研究領域：

• 開發新式生物資訊輔助質譜學技術，研究膜蛋白體、磷酸化蛋白質體及亞硝基化蛋白質體在疾病所扮演角色。
  
• 發展功能化奈米粒子結合質譜技術，應用於疾病標記蛋白質定量、轉譯後修飾分析及藥物－ 蛋白質作用之研究。

代表作：

1. Ku, W.-C. ; Chiu, S.-K.; Chen, Yi-J.; Huang, H.-H.; Wu, W.-G.; Chen, Y.-J. Complementary quantitative proteomics reveals that transcription factor AP-4 mediates E-box-dependent complex formation for transcriptional repression of HDM2. Mol. Cell. Proteomics 2009 8, 2034.

2. 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 2009, in press.

3. 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, in press.

4. Tsai, C.-F.; Wang Y.-T.; Chen, Y.-R.; Lai, C.-Y.; Lin, P.-Y.; Pan, K.-T.; Chen, J.-Y.; Khoo, K.-H.; Chen, Y.-J. Immobilized Metal Affinity Chromatography Revisited: pH/acid Control toward High Selectivity in Phosphoproteomics. J. Proteome Res. 2008, 7, 4058.

5. 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)

6. 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.

7. Wang, K.-Y.; Chuang, S.-A.; Lin, P.-C.; Huang, L.-S.; Chen, S.-H.; Saib Ouarda; Pan, W.-H.; Lee, P.-Y.; Lin, C.-C.; Chen, Y.-J. A Rapid Multiplexed Immunoassay: Quantitation and Profiling of Serum Biomarkers using Magnetic Nanoprobes and MALDI-TOF MS. Anal. Chem. 2008, 80, 6159.

8. Lu, Y.-T.; Han, C.-L.; Wu, C.-L.; Yu, T.-M.; Chien, C.-W.; Liu, C.-L.; Chen, Y.-J. Proteomic Profiles of Bronchoalveolar Lavage Fluid from Patients with Ventilator-associated Pneumonia by Gel-assisted Digestion and 2DLC/MS/MS. Proteomics 2008, 2, 1208.

9. Lin, P.-C.; Tseng, M.-C.; Su, A.-K.; Chen, Y.-J.; Lin, C.-C. Functionalized Magnetic Nanoparticles for Small Molecule Isolation, Identification and Quantification. Anal. Chem. 2007, 79, 3401.

10. Chen, S.-H.; Liao, H.-K.; Chang, C.-Y.; Juo, C.-G.; Chen, J.-H.; Chan, S.-l.; Chen, Y.-J. Targeted Protein Quantitation and Profiling Using PVDF Affinity Probe and MALDI-TOF MS. Proteomics 2007, 7, 3038. (Cover story)

11. Chen, Y.-R.; Juan, H.-F.; Huang, H.-C.; Huang, H.-H.; Lee, Y.-J.; Liao, M.-Y.; Tseng, C.-W.; Lin, L.-L.; Chen, J.-Y.; Wang, M.-J.; Chen, J.-H.; Chen, Y.-J. Quantitative Proteomic and Genomic Profiling Reveals Metastasis-Related Protein Expression Patterns in Gastric Cancer Cells. J. Proteome Res. 2006, 5, 2727.

12. Lina, W.-T.; Hung, W.-N.; Yian, Y.-H.; Wua, K.-P.; Han, C.-L.; Chen, Y.-R.; Chen, Y.-J.; Sung, T.-Y.; Hsu, W.-L. Multi-Q: A Fully Automated Tool for Multiplexed Protein Quantitation. J. Proteome Res. 2006, 5, 2328.

13. Chou, P.-H.; Chen, S.-H.; Liao, H.-K.; Lin, P.-C.; Her, G. R.; Lai, A. C.-Y.; Lin, C.-C.; Chen, Y.-J. Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human Plasma. Anal. Chem. 2005, 77, 5990.

14. Chen, Y.-J.; Chen, S.-H.; Chien, Y.-Y.; Chang, Y.-W.; Liao, H.-K.; Chang, C.-Y.; Jan, M.-D.; Wang, K.-T.; Lin, C.-C. Carbohydrate-Encapsulated Gold Nanoparticle for Rapid Target Protein Identification and Binding Epitope Mapping. ChemBioChem, 2005, 6, 1169.

15. Chen, J.-H.; Chang, Y.-W.; Yao, C.-W.; Chiueh, T.-S.; Huang, S.-C.; Chien, K.-Y.; Chen, An; Chang, F.-Y.; Wong, C.-H.; Chen,Y.-J. Plasma Proteome of Severe Acute Respiratory Syndrome (SARS) Analyzed by Two-dimensional Gel Electrophoresis and Mass Spectrometry. Proc. Natl. Acad. Sci. USA 2004, 101, 17039.

Update： 2010-03-18