| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 2010 | IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation | Tsou, Chih-Chiang; Tsai, Chia-Feng; Tsui, Ying-Hao; Sudhir, Putty-Reddy; Wang, Yi-Ting; Chen, Yu-Ju ; Chen, Jeou-Yuan ; Sung, Ting-Yi ; Hsu, Wen-Lian | Molecular and Cellular Proteomics 9(1), 131-144 | | | |
| 2020 | Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations | Itang, Corazon Ericka Mae M.; Gaza, Jokent T.; Masacupan, Dan Jethro M.; Batoctoy, Dessa Camille R.; Chen, Yu-Ju ; Nellas, Ricky B.; Yu, Eizadora T. | Marine Drugs 18(10), 503 | | | |
| 2010 | Identification of in vivo phosphorylation sites of lens proteins from porcine eye lenses by a gel-free phosphoproteomics approach | Chiou, SH ; Huang, CH; Lee, IL; Wang, YT; Liu, NY; Tsay, YG; Chen, YJ | MOLECULAR VISION 16, 294-302 | | | |
| 2017 | Identification of Potential Plasma Biomarkers for Nonalcoholic Fatty Liver Disease by Integrating Transcriptomics and Proteomics in Laying Hens | Meng-Tsz Tsai; Yu-Jen Chen; Ching-Yi Chen; Mong-Hsun Tsai; Chia-Li Han; Yu-Ju Chen ; Harry J Mersmann; Shih-Torng Ding | The Journal of Nutrition 147(3), 293-303 | | | |
| 2011 | Identification of SEC61 Beta and Its Autoantibody As Biomarkers for Colorectal Cancer | Fan, Chung-Wei; Chan, Chung-Chuan; Chen, Kuei-Tien; Twu, Jen; Huang, Ya-Shu; Han, Chia-Li; Chen, Yu-Ju ; Yu, Jau-Song; Chang, Yu-Sun; Kuo, Yung-Bin; Chan, Err-Cheng | CLINICA CHIMICA ACTA 412 (11-12), 887–893 | | | |
| 2004 | Identification of Tumor-associated Plasma Biomarkers Using Proteomic Techniques: From Mouse to Human | Juan, Hsueh-Fen; Chen, Jenn-Han; Hsu, Wei-Tse; Huang, Su-Ching; Chen, Shui-Tein; Lin, John Yi-Chung; Chang, Yu-Wang; Chiang, Chih-Yin; Wen, Li-Li; Chan, De-Chuan; Liu, Yao-Chi; Chen, Yu-Ju | PROTEOMICS 4, 2766-2775 | | | |
| 2008 | Immobilized Metal Affinity Chromatography Revisited: pH/acid Control toward High Selectivity in Phosphoproteomics | Tsai, Chia-Feng; Wang, Yi-Ting; Chen, Yet-Ran; Lai, Chen-Yu; Lin, Pei-Yi; Pan, Kuan-Ting; Chen, Jeou-Yuan ; Khoo, Kay-Hooi ; Chen, Yu-Ju | JOURNAL OF PROTEOME RESEARCH 7(9), 4058-4069 | | | |
| 2006 | Improved Analysis of Membrane Protein by PVDF-Aided, Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry | Chang, Chih-Yang; Liao, Hsin-Kai; Juo, Chiun-Gung; Chen, Shu-Hua; Chen, Yu-Ju | ANALYTICA CHIMICA ACTA 556,237-246 | | | |
| 2011 | 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 | Cho, Young-Eun; Singh, Thoudam S. K.; Lee, Hyun-Chul; Moon, Pyong-Gon; Lee, Jeong-Eun; Lee, Myung-Hoon; Choi, Eung-Chil; Chen, Yu-Ju ; Kim, Sang-Hyun; Baek, Moon-Chang | MOLECULAR & CELLULAR PROTEOMICS 10, 1074 | | | |
| 2014 | Incorporating Amino Acids Composition and Functional Domains for Identifying Bacterial Toxin Proteins | Min-Gang Su; Chien-Hsun Huang; Tzong-Yi Lee; Yu-Ju Chen ; Hsin-Yi Wu | BioMed Research International 2014, 972692 | | | |
| 2018 | Inducing hair follicle neogenesis with secreted proteins enriched in embryonic skin | Fan, Sabrina Mai-Yi; Tsai, Chia-Feng; Yen, Chien-Mei; Lin, Miao-Hsia; Wang, Wei-Hung; Chan, Chih-Chieh; Chen, Chih-Lung; Phua, Kyle K.L.; Pan, Szu-Hua; Plikus, Maksim V.; Yu, Sung-Liang; Chen, Yu-Ju ; Lin, Sung-Jan | Biomaterials 167, 121-131 | | | |
| 2015 | Informatics View on the Challenges of Identifying Missing Proteins From Shotgun Proteomics | Wai-Kok Choong; Hui-Yin Chang; Ching-Tai Chen; Chia-Feng Tsai; Wen-Lian Hsu ; Ting-Yi Sung ; Yu-Ju Chen | Journal of Proteome Research 14(12), 5396-5407 | | | |
| 2015 | Integrating proteomics with electrochemistry for identifying kinase biomarkers | 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 | Chemical Science 6, 4756-4766 | | | |
| 2021 | Integrating site-specific peptide reporters and targeted mass spectrometry enables rapid substrate-specific kinase assay at the nanogram cell level | Reyes Aaron James F.; Kitata Reta Birhanu; dela Rosa Mira Anne C.; Wang Yi-Ting; Lin Pei-Yi; Yang Pan-Chyr; Friedler Assaf; Yitzchaik Shlomo; Chen Yu-Ju | Analytica Chimica Acta 1155, 338341 | | | |
| 2013 | Interaction Modes and Approaches to Glycopeptide and Glycoprotein Enrichment | Chen-Chun Chen; Wan-Chih Su; Bao-Yu Huang; Yu-Ju Chen ; Hwan-Ching Tai; Rofeamor Palarca Obena | ANALYST 139 (4), 688-704 | | | |
| 2011 | Interplay between SIN3A and STAT3 mediates chromatin conformational changes and GFAP expression during cellular differentiation. | Cheng, PY; Lin, YP; Chen, YL; Lee, YC; Tai, CC; Wang, YT; Chen, YJ ; Kao, CF ; Yu, J | PloS one 6(7), e22018 | | | |
| 2011 | Iron Oxide Nanomatrix Facilitates Metal Ionization in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry | Obena, Rofeamor; Lin, Po-Chiao; Lu, Ying-Wei; Li, I-Che; del Mundo, Florian; Arco, Susan; Nuesca, Guillermo; Lin, Chun-Cheng; Chen, Yu-Ju | ANALYTICAL CHEMISTRY 83(24), 9337-9343 | | | |
| 2017 | iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm | Hui-Yin Chang; Ching-Tai Chen; Chu-Ling Ko; Yi-Ju Chen; Yu-Ju Chen ; Wen-Lian Hsu ; Chiun-Gung Juo; Ting-Yi Sung | Analytical Chemistry 89(24), 13128-13136 | | | |
| 2015 | Large-Scale Determination of Absolute Phosphorylation Stoichiometries in Human Cells by Motif-Targeting Quantitative Proteomics | 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; Chen, Yu-Ju | NATURE COMMUNICATIONS 6, 6622 | | | |
| 2018 | Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function | Paik, Young-Ki; Lane, Lydie; Kawamura, Takeshi; Chen, Yu-Ju ; Cho, Je-Yoel; LaBaer, Joshua; Yoo, Jong Shin; Domont, Gilberto; Corrales, Fernando; Omenn, Gilbert S.; Archakov, Alexander; Encarnación-Guevara, Sergio; Lui, Siqi; Salekdeh, Ghasem Hosseini; Cho, Jin-Young; Kim, Chae-Yeon; Overall, Christopher M. | Journal of Proteome Research 17(12), 4042-4050 | | | |
