JOURNAL OF PROTEOME RESEARCH 20065(10), 2727-2742.
  110. Chiung-Cheng Huang, Ying-Chih Lin, Ping-Yu Lin, Yu-Ju Chen Star-shaped Molecules Containing Polyalkynyl Groups with Metal Moieties on Benzene and Triphenylene Cores. EUROPEAN JOURNAL OF ORGANIC CHEMISTRY 200619, 4510-4518.
  111. Wen-Ting Lin, Wei-Neng Hung, Yi-Hwa Yian, Kun-Pin Wu*, Chia-Li Han, Yet-Ran Chen, Yu-Ju Chen, Ting-Yi Sung* and Wen-Lian Hsu Multi-Q: A Fully Automated Tool for Multiplexed Protein Quantitation. JOURNAL OF PROTEOME RESEARCH 20065(9), 2328-2338.
  112. Yuan-Chen Chang, Hsiao-Hui Lee, Yu-Ju Chen, Gary M. Bokoch, and Zee-Fen Chang* Contribution of Guanine Exchange Factor H1 in Phorbol Ester-induced Apoptosis. CELL DEATH AND DIFFERENTIATION 200613, 2023-2032.
  113. Yu-Wang Chang, Shu-Hua Chen, Yu-Ju Chen Application of Mass Spectrometry in Clinical Proteomics. Formosan Journal of Medicine 20059, 637-649.
  114. Lee-Chiang Lo*, Ying-Ling Chiang, Chi-Hsien Kuo, Hsin-Kai Liao, Yu-Ju Chen, and Jing-Jer Lin* Study of the Preferred Modification Sites of the Quinone Methide Intermediate Resulting from the Latent Trapping Device of the Activity Probes for Hydrolases. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2005326, 30-35.
  115. Hsin-Yuan Cheng, Yu-Yu Lin, Chun-Ying Yu, Jen-Yau Chen, Kuo-Fang Shen, Wei-Ling Lin, Hsin-Kai Liao, Yu-Ju Chen, Chen-Hsuan Liu, Victor Fei Pang and Tzuu-Shuh Jou* Molecular Identification of Canine Podocalyxin-like Protein 1 as a Renal Tubulogenic Regulator. JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY 200516, 1612-1622.
  116. Hsin-Kai Liao, Yi-Ning Su, Hung-Yi Kao, Chia-Cheng Hung, Hsueh-Ting Wang and Yu-Ju Chen* Parallel Minisequencing Followed by Multiplex Matrix-assisted Laser Desorption/ Ionization Mass Spectrometry Assay for Beta-thalassemia Mutations. JOURNAL OF HUMAN GENETICS 200550, 139-150.
  117. Fang-Yuan Lee, Jiann-Jyh Huang, Yu-Ju Chen, Kuan-Jiuh Lin, Gene-Hsiang Lee, Shie-Ming Peng, Jih-Ru Hwu, and Kuang-Lieh Lu* Os(CO)2(η2-SC5H4N(O))(η2-SCSH4N): Structural Evidence for the Transformation of Pyridine-2-thione N-Oxide to Pyridine-2-thiolate in Osmium Complexes. JOURNAL OF ORGANOMETALLIC CHEMISTRY 2005690, 441-449.
  118. Hsin-Hung Huang, Hsin-Kai Liao, Tzann-Shun Hwang, Yi-Han Lin, Chun-Hung Lin and Yu-Ju Chen* Structural Characterization of Sialic Acid Synthase by Electrospray Mass Spectrometry- a Tetrameric Enzyme Composed of Dimeric Dimers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 200516, 324-332.
  119. Yu-Ju Chen*, Shu-Hua Chen, Yuh-Yih Chien, Yu-Wan Chang, Hsin-Kai Liao, Chih-Yang Chang, Mi-Dan Jan, Ken-Tseng Wang, and Chun-Cheng Lin* Carbohydrate-Encapsulated Gold Nanoparticles for Rapid Target Protein Identification and Binding Epitope Mapping. CHEMBIOCHEM 20056, 1169-1173.
  120. Po-Hung Chou, Shu-Hua Chen, Hsin-Kai Liao, Po-Chiao Lin, Gour-Rong Her, Alan Chuan-Ying Lai, Jenn-Han Chen, Chun-Cheng Lin*, and Yu-Ju Chen* Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human Plasma. ANALYTICAL CHEMISTRY 200577, 5990-5997.
  121. Tung-Kung Wu*, Chiao-Yin Huang, Cheng-Yu Ko, Cheng-Hsiang Chang, Yu-Ju Chen, and Hsin-Kai Liao Purification, Tandem Mass Characterization, and Inhibition Studies of Oxidosqualene- lanosterol Cyclase Enzyme from Bovine Liver. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS 2004421, 42-53.
  122. Po-Jui Chen, Hsueh-Ting Wang, Chien-Chung Cheng, and Yu-Ju Chen* Specific Recognition of DNA Bulge Structure by Matrix-assisted Laser Desorption/ Ionization Time-of-flight Mass Spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY 200418, 609-616.
  123. Hsueh-Fen Juan, Jenn-Han Chen*, Wei-Tse Hsu, Su-Ching Huang, Shui-Tein Chen, John Yi-Chung Lin, Yu-Wang Chang, Chih-Yin Chiang, Li-Li Wen, De-Chuan Chan, Yao-Chi Liu, Yu-Ju Chen* Identification of Tumor-associated Plasma Biomarkers Using Proteomic Techniques: From Mouse to Human. PROTEOMICS 20044, 2766-2775.
  124. Chen-Hsiung Hung*, Cheng-Yu Lin, Ping-Yu Lin, and Yu-Ju Chen Synthesis and Crystal Structure of Core-Modified Benziporphyrin: Thia-ρ- Benziporphyrin. TETRAHEDRON LETTERS 2004 45, 129-132.
  125. ei-Chun Kao, Yat-Ren Chen, Eugene C. Yi, Hookeun Lee, Qiang Tian, Keh-Ming Wu, Shih-Feng Tsai, Steve S. -F. Yu, Yu-Ju Chen, Ruedi Aebersold, and Sunney I. Chan* Quantitative Proteomic Analysis of Metabolic Regulation by Copper Ions in Methylococcus Capsulatus (Bath). JOURNAL OF BIOLOGICAL CHEMISTRY 2004279, 51554-51560.
  126. Jenn-Han Chen*, Yu-Wang Chang, Chen-Wen Yao, Tzong-Shi Chiueh, Su-Chin Huang, Ko-Yi Chien, An Chen, Feng-Yee Chang, Chi-Huey Wong, and Yu-Ju Chen* Plasma proteome of Severe Acute Respiratory Syndrome (SARS) analyzed by two-dimensional gel electrophoresis and mass spectrometry.. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2004101, 17039-17044.
  127. Hsiao-Hui Lee, Chung-Liang Chien, Hsin-Kai Liao, Yu-Ju Chen and Zee-Fen Cheng* Nuclear Efflux of Heterogeneous Nuclear Ribonucleoprotein C1/C2 in Apoptotic Cells: A Novel Nuclear Export Dependent on Rho-Associated Kinase Activation. JOURNAL OF CELL SCIENCE 2004117, 5579-5589.
  128. Chien-Tai Ren, Chien-Sheng Chen, Yi-Ping Yu, Yow-Fu Tsai, Ping-Yu Lin, Yu-Ju Chen, Wei Zou, and Shih-Hsiung Wu* Synthesis of α-(2→5) Neu5Gc Oligomers. CHEMISTRY- A EUROPEAN JOURNAL 2003 9, 1085-1095.
  129. Yu-Ju Chen*, Hsin-Kai Liao Mass Spectrometry – Based Proteomics. CHEMISTRY 200361,235-247.
  130. Steve S.-F Yu, Kelvin H.-C. Chen , Mandy Y.-H., Yane-Shih Wang, Chiu-Feng Tseng, Yu-Ju Chen, Ded-Shih Huang*, Sunney I. Chan* Production of High-Quality Particulate Methane Monooxygenase in High Yields from methylococcus capsulatus (bath) with a Hollow-Fiber Membrane Bioreactor. JOURNAL OF BACTERIOLOGY 2003, 185(5915-24).
  131. Wei-Chun Huang-Fu, Kuo-Chan Hung, Po-Jui Chen, Wen-Jwu Wang, and Yu-Ju Chen* Mechanistic aspect of Co(HAPP)(TFA)2 in DNA bulge-specific recognition.. NUCLEIC ACIDS RESEARCH 200331, 2227-2233.
  132. Yu-Ju Chen, P. T. Fenn, Kai-Chung Lau, C. Y. Ng*, Chi-Kin Law, and Wai-Kee Li* Study of the Dissociation of CH3SCH3+ by Collisional Activation: Evidence of Nonstatistical Behavior. JOURNAL OF PHYSICAL CHEMISTRY A 2002106, 9729-9736.
  133. Tzann-Shun Hwang, Chih-Hung Hung, Chin-Fen Teo, Guan-Ting Chen, Lee-Shang Chang, Sung-Fang Chen, Yu-Ju Chen*, Chun-Hung Lin* Structural Characterization of Escherichia Coli Sialic Acid Synthase. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2002295, 167-173.
  134. Yu-Ju Chen, P. T. Fenn, and C. Y. Ng* Direct Identification of Product CH2SH+/CH3S+ Structures in the Dissociation of CH3CH2SH+ and CH3SCH3+ via Collisional Activation. CHEMICAL PHYSICS LETTERS 2001336, 105-108.
  135. Shih-Hao Chen, Li-Kung Chu, Yu-Ju Chen, I-Chia Chen and Yuan-Pern Lee* Detection of ClCO with Time-resolved Fourier-transform Infrared Absorption Spectroscopy. CHEMICAL PHYSICS LETTERS 2001333, 365-370.
  136. Yu-Ju Chen, Shiaw-Ruey Lin, and Yuan-Pern Lee* Observation of CH4 (v(2)=1 or v(4)=1) in the Reaction Cl + CH4 by Time-resolved Fourier-transform Absorption Spectroscopy. JOURNAL OF CHEMICAL PHYSICS 2001115, 6513-6521.
  137. T. Rajendran, Bala Manimaran, Fang-Yuan Lee, Po-Jui Chen, Su-Ching Lin, Gene-Hsiang Lee, Shie-Ming Peng, Yu-Ju Chen*, and Kuang-Lieh Lu* Self-assembly of Tetrametallic Square [Re-4(CO)(12)Br-4(mu-pz)(4)] (pz = pyrazine) from [Re(CO)(4)Br(pz)]. A Mechanistic Approach. J. Chem. Soc., Dalton Transactions 200122, 3346 -3351.
  138. S. Stimson, Yu.-Ju Chen, M. Evans, C.-W. Hsu, P. Heimann, C.-L. Liao, and C. Y. Ng* Rotational-Resolved Pulsed Field Ionization Photoelectron Bands of H-2(+)(X-2 Sigma(+)(g), v(+) = 0, 2, 9, and 11) Using Multibunch Synchrotron Radiation . CHEMICAL PHYSICS LETTERS 1998289, 507-515.
  139. P. T. Fenn, Yu-Ju Chen, S. Stimson, C. Y. Ng, Wai- Kee Li and N.L. Ma A study of Dissociation of CH3CH2SH+ by Collisional Activation: Evidence of Non-Statistical Behavior. JOURNAL OF CHEMICAL PHYSICS 1998108, 8020-8028.
  140. P. T. Fenn, Yu-Ju Chen, S. Stimson, and C. Y. Ng* Dissociation of CH3SH+ by Collisional Activation: Evidence of Non-Statistical Behavior. JOURNAL OF PHYSICAL CHEMISTRY A 1997101, 6513-6522.
  141. Yu-Ju Chen, P. T. Fenn, and C. Y. Ng* Bond Selective Dissociation of CH3SH+ and C2H5SH+ via Collisional Activation. JOURNAL OF CHEMICAL PHYSICS 1997106, 8274-8277.
  142. Yu-Ju Chen, C. L. Liao, and C. Y. Ng* A Molecular Beam Photoionization Mass Spectrometric Studies of Cr(CO)6, Mo(CO)6, and W(CO)6. JOURNAL OF CHEMICAL PHYSICS 1997107, 4527-4536.
  143. C.-W. Hsu, K. T. Lu, M. Evans, Yu-Ju Chen, C. Y. Ng*, and P. Heimann A High Resolution Photoionization Study of Ne and Ar: Observation of Mass Analyzed Threshold Ions Using Synchrotron Radiation and Direct Current Electric Fields. JOURNAL OF CHEMICAL PHYSICS 1996105, 3950-3961.
  144. Y.-S. Cheung, Yu-Ju Chen, C. Y. Ng*, See-Wing Chiu, and Wai- Kee Li Combining Theory with Experiment: Assessment of the Thermochemistry of SFn, SFn+, and SFn-. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1995117,9725-9733.
  1. 何國榮、陳玉如、廖寶琪、王亦生、陳逸然、曾美郡、黃友利、賴建成、彭文平、何彥鵬、許邦弘、李福安、陳朝榮、林俊利、陳頌方、李茂榮、謝建台、卓群恭、丁望賢、王家麟、游鎮烽、陳皓君、王勝盟、蔡東湖、陳月枝、卓怡孜, 2015, 質譜分析技術-原理與應用, 512 pages, 新北市: 全華圖書.
Chapter of Publication
  1. Li-Shing Huang, Yuh-Yih Chien, Shu-Hua Chen, Po-Chiao Lin, Kai-Yi Wang, Po-Hung Chou, Chun-Cheng Lin, Yu-Ju Chen, 2007, “Nanoprobe-Based Affinity Mass Spectrometry for Cancer Marker Protein Profiling”, editor(s): Challa S. S. R. Kumar, Nanomaterials for Cancer Diagnosis., pp. 338-376, U.S.A: Wiley-VCH.