Chen, Yu-Ju

Proteomics and Mass Spectrometry

Chen, Yu-Ju (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. 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,.
  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. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  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. 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.
  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 Fang* 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. 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.
  18. 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).
  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, Fernando Corrales, Victor Segura, José Ignacio Casal, Alberto Pascual-Montano, Juan Albar, Manuel Fuentes, Maria Gonzalez-Gonzalez, Paula Diez, Nieves Ibarrola, Rosa Degano, Yassene Mohammed, Christoph Borchers, Andrea Urbani, Alessio Soggiu, Tadashi Yamamoto, Alexander Archakov, Elena Ponomarenko, Andrey Lisitsa, Cheryl Lichti, Ekaterina Mostovenko, Roger Kroes, Melinda Rezeli, Akos Vegvari, Thomas Fehniger, Rainer Bischoff, Juan Antonio Vizcaíno, Eric Deutsch, Lydie Lane, Carol Nilsson, György Marko-Varga, Gilbert Omenn, Seul-Ki Jeong, Jin-Young Cho, Young-Ki Paik, William Hancock  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. 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.
  28. 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, Fernando Corrales, Victor Segura, José Ignacio Casal, Alberto Pascual-Montano, Juan Albar, Manuel Fuentes, Maria Gonzalez-Gonzalez, Paula Diez, Nieves Ibarrola, Rosa Degano, Yassene Mohammed, Christoph Borchers, Andrea Urbani, Alessio Soggiu, Tadashi Yamamoto, Alexander Archakov, Elena Ponomarenko, Andrey Lisitsa, Cheryl Lichti, Ekaterina Mostovenko, Roger Kroes, Melinda Rezeli, Akos Vegvari, Thomas Fehniger, Rainer Bischoff, Juan Antonio Vizcaíno, Eric Deutsch, Lydie Lane, Carol Nilsson, György Marko-Varga, Gilbert Omenn, Seul-Ki Jeong, Jin-Young Cho, Young-Ki Paik, William Hancock Quest for Missing Proteins: Update 2015 on Chromosome-Centric 2 Human Proteome Project. JOURNAL OF PROTEOME RESEARCH 2015-0714(9), 3415-31.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  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/gku1176.
  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. 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.
  39. 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.
  40. 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.
  41. 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.
  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. 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 Lee, Pei-Jung Lee, Ker-Chau Li, Huei-Wen Chen*, Pan-Chyr Yang* Cancer-Associated Fibroblasts Regulate the Plasticity of Lung Cancer Stemness via Paracrine Signalling. Nature Communications 2014-035:3472, DOI: 10.1038/ncomms4472.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  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. 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.
  53. 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.
  54. 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.
  55. 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.
  56. 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.
  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. 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.
  59. 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.
  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. 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.
  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. 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.
  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. 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.
  69. 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.
  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. 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.
  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. 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.
  79. 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.
  80. 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.
  81. 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.
  82. 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.
  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. 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.
  85. 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 Nakamura, Sai Ming Ngai, Young-Ki Paik, Tai-Long Pan, Terence C. W. Poon, Ghasem Hosseini Salekdeh, Richard J. Simpson, Ravi Sirdeshmukh, Chantragan Srisomsap, Jisnuson Svasti, Yu-Chang Tyan, Florian S. Dreyer, Danyl McLauchlan, Pisana Rawson, T. William Jordan* The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate-washed membrane standard. PROTEOMICS 2010-1110, 4142–4148.
  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. 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..
  90. 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.
  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. 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.
  97. 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.
  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. 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.
  100. 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.
  101. 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.
  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. 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.
  105. 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.
  106. 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.
  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. 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.
  110. 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.
  111. 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.
  112. 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.
  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. 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.
  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. 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.
  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-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.
  119. 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.
  120. 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.
  121. 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.
  122. 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.
  123. 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.
  124. 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.
  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. 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.
  127. 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.
  128. Yu-Ju Chen*, Hsin-Kai Liao Mass Spectrometry – Based Proteomics. CHEMISTRY 200361,235-247.
  129. 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.
  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. 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.
  132. 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.
  133. 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.
  134. 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.
  135. 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.
  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.
  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.