Year Graduated: 2014

Student's Name Thesis Advisor(s) List of Published Papers During Study Time
**Equally Contributing Authors
* Corresponding Author(s)
Jason Ching-Yao Lin
Dr. Chun-Hung Lin
  1. Chiang BY, Chou CC, Hsieh FT, Gao S, Lin JC, Lin SH, Chen TC, Khoo KH, Lin CH, ¡§In vivo tagging and characterization of S-glutathionylated proteome by a chemoenzymatic method.¡¨ Angew. Chem. Intl. Ed. 51(24): 5871-5875, 2012.
  2. Lin JC, Chou CC, Gao S, Wu SC, Khoo KH, Lin CH, ¡§An in vivo tagging method reveals that Ras undergoes sustained activation upon transglutaminase-mediated protein serotonylation.¡¨ ChemBioChem 14: 813-817, 2013.
  3. Lin JC, Chou CC, Tu Z, Yeh LF, Wu SC, Khoo KH, Lin CH, ¡§Characterization of protein serotonylation via bioorthogonal labeling and enrichment.¡¨ J. Proteome Res. 13(8): 3523-3529, 2014.
Chang, Hon-Ju
Dr. An-Suei Yang

Not Available

Liao, Yi-Hung
Dr. Yun-Ru Ruby Chen
Dr. Ming-Daw Tsai
  1. Liao, Y.-H., Chang, Y.-J., Yoshiike, Y., Chang, Y.-C. and Chen, Y.-R. (2012). Negatively Charged Gold Nanoparticles Inhibit Alzheimer's Amyloid-£] Fibrillization, Induce Fibril Dissociation, and Mitigate Neurotoxicity. Small, 8: 3631¡V3639. doi: 10.1002/smll.201201068
  2. Chen W. T., Liao, Y. H., Yu, H. M., Cheng, I. H., and Chen, Y. R. (2011) Distinct Effects of Zn2+, Cu2+, Fe3+, and Al3+ on Amyloid-£] Stability, Oligomerization, and Aggregation: Amyloid-£] Destabilization Promotes Annular Protofibril Formation. J Biol. Chem. 286, 9646-9656. (2011)
Camy Chia Hsuan Kung
Dr. Tai-Huang Huang

Kung, C.C.H., Naik, M.T., Wang, S.H. Shih, H.M. Chang, C.C., Lin, L.Y. Chen, Ma, C., Chang, C.-F. and Huang, .T.-h. *. Structural Analysis of Poly-SUMO Chain Recognition by RNF4-SIMs Domain, Biochem. J. 462(1):53-65 (2014)

Lin, Hsin-Hung
Dr. Alice Lin-Tsing Yu
  1. Liao, H.S., Huang, K.Y., I.-S. Hwang, I.S., Chang, T.J., Wesley W. Hsiao, W.W., Lin, H.H., E.-T. Hwu, E.T., Chang, C.S. (2013) ¡§Operation of Astigmatic-Detection Atomic Force Microscopy in Liquid Environments.¡¨ Rev. Sci. Instrum. 84(10), 103709.
  2. Hsiao, W.W., Liao, H.S., Lin, H.H., Lee, Y.L., Fan, C.K., Liao, C.W., Lin, P.Y., En-Te Hwu, E.T., Chia-Seng Chang, C.S. (2013) ¡§Biophysical Analysis of Astrocytes Apoptosis Triggered by Larval E/S Antigen from Cerebral Toxocarosis-Causing Pathogen Toxocara canis.¡¨ Anal. Sci. 29(9), 885-892.
  3. Lin, H.H.**, Chang, B.M.**, Su, L.J., Lin, W.D., Lin, R.J., Tzeng, Y.K., Lee, R.T., Lee, Y.C., Yu, A.L., Chang, H.C. (2013) ¡§Highly Fluorescent Nanodiamonds Protein-Functionalized for Cell Labeling and Targeting.¡¨ Adv. Funct. Mater. doi: 10.1002/adfm.201301075
  4. Hsiao, W.W., Liao, H.S., Lin, H.H., Ding, R.F., Huang, K.Y., Chang, C.S. (2013) ¡§Motility Measurement of a Mouse Sperm by Atomic Force Microscopy.¡¨ Anal. Sci. 29(1), 3-8.
  5. Lin, H.C., Lin, J.L., Lin, H.H., Tsai, S.W., Yu, A.L., Chen, R., Chen, C.H. (2012) ¡§High Speed Mass Measurement of Nanoparticle and Virus.¡¨ Anal. Chem. 84(11), 4965-4969.
  6. Lin, H.H., Li, Y.C., Chang, C.H., Liu, C., Yu, A.L., Chen, C.H. (2012) ¡§Single Nuclei Raman spectroscopy for Drug Evaluation.¡¨ Anal. Chem. 84(1):113-120.
  7. Lin, H.C., Lin, H.H., Kao, C.Y., Yu, A.L., Peng, W.P., Chen, C.H. (2010) ¡§Quantitative measurement of nano-/microparticle endocytosis by cell mass spectrometry.¡¨ Angew. Chem. Int. Ed. 49(20): 3460-3464.
  8. Lai, C.Y., Hung, J.T., Lin, H.H., Yu, A.L., Chen, S.H., Tsai, Y.C., Shao, L.E., Yang, W.B., Yu, J. (2010) ¡§Immunomodulatory and adjuvant activities of a polysaccharide extract of Ganoderma luciduminvivo and in vitro¡¨ Vaccine 28(31):4945-4954.
  9. Kuo, M.W., Wang, S.H., Chang, J.C., Chang, C.H., Lin, H.H., Yu, A.L., Li, W.H. and Yu, J. (2009) ¡§A novel puf-A gene predicted from evolutionary analysis is involved in the development of eyes and primordial germ-cells.¡¨ PLoS ONE 4(3):e4980.
  10. Peng, W.P., Lin, H.C., Chu, M.L., Chang, H.C., Lin, H.H., Yu, A. L., and Chen, C.-H. (2008) ¡§Charge Monitoring Cell Mass Spectrometry¡¨ Analytical Chemistry. 80: 2524-2530.
  11. Nie, Z., Cui, F., Tzeng, Y.K., Chang, H.C., Chu, M., Li,n H.C., Chen, C.H., Lin, H.H., Yu, A.L. (2007) ¡§High-speed mass analysis of whole erythrocytes by charge-detection quadrupole ion trap mass spectrometry.¡¨ Analytical Chemistry. 79: 7401-7407.
  12. Peng, W.P., Lin, H.C., Lin, H.H., Chu, M.L., Yu, A.L., Chang, H.C., Chen, C.H. (2007) ¡§Charge-Monitoring Laser-induced Acoustic Desorption Mass Spectrometry for Cell and Microparticle Mass Distribution Measurement.¡¨ Angew. Chem. Int. Ed. 46(21): 3865-3869.
  13. Lin, Y.C., Diccianni, M.B., Kim, Y., Lin, H.H., Lee, C.H., Lin, R.J., Joo, S.H., Li, J., Chuang, T.J., Yang, A.S., Kuo, H.H., Tsa,i M.D., Yu, A.L. (2007) ¡§Human p16£^, a novel transcriptional variant of p16INK4A, co-expresses with p16INK4A in cancer cells and inhibits cell cycle progression.¡¨ Oncogene. 26: 7017-7027.
Kuei-Chen Wang
Dr. Tsung-Lin Li
  1. Wang, K.C., Lyu, S.Y., Liu, Y.C., Chang, C.Y., Wu, C.J., LI, T.L. Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple reaction complexes. Acta Cryst. D70, 1401¡V1410 (2014)
  2. Chien, K.L., Wang, K.C., Chen, Y.C., Chao, C.L., Hsu, H.C., Chen, M.F. & Chen, W.J. Common sequence variants in pharmacodynamic and pharmacokinetic pathway-related genes conferring LDL cholesterol response to statins. Pharmacogenomics 11, 309¡V317 (2010)
  3. Janmanchi, D., Tseng, Y.P., Wang, K.C., Huang, R.L., Lin, C.H., Yeh, S.F. Synthesis and the biological evaluation of arylnaphthalene lignans as anti-hepatitis B virus agents. Bioorganic & Medicinal Chemistry 18 1213¡V1226 (2010)
Yi Ting Wang
Dr. Yu-Ju Chen
  1. Yi-Ting Wang, Chia-Feng Tsai, Hsin-Yi Wu, Szu-Hua Pan, Ting-Chun Kuo, Hsin-Yung Yen, Wai-Kok Choong, Pan-Chyr Yang, Ting-Yi Sung, Chi-Huey Wong and Yu-Ju Chen*. Phosphoproteomics Reveals CK2 Substrate, HMGA1, as a Drug Resistant Target in Non-Small Cell Lung Cancer. manuscript in preparation
  2. Chia-Feng Tsai, Yi-Ting Wang, Hsin-Yung Yen, Chih-Chiang Tsou, Wei-Chi Ku, Pei-Yi Lin, Alexey I. Nesvizhskii, Yasushi Ishihama*, Yu-Ju Chen*. ¡§Motif-targeting Quantitative Proteomics for Absolute Phosphorylation Stoichiometry Measurement¡¨ manuscript in preparation
  3. Li Kao, Yi-Ting Wang, Yu-Chen Chen, Shun-Fu Tseng, Jia-Cin Jhang, Yu-Ju Chen**, and Shu-Chun Teng**. Global Analysis of Cdc14 Dephosphorylation Sites Reveals Essential Regulatory Role in Mitosis and Cytokinesis. Mol. Cell. Proteomics, 2014, 13, 594-605.
  4. 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, and Yu-Ju Chen* Sequential Phosphoproteomic Enrichment through Complementary Metal-Directed Immobilized Metal Ion Affinity Chromatography. Anal. Chem., 86, 685-693 (2014)
  5. 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. Oncogene2014, 1-10. doi: 10.1038/onc.2014.58, 1¡V10
  6. Shih-Han Kao, Wen-Lung Wang, Chi-Yuan Chen, Yih-Leong Chang, Yi-Ying Wu, Yi-Ting Wang, Shu-Ping Wang, Alexey I Nesvizhskii, Yu-Ju Chen, Tse-Ming Hong, Pan-Chyr Yang. GSK3£] controls epithelial¡Vmesenchymal transition and tumor metastasis by CHIP-mediated degradation of Slug. Oncogene 2013, 1-11, doi:10.1038/onc.2013.279
  7. 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. J. Proteome Res., 2012, 11, 586¡V598.
  8. Yi-Ting Wang Chun-Hao Huang, Chia-Feng Tsai, Yu-Ju Chen, Jiahn-Shing Lee, Shyh-Horng Chiou*. (The first three authors contributed equally to this work) Phosphoproteomics characterization of novel phosphorylated sites of lens proteins from normal and cataractous human eye lenses. Molecular Vision, 2011, 17, 186-198.
  9. 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, 6, e20199.
  10. 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, 6, e22018.
  11. Yi-Ting Wang**, Chia-Feng Tsai**, Tzu-Chan Hong, Chih-Chiang Tsou, Pei-Yi Lin, Szu-Hua Pan, Che-Ming Hong, Pan-Chyr Yang, Ting-Yi Sung, Wen-Lian Hsu, Yu-Ju Chen*. An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion J. Proteome Res., 2010, 9, 5582¡V5597.
  12. Shyh-Horng Chiou*, Yi-Ting Wang**, Chun-Hao Huang**, I-Liang Lee**, Nai-Yu Liu, Yeou-Guang Tsay, 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, 16, 294-302.
  13. Chih-Chiang Tsou, Chia-Feng Tasi, 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. Mol. Cell. Proteomics, 2009, 9, 131-144.
  14. Ta-Wei Liu, Ching-Wen Ho, Hsin-Hung Huang, Sue-Ming Chang, Shide D. Popat, Yi-Ting Wang, Ming-Shiang Wu, Yu-Ju Chen and Chun-Hung Lin*. Role for £\-L-fucosidase in the control of Helicobacter pylori-infected gastric cancer cells. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 14581-14586.
  15. Chi-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. J. Proteome Res. 2008, 7, 4058¡V4069.
Vathan Kumar
Dr. Po-Huang Liang
  1. Vathan Kumar et al. Anti-SARS coronavirus agents: a patent review (2008-present). Expert Opin. Ther. Patents (2013) 23 (10).
  2. Vathan Kumar et al. Identification, synthesis, and evaluation of novel neuraminidase inhibitors. Org. Lett., 2014, 16 (19), pp 5060¡V5063.
Jiri Koubek
Dr. Joseph Jen-Tse Huang
  1. Koubek J., Lin K.F., Chen Y.R., Cheng R.P., Huang J.J.: Strong anion-exchange fast performance liquid chromatography as a versatile tool for preparation and purification of RNA produced by in vitro transcription. RNA 19, 2013: 1449-59.
  2. Koubek J., Uhlik O., Macek T., Mackova M.: Diversity of chlorobiphenyl-metabolizing bacteria and their biphenyl dioxygenases in contaminated sludge. Chemosphere 92, 2013.
  3. Huang Y.C., Lin K.F., He R.Y., Tu P.H., Koubek J., Hsu Y.C., Huang J.J.: Inhibition of TDP-43 Aggregation by Nucleic Acid Binding. PLoS One. 8, 2013: e64002.
  4. Uhlik O., Musilova L., Ridl J., Hroudova M., Vlcek C., Koubek J., Holeckova M., Mackova M., Macek T.: Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil. Appl Microbiol Biotechnol. 97 2013 9245-56.
  5. Lin K.F., Sun C.S., Huang Y.C., Chen S.I., Koubek J., Wu T.H., Huang J.J.T.: Cotranslational Protein Folding within the Ribosome Tunnel Influences Trigger-Factor Recruitment, Biophys J. 102, 2012, 2818-2827.
  6. Koubek J., Uhlik O., Jecna K., Junkova P., Vrkoslavova J., Lipov J., Kurzawova V., Macek T., Mackova M.: Whole-cell MALDI-TOF: Rapid screening method in environmental microbiology, Int. Biodeterior. Biodegrad. 69, 2012, 82-86.
  7. Strursa P., Uhlik O., Kurzawova V.,Koubek J., Ionescu M., Strohalm M., Lovecka P., Macek T., Mackova M.: Approaches for diversity analysis of cultivable and non-cultivable bacteria in real soil, Plant Soil Environ 55, 2009, 389¡V396.