國立中興大學基因體暨生物資訊學研究所

　　

　　 　　

　　　　　　　

　　　　　　　

　　　　　　　

基因體暨生物資訊學研究所

Graduate Institute of Genomics and Bioinformatics

Chinese
English

興大首頁

National Chung Hsing University

醫科博班

Doctoral Program in Medical Biotechnology

生命科學院

College of Life Sciences

Archives: Team Showcase

Post Type Description

CHANG, YING-LIN

Fax :(04)2285-9329

Honors:

  • 國立中興大學97年績效獎
  • 國立中興大學102年績效獎
  • 國立中興大學104年績效獎
  • 國立中興大學109年績效獎

 

Hou, Ming-Hon

Lab: Drug Design and Chemical Biology Core Lab

Experience

Title Department Period
Professor NCHU, Institute of Genomics and Bioinformatics 2013.08–Now
Associate Professor NCHU, Institute of Genomics and Bioinformatics 2010.02– 2013.07
Adjunct Assistant Professor NCHU, Graduate Institute of Biotechnology 2008.8-2010.01
Joint Assistant Professor NCHU, Department of Life Sciences 2008.8-2010.01
Joint Assistant Professor NCHU, Biotechnology Center 2008.8-2010.01
Assistant Professor NCHU Institute of Genomics and Bioinformatics 2008.08 – 2010.01
Assistant Professor NCHU, Biotechnology Center 2007.02-2008.07
Assistant Professor Shih Chien University, Department of Food Science, Nutrition, and Nutraceutical Biotechnology 2004.8-2007.1
Postdoctoral Fellow Institute of Biological Chemistry, Academia Sinica 2003.8-2004.7
Ph.D. NTU, Institute of Biochemical Sciences 1999.09-2003.07
M.S. NCHU, Graduate Institute Of Biochemistry 1997.09-1999.07

Research

Research Interests
  1. Protein Engineering
  2. Structural Biology
  3. Drug Design
  4. Biophysics

Lectures:

Course

Genetics, Bioinformatics: Lecture and Experiment, Protein Engineering, Structural Bioinformatics, Special Topics in Biotechnology, Applied Genomics and Bioinformatics: Lecture and Experiment, Special Topics in Biotechnology

Research

Lab Research
Our major research projects include:

  • Development of antiviral drugs targeting the nucleoside protein against emerging viruses.
  • Development of anticancer drugs targeting DNA or RNA.
  • Development of diagnostic tools for genetic diseases associated with unusual DNA structures.

 

In order to solve the health problems that human beings are facing today, our lab focuses on the development of novel drugs against several important infectious diseases, genetic diseases, and cancers. Our specialty research field can be divided into two parts: (1) Developing nucleic acid-binding drugs for cancer therapy and investigating the mechanisms of these anti-cancer drugs and (2) Investigating the function and structure of nucleoside proteins from viruses, such as coronavirus and influenza virus, and developing new anti-viral drugs. These two aspects of our research focus on developing essential therapy drugs for important diseases that affect all humankind.

Our group showed that the binding of Chromomycin A3 to the repetitive DNA duplex can induce the conformational changes in the DNA structure in presence of the metal ions. This study is a useful contribution towards the use of the metalloantibiotic not only for the therapeutic but also for the diagnostic purposes in neurological diseases (Angew Chem Int Ed Engl in 2017). On the other hand, we solve the crystal structure of the CCG triplet repeats sequence with i-motif structure related to neurological disease. Our observation of this i-motif structure provides a molecular-level pathological consequence of DNA expansion (Angew Chem Int Ed Engl in 2014). Furthermore, we discovered that the drug actinomycin D can also bind to repetitive DNA sequences to induce the sharp bends in the DNA with flipping out of the bases. This study was a very useful contribution from our group against the drug development for the neurological diseases due to DNA repeat expansions (NAR in 2013).

In addition, we are also interested in developing the novel antiviral agents against the various respiratory viruses including coronavirus and influenza virus. We have studied the coronaviruses 229E and OC43 as experimental models, specifically focusing on nucleocapsid protein. In these analyses, we have examined its biochemistry, biophysics, immunology, and its potential as a target for antiviral drugs. In our recent findings of the N protein of coronavirus, we propose guidelines for developing new N protein-based antiviral agents that target CoVs (Journal of medicinal chemistry, 2014). Influenza spreads very rapidly and has a high mortality rate. Tamiflu (oseltamivir), which is a neuraminidase inhibitor, is used to treat patients. However, several H1N1 influenza strains are known to be resistant to Tamiflu because of the H274Y mutation in neuraminidase. In order to find out the new drugs acting on the nucleoprotein of the influenza virus, we develop a fluorescence-based assay to monitor nucleoprotein binding to a potential inhibitor. This assay can also be useful in screening the new drugs against the other viral proteins also such as HBV or HIV (Analytical Chemistry in 2012).

Publications

Journal(*Corresponding author)
    1. Roshan Satange, Chien-Ying Chuang, Stephen Neidle and Ming-Hon Hou*. (2019) Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Nucleic Acids Research, 47(16):8899–8912.
    2. Chen YW; Satange R; Wu PC; Jhan CR; Chang CK; Chung KR; Waring MJ; Lin SW; Hsieh LC; Hou MH*.(2018) CoII(Chromomycin)2 complex induces a conformational change of CCG repeats from i-Motif to base-extruded DNA duplex. International Journal of Molecular Sciences
    3. Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou MH*. (2018) Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex Nucleic Acids Research
    4. Satange R; Chang CK; Hou, MH*. (2018) A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic acids research
    5. Liu CH, Chen YT, Hou MH, Hu NJ, Chen CS, Shaw JF. (2018) Crystallographic analysis of the Staphylococcus epidermidis lipase involved in esterification in aqueous solution. Acta Crystallographica Section F-Structural Biology Communications
    6. Huang TY; Chang CK; Kao YF; Chin CH; Ni CW; Hsu HY; Hu NJ; Hsieh LC; Chou SH; Lee IR; Hou MH*. (2017) Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion. Proceedings of the National Academy of Sciences of the United States of America
    7. Tseng WH; Chang CK; Wu PC; Hu NJ; Lee GH; Tzeng CC; Neidle S; Hou MH*. (2017) Induced-fit recognition of CCG trinucleotide repeats by a nickel chromomycin complex results in large-scale DNA deformation. Angewandte Chemie-International Edition
    8. Lin YH; Chuang SM; Wu PC; Chen CL; Jeyachandran S; Lo SC; Huang HS; Hou MH*. (2016) Selective recognition and stabilization of new ligands targeting the potassium form of the human telomeric G-quadruplex DNA. Scientific Reports
    9. Liu CL; Hung HC; Lo SC; Chiang CH; Chen IJ; Hsu JT; Hou MH*. (2016) Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development. Scientific Reports
    10. Hou MH; Chuang CY; Ko TP; Hu NJ; Chou CC; Shih YP; Ho CL; Wang AH. (2016) Crystal structure of vespid phospholipase A(1) reveals insights into the mechanism for cause of membrane dysfunction. Insect Biochemistry And Molecular Biology
    11. Chang CK; Jeyachandran S; Hu NJ; Liu CL; Lin SY; Wang YS; Chang YM; Hou MH*. (2016) Structure-based virtual screening and experimental validation of the discovery of inhibitors targeted towards the human coronavirus nucleocapsid protein. Molecular Biosystems
    12. Wang YS; Chang CK; Hou MH*. (2015) Crystallographic analysis of the N-terminal domain of Middle East respiratory syndrome coronavirus nucleocapsid protein. Acta Crystallographica Section F-Structural Biology Communications
    13. Lin, S.Y., Liu, C.L., Chang, Y.M., Zhao, J., Perlman, S. and Hou,M.H.(2014) Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target. Journal of medicinal chemistry, 57, 2247-2257.
    14. Chang, C.K., Hou, M.H., Chang, C.F., Hsiao, C.D. and Hou,M.H.(2014) The SARS coronavirus nucleocapsid protein–forms and functions. Antiviral research, 103, 39-50.
    15. Chen, I.J., Yuann, J.M., Chang, Y.M., Lin, S.Y., Zhao, J., Perlman, S., Shen, Y.Y., Huang, T.H. and Hou,M.H.(2013) Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein. Biochimica et biophysica acta, 1834, 1054-1062.
    16. Lo, Y.S., Tseng, W.H., Chuang, C.Y. and Hou,M.H.(2013). The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats. Nucleic Acids Res 41, 4284-94.
    17. Chen, Y.W. and Hou,M.H.(2013) The binding of the Co(II) complex of dimeric chromomycin A3 to GC sites with flanking G:G mismatches. Journal of inorganic biochemistry, 121, 28-36.
    18. Lo, Y.S., Lin, S.Y., Wang, S.M., Wang, C.T., Chiu, Y.L., Huang, T.H. and Hou,M.H.(2013). Oligomerization of the carboxyl terminal domain of the human coronavirus 229E nucleocapsid protein. FEBS Lett 587, 120-7.
    19. Liang, F.Y., Lin, L.C., Ying, T.H., Yao, C.W., Tang, T.K., Chen, Y.W. and Hou,M.H.(2013). Immunoreactivity characterisation of the three structural regions of the human coronavirus OC43 nucleocapsid protein by Western blot: implications for the diagnosis of coronavirus infection. J Virol Methods 187, 413-20.
    20. Kuo, S.M., Kao, H.W., Hou,M.H., Wang, C.H., Lin, S.H. and Su, H.L. (2013). Evolution of infectious bronchitis virus in Taiwan: positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity. Vet Microbiol 162, 408-18.
    21. Hsu, C.W., Kuo, C.F., Chuang, S.M. and Hou,M.H.(2013). Elucidation of the DNA-interacting properties and anticancer activity of a Ni(II)-coordinated mithramycin dimer complex. Biometals 26, 1-12.
    22. Chen, Y.W. and Hou,M.H.(2013). The binding of the Co(II) complex of dimeric chromomycin A3 to GC sites with flanking G:G mismatches. J Inorg Biochem 121, 28-36.
    23. Yuann, J.M., Tseng, W.H., Lin, H.Y. and Hou,M.H.(2012). The effects of loop size on Sac7d-hairpin DNA interactions. Biochim Biophys Acta 1824, 1009-15.
    24. Wu, M.R.,Hou,M.H., Lin, Y.L. and Kuo, C.F. (2012). 2,4,5-TMBA, a natural inhibitor of cyclooxygenase-2, suppresses adipogenesis and promotes lipolysis in 3T3-L1 adipocytes. J Agric Food Chem 60, 7262-9.
    25. Wang, S.Y. et al. (2012). Spermine attenuates the action of the DNA intercalator, actinomycin D, on DNA binding and the inhibition of transcription and DNA replication. PLoS One 7, e47101.
    26. Hung, H.C. et al. (2012). Development of an anti-influenza drug screening assay targeting nucleoproteins with tryptophan fluorescence quenching. Anal Chem 84, 6391-9.
    27. Hsu, C.W., Chuang, S.M., Wu, W.L. and Hou,M.H. (2012). The crucial role of divalent metal ions in the DNA-acting efficacy and inhibition of the transcription of dimeric chromomycin A3. PLoS One 7, e43792.
    28. Chang, Y.M., Chen, C.K. and Hou,M.H.(2012). Conformational Changes in DNA upon Ligand Binding Monitored by Circular Dichroism. Int J Mol (SCI) 13, 3394-413.
  • Chang, Y.M., Chen, C.K., Chang, Y.C., Jeng, W.Y.,Hou,M.H. and Wang, A.H. (2012). Functional studies of ssDNA binding ability of MarR family protein TcaR from Staphylococcus epidermidis. PLoS One 7, e45665.
  • Kuo, S.M., Wang, C.H.,Hou,M.H., Huang, Y.P., Kao, H.W. and Su, H.L. (2010). Evolution of infectious bronchitis virus in Taiwan: characterisation of RNA recombination in the nucleocapsid gene. Vet Microbiol 144, 293-302.
  • Chen, I.J., Chou, C.C., Liu, C.L., Lee, C.C., Kan, L.S. and Hou,M.H.(2010). Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of human coronavirus OC43 nucleocapsid protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 66, 815-8.
  • Lu, W.J., Wang, H.M., Yuann, J.M., Huang, C.Y. andHou, M.H.(2009). The impact of spermine competition on the efficacy of DNA-binding Fe(II), Co(II), and Cu(II) complexes of dimeric chromomycin A(3). J Inorg Biochem 103, 1626-33.>
  • Huang, C.Y., Hsu, Y.L., Chiang, W.L. and Hou, M.H.(2009). Elucidation of the stability and functional regions of the human coronavirus OC43 nucleocapsid protein. Protein (SCI) 18, 2209-18.
  • Hou, M.H., Lu, W.J., Lin, H.Y. and Yuann J.M. (2008) Studies of sequence-specific DNA binding, DNA cleavage, and topoisomerase I Inhibition by the dimeric chromomycin A3 complexed with Fe(II). Biochemistry., 47, 5493-5502.
  • Tang, T.K., Wu, P.J., Chen, S.T., Hou, M.H., Hong, M.H., Pan, F.M., Yu, H.M., Chen, J.H., Yao, C.W. and Wang, A.H.-J. (2005) Biochemical and immunological studies of nucleocapsid proteins of severe acute respiratory and 229E human coronaviruses.. Proteomics 5,925-37.
  • Hou, M.H. and Wang A.H.-J. (2005) Mithramycin forms a stable dimeric complex by chelating with Fe(II): DNA-interacting characteristics, cellular permeation and cytotoxicity. Nucleic Acids Res. 33,1352-61
  • Hou, M.H., Robinson H., Gao Y.G. and Wang A.H.-J. (2004) Crystal structure of the Mg2+-(chromomycin A3)2-d(TTGGCCAA)2 complex reveals GGCC binding specificity of the drug dimer chelated by metal ion. Nucleic Acids Res, 32, 2214-2222. (Featured on Cover)
  • Hou, M.H., Robinson H., Gao Y.G. and Wang A.H.-J. (2002). Crystal structure of actinomycin D bound to the CTG triplet repeat sequences linked to neurological diseases. Nucleic Acids Res., 30, 4910-4917. (Featured on Cover)
  • Hou, M.H., Lin, S.B., Yuann J.M., Lin W.C., Wang A.H.-J. and Kan L.S. (2001) Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure. Nucleic Acids Res., 29, 5121-5128.

 

Conference (*Invited speaker)
      1. Ming-Hon Hou (2019, Feb) Structure-based virtual screening and experimental validation of novel human coronavirus nucleocapsid protein anti-viral inhibitors. In: Structure Assisted Development of Novel Therapeutics 2019; 2019 Feb 12-16. Faridabad, India (Speech, Feb 15 , VI).
      2. Roshan Satange and Ming-Hon Hou*(2019, Feb) Structural heterogeneity in DNA duplex with symmetric G:G mismatches upon CoII(Chromomycin A3)2 and Actinomycin D binding.In: Structure Assisted Development of Novel Therapeutics 2019; 2019 Feb 12-16. Faridabad, India. (Poster)
      3. Roshan Satange and Ming-Hon Hou*(2018, May) Synergistic intercalation of echinomycin and actinomycin D to DNA duplex with T:T mismatch causes single strand deformation. pp.104(Poster). In: The 23rd Biophysics Conference; 2018 May 23-25; Taichung, Taiwan
      4. Yun-Jean Lin and Ming-Hon Hou*(2018, May) Structural study of the specific interactions between echinomycin and methylated DNA containing the CCG motif .pp.103(Poster). In: The 23rd Biophysics Conference; 2018 May 23-25; Taichung, Taiwan
      5. Hsiang-Ti Huang and Ming-Hon Hou*(2018, May) Structural basis for the binding of Echinomycin to DNA duplex containing I:C mismatch. pp.91(Poster). In: The 23rd Biophysics Conference; 2018 May 23-25; Taichung, Taiwan
      6. Pei-Ching Wu, Shu-Ling Tzeng, Chung-ke Chang, Ya-Fen Kao, Michael J. Waring and Ming-Hon Hou* (2018, May) Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex. pp.106(Poster). In: The 23rd Biophysics Conference; 2018 May 23-25; Taichung, Taiwan
      7. Ching-Ming Chien, Jia-Ning Hsu and Ming-Hon Hou* (2018, May) Homology Modeling and Crystallization of N-terminal domain of Porcine Epidemic Diarrhea Virus Nucleocapsid Protein. pp.90(Poster). In: The 23rd Biophysics Conference; 2018 May 23-25; Taichung,Taiwan
      8. Jing-Yi Zeng, Tzu-Jung Huang and Ming-Hon Hou* (2018, May) The terminal base pairs determine the conformation of DNA duplex with G:T mismatch. pp.117(Poster). In: The 23rd Biophysics Conference; 2018 May 23-25; Taichung, Taiwan
      9. Ming-Hon Hou (2018, May) Binding of small molecules to trinucleotide DNA repeats associated with fragile X syndrome. pp.34(Oral). In: The 23rd Biophysics Conference; 2018 May 23-25; Taichung, Taiwan
      10. Hou, MH; Hsu, CN (Dec, 2017) Structural basis for identification of the interface of the N-terminal domain of CoV N protein dimer as a target for drug development. pp. 196 (Abstract POS501). In: the 31st Annual Symposium ofThe Protein Society, 2017 July 24–27, Montreal, Canada.
      11. Lin, S.Y., Liu, C.L., Chang, Y.M., and Hou, M.H.*(2012, Dec). Probing the N-terminal domain of coronavirus nucleocapsid protein as a potent target for antiviral drug development.. 2012 Taiwan Society for Biochemistry and Molecular Biology.
      12. Lin, Y.H., Chen, C.L., Huang, H.S., and Hou, M.H.* (2012, Dec). The study of anthrax[1, 2-d] imidazole-6,11-dione derivatives bound to the potassium form of human telomere G-quadruplex.. 2012 Taiwan Society for Biochemistry and Molecular Biology.
      13. Chen, Y.W., andHou, M.H.* (2012, Dec). The binding of the Co(II) complex of dimeric chromomycin A3 to GC sites with flanking G:G mismatches.. 2012 Taiwan Society for Biochemistry and Molecular Biology.
      14. Tseng, W. H., Yuann, J. M., Lin, H. Y., and Hou, M.H.*(2012). The effects of loop size on Sac7d-hairpin DNA interactions.. 17th Joint International Conference of Biophysics and Annual Conference of the Biophsical Society of ROC.
      15. Hou, M.H.*., Liu, C.L., Chen, I.J. and Chou, C.C. (2011). Identification of the N-terminal domain of human coronaviral nucleocapsid protein as a potential antiviral target. The 36th FEBS congress.
      16. Hsu, CW., Chuang, S.M. and Hou, M.H.* (2011). Comparison of DNA-binding properties and ant proliferative effects for chromomycin A3 dimer chelated with various divalent metal ions. 22nd FAOBMB conference.
      17. Liu, C.L., Chen, I.J. and Hou, M.H.*(2011). Identification of the N-terminal domain of human coronaviral nucleocapsid protein as a potential antiviral target . 22nd FAOBMB conference.
      18. Chen, Y.W. and Hou, M.H.*(2010). Probing the interaction of the residue Y148 in influenza A virus nucleoprotein involved in RNA-binding. The Taiwan society for biochemistry and molecular biology.
      19. Hou, M.H.* Lu,W.J., Wang, H.M., Yuann, J.M., and Huang, C.Y. (2010). The impact of spermine competition on the efficacy of DNA-binding Fe(II), Co(II), and Cu(II) complexes of dimeric chromomycin A(3). 4th Asian Bioinorganic Chemistry Conference.
      20. Hou, M.H.*, Lu,W.J., Huang, C.Y., Fan, R.J., and Yuann, J.M. (2010). Effects of polyamines on the DNA-reactive properties of dimeric mithramycin complexed with cobalt(II): implications for anticancer therapy . 24th International Conference on Organometallic Chemistry.
      21. Lo, Y.S., Chiu, Y.L. and Hou, M.H.*(2010). The crucial role of C-terminal tail of human coronavirus 229E nucleocapsid protein in oligomerization. The Taiwan society for biochemistry and molecular biology.
      22. Chiang, C.H., Wu, F.C. and Hou, M.H.*(2009). Probing the crucial residues of influenza virus (H1N1) nucleocapsid for RNA-bunding. 14th Joint International Conference of Biophysics and Annual Conference of the Biophsical Society of ROC.
      23. Chiu, Y.L, Lo, Y.S. and Hou, M.H.*(2009). Characterization of the C-terminal domain of human coronavirus 229E nucleocapsid protein in RNA-binding and oligomerization. 14th Joint International Conference of Biophysics and Annual Conference of the Biophisical Society of ROC.
      24. Hou, M.H.* Chiang, C. H., Wu, F. C. and Lo, Y. S. (2009). Probing the crucial residues of influenza virus (H1N1) nucleoprotein for RNA-binding. VIII European Symposium of The Protein Society.

 

 

Chu, Yen-Wei

Lab: Natural Computing & Bioinformatics Laboratory

Experience

Title Department Period
Review Editor Frontiers in Digital Public Health 2021/07 – present
Editor International Journal of Genomics, Proteomics, Metabolomics & Bioinformatics 2017/12 – present
Editor International Journal of Pharmacology, Phytochemistry & Ethnomedicine 2015/11 – present
Editor Journal of Biochemistry and Molecular Biology Research 2014/10 – present
Editor Journal of Computation in Biosciences and Engineering 2013/11 – present
Lead Guest Editor Journal of Neuroscience and Neuroengineering 2012 – 2013
Professor NCHU, Institute of Genomics and Bioinformatics 2019/08 -present
Associate Professor NCHU, Institute of Genomics and Bioinformatics 2012/08 -2019/07
Assistant Professor NCHU, Institute of Genomics and Bioinformatics 2008/08 – 2012/07
Advisory Committee Member ROC, Ministry of Health and Welfare 2006 – present
Assistant Professor Asia University, Department of Bioinformatics and Medical Engineering 2006/08 – 2008/07
Lecturer YUMT, Department of Information Management 2005/08 – 2006/07
Lecturer CUTE, Department of Information Management 2003/09 – 2005/07
Consultant IT Division, Transformer Bobbin Industrial Co., LTD 1998/03 – 2000/03
Lecturer Association of Electronic Multi-education, R.O.C. 1997/03 – 1999/06
PhD NCTU, Department of Computer Science 1998/09 – 2006/07
M.S. Department of Computer Science,
National Chiao Tung University		 1996/09 – 1998/07
B.S. Department of Computer Science,
National Chiao Tung University		 1992/09 – 1996/07

Research

Research Interests
  1. Bioinformatics Algorithms
  2. Computational Epigenetics
  3. Artificial Intelligence
  4. Intelligent Systems

Lectures:

Course

Special Topics in The Application of Natural Computing, Machine Learning, Current Approaches in Bioinformatics, Bioinformatics Programming, Bioinformatics: Lecture and Experiment, Applied Genomics and Bioinformatics: Lecture and Experiment

Publications

Journal (*Corresponding author)
  1. Jone-Han Liu, Chi-Chang Chang, Chi-Wei Chen, Li-Ting Wong and Yen-Wei Chu* (2019) Conservation region finding for influenza A viruses by machine learning methods of N-linked glycosylation sites and B-cell epitopes, Mathematical Biosciences, 315:108217. (SCI)
  2. Chi-Chou Liao, Liang-Jwu Chen, Shuen-Fang Lo, Chi-Wei Chen and Yen-Wei Chu* (2019) EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches, PLoS Comput Biol, 15(5):e1006942. (SCI)
  3. Kai-Po Chang, Yen-Wei Chu* and John Wang (2019) Analysis of Hormone Receptor Status in Primary and Recurrent Breast Cancer Via Data Mining Pathology Reports, Open Medicine, 20(14): 91-98. (SCI)
  4. Jehn-Hwa Kuo, Chi-Chang Chang, Chi-Wei Chen, Heng-Hao Liang, Chih-Yen Chang and Yen-Wei Chu* (2019) Sequence-Based Structural B-cell Epitope Prediction by Using Two Layer SVM Model and Association Rule Features, Current Bioinformatics, DOI: 10.2174/1574893614666181123155831 (SCI)
  5. Yu-Ting Chen, Chi-Chang Chang, Chi-Wei Chen, Kuan-Chun Chen and Yen-Wei Chu* (2019) MADS-Box Gene Classification in Angiosperms by Clustering and Machine Learning Approaches, Frontiers in Genetics, 8(9): 707. (SCI)
  6. Chi-Wei Chen, Kai-Po Chang, Cheng-Wei Ho, Hsung-Pin Chang and Yen-Wei Chu* (2018) KStable: A Computational Method for Predicting Protein Thermal Stability Changes by K-Star with Regular-mRMR Feature Selection, Entropy, 20(12): 988. (SCI)
  7. Chi-Chang Chang,Chi-Hua Tung,Chi-Wei Chen,Chin-Hau Tu and Yen-Wei Chu* (2018) SUMOgo: Prediction of sumoylation sites on lysines by motif screening models and the effects of various post-translational modifications. scientific report, 19;8(1):15512. doi: https://doi.org/10.1038/s41598-018-33951-5 (SCI)
  8. Quan Zou, Chi-Wei Chen, Hao-Chen Chang and Yen-Wei Chu* (2018) Identifying Cleavage Sites of Gelatinases A and B by Integrating Feature Computing Models. Journal of Universal Computer Science, Vol. 24, No. 6, pp. 711-724 (SCI)
  9. Chi-Chou Huang, Chi-Chang Chang, Chi-Wei Chen, Shao-yu Ho, Hsung-Pin Chang and Yen-Wei Chu* (2018) PClass: Protein Quaternary Structure Classification by Using Bootstrapping Strategy as Model Selection. Genes, Vol. 9, No. 2, pii: E91. doi: 10.3390/genes9020091 (SCI)
  10. Chi-Wei Chen, Chi-Chang Chang, Hui-Chih Hung, Hsung-Pin Chang and Yen-Wei Chu* (2018) Constructing Feature Models for Citrullination Sites Prediction. Journal of Quality, Vol. 25, No. 3, doi:10.6220/joq.201806_25(3).0004 (EI)
  11. Chi-Hua Tung, Pei-Wei Shueng, Yen-Wei Chu*, Chi-Wei Chen, Chian-Ying Chen (2017) Identifying Post-Translational Modification Crosstalks for Breast Cancer. Journal of Computing Science and Engineering, Vol. 11, No. 4, pp. 111-120 (EI)
  12. Chi-Hua Tung, Chi-Wei Chen, Han-Hao Sun, Yen-Wei Chu* (2017) Predicting human protein subcellular localization by heterogeneous and comprehensive approaches, PLoS ONE, 12(6):e0178832. doi: 10.1371/journal.pone.0178832 (SCI)
  13. Chi-Hua Tung, Chi-Wei Chen, Ren-Chao Guo, Hui-Fuang Ng, Yen-Wei Chu* (2016) QuaBingo: A Prediction System for Protein Quaternary Structure Attributes Using Block Composition, BioMed Research International, 2016:9480276, doi:10.1155/2016/9480276 (SCI : 2.134)
  14. Han-Ju Chien+, Yen-Wei Chu+, Chi-Wei Chen, Yu-Min Juang, Min-Wei Chien, Chih-Wei Liu, Chia-Chang Wu, Jason T.C. Tzen and Chien-Chen Lai* (2016) 2-DE combined with two-layer feature selection accurately establishes the origin of oolong tea, Food Chemistry, 211:392-9, doi:10.1016/j.foodchem.2016.05.043 (SCI: 4.052 , Co-first Author)
  15. Chi-Wei Chen, Jerome Lin, Yen-Wei Chu* (2013) iStable: Off-the-shelf Predictor Integration for Predicting Protein Stability Changes, BMC Bioinformatics, 14(suppl 2):S5, doi:10.1186/1471-2105-14-S2-S5 (SCI:2.435, ranking: 17.9%)
  16. Wei-Jie Pan, Chi-Wei Chen, Heng-Hao Liang, Yen-Wei Chu* (2012) Selecting High Efficacy siRNAs by Computational Models, Advanced Science Letters, 18: 141-144. (SCI:1.253, ranking: 25%)
  17. Chang-Hsien Yang, Yu-Yun Chang, Chi-Wei Chen, Min-Cheng Chan, Yen-Wei Chu* (2012) iMADS: The Class Identification of MADS-box Gene on Angiosperm, Advanced Science Letters, 18: 170-175.(SCI:1.253, ranking: 25%)
  18. Po-Chang Chang, Wei-Jie Pan, Chi-Wei Chen,Yu-Ting Chen and Yen-Wei Chu* (2012) DEsi: an design engine of siRNA that integrates SVMs prediction and feature filters, Biocatalysis and Agricultural Biotechnology, doi: 10.1016/j.bcab.2012.01.005
  19. Wei-Jie Pan, Chi-Wei Chen and Yen-Wei Chu* (2011)siPRED: Predicting siRNA efficacy using various characteristic methods, PLoS ONE, doi: 10.1371/journal.pone.0027602 (SCI :3.057)
  20. Yu-Yun Chang+,Yen-Wei Chu+, Chi-Wei Chen, Wei-Ming Leu, Hsing-Fun Hsu and Chang-Hsien Yang* (2011) Characterization of Oncidium ‘Gower Ramsey’ Transcriptomes using 454 GS-FLX Pyrosequencing and Their Application to the Identification of Genes Associated with Flowering Time, Plant and Cell Physiology, 52(9): 1532-1545 (SCI: 4.319 , Co-first Author)
  21. Hui-Fuang Ng, Zeng-Wei Hong and Yen-Wei Chu (2008) “Pose and Expression Invariant Face Recognition from a Single Training Sample Using Similarity Vector”, Journal of Cybernetics and Systems, 1(1): 21-26. (International Journal)
  22. Yen-Wei Chu* and Chuen-Tsai Sun (2007) Problem-based Approach for Bioinformatics. International Journal of Instructional Media,Vol. 34 #4. (International Journal)
  23. Yen-Wei Chu*, Chuen-Tsai Sun, and Chung-Yuan Huang (2006) Regularity of Protein Secondary Structures and Its Prediction. WSEAS Transactions on Systems, 2(5), pp. 380-387. (EI)
  24. Chung-Yuan Huang, Chuen-Tsai Sun, and Yen-Wei Chu (2006) A Co-adaptive Approach to XCS Classifier Systems. WSEAS Transactions on Systems, 2(5), pp. 388-394. (EI)
  25. Yen-Wei Chu* and. Jinn-Moon Yang (2003) Finding Regularity in Various Types of Secondary Protein Structures, Journal of Information Science and Engineering, vol. 19, pp.943-952.(SCI)

 

Conference (*Invited speaker)
  1. Chen Chi-Wei, Chin-Hau Tu and Yen-Wei Chu* (2018) SUMOylation Sites Prediction by Machine Learning Approaches, IEEE International Conference on Consumer Electronics-Taiwan. (http://edas.info/p24335#S1569554145)
  2. Kai-Po Chang, Chi-Chang Chang, Yen-Wei Chu* and John Wang* (2018) BreastExtractor: A Word/Phrase Matching-Based Text Mining Program for Automatic Extraction of Hormone Receptor Data from Free-text Pathology Reports on Breast Cancer, the second International Conference on Medical and Health Informatics. (Best Paper Award)
  3. Kai-Po Chang, John Wang* and Yen-Wei Chu* (2016) Big data in pathologists’ office: large-scale extraction and analysis of immunohistochemical study result in free-text pathology reports by a client-side Python script, Paper presented at 2016 Annual Meeting of Taiwan Society Of Pathology, Taipei, Taiwan.
  4. Ci-Jhou Liao, Liang-Jwu Chen, Yen-Wei Chu* (2014) Using machine learning approach to predict the flanking genes expression in T-DNA insertion activation-tagged rice lines, Summer Workshop on Plant Molecular Biology, Nantou County, Taiwan, July 4-6.
  5. Chi-Wei Chen, Hui-Chih Hung, Yen-Wei Chu* (2014) Citrullination Sites Prediction by Machine Learning Approaches, Proceedings of the 25th International Conference on Information Management (ICIM 2014), pp. 1-13. (Best Paper Award)
  6. Chi-Wei Chen, Hui-Chih Hung, Yen-Wei Chu* (2013) Feature Model Integration by Evolutionary Computation for Predicting Protein Citrullination sites, Proceedings of the Taiwan Academic Network Conference 2013 (TANet 2013), pp. 1047-1052.
  7. Hao-Chen Chang and Yen-Wei Chu* (2013) Gelatinase Substrate Cleavage Sites Prediction Using Machine Learning and Feature Selection, Proceedings of the Taiwan Academic Network Conference 2013 (TANet 2013), pp. 1053-1058.
  8. Chi-Wei Chen, Jerome Lin, Yen-Wei Chu* (2013) iStable: Off-the-shelf Predictor Integration for Predicting Protein Stability Changes, The Eleventh Asia Pacific Bioinformatics Conference, Vancouver, BC, Canada, January 21-23.
  9. Wen-Pin Hu, Chi-Wei Chen, Jian-Shiun Chen, and Yen-Wei Chu* (2012) Evaluating various machine learning approaches for the sunspot number prediction. Symposium of university league in Changhua, Yunlin, and Chiayi, Taiwan, December 7.
  10. Yu-Yun Chang, Yen-Wei Chu, Wei-Ming Leu and Chang-Hsien Yang* (2011) Characterization of Oncidium ‘Gower Ramsey’ transcriptome for using GS-FLX 454 pyrosequencing and its application for studies of flowering time associate genes. The International Conference Plant Gene Discovery Technologies. Venue. February 23- 26.
  11. Yu-Yun Chang, Yen-Wei Chu, Hsing-Fun Hsu, Chi-Wei Chen, Wei-Ming Leu and Chang-Hsien Yang* (2011) Characterization of Oncidium ‘Gower Ramsey’ transcriptomes using 454 GS-FLX pyrosequencing and their application to theidentification of genes associated with flowering time. 2011 Canadian Plant Genomics Workshop, Niagara Falls, Ontario. Canada, August 22-25.
  12. Wei-Jie Pan, Chi-Wei Chen and Yen-Wei Chu* (2011) High efficacy siRNA selection using machine learning approach, Proceedings of 2011 Joint Conference on 7th Taiwan Software Engineering (TCSE) and 22nd Object-Oriented Technology and Applications (OOTA), pp. 94-99
  13. Qiu-Hui Lin, Chi-Wei Chen, Zeng-Wei Hong,* and Yen-Wei Chu* (2009) PredPhosGrid – A Grid-based Phosphorylation Prediction System by Reengineering off-the-shelf Bioinformatic Websites, Proceedings of the 20th Workshop on Object-Oriented Technology and Applications, pp. 1-6.
  14. Cheng-Yu Liao, Wei-Fu Lu and Yen-Wei Chu* (2009) Using Genetic Algorithms to Assist the Classification of Biological Documents: An Example of Mushroom and Toadstool Data, Information Management and Commerce Technology Conference, pp. 559, Yunlin, Taiwan.
  15. Yen-Wei Chu*, Chin-Sheng Yu. and Hui-Fuang Ng. (2008) Protein Secondary Structures Prediction Using Data Fusion Approach, Proceedings of the 7th IEEE World Congress on Intelligent Control and Automation (WCICA), v. 4, pp. 1885-1890. (EI, NSC 96-2218-E-468-001)
  16. Hui-Fuang Ng* and Yen-Wei Chu (2008) Illumination Invariant Color Model for Image Matching and Object Recognition, The Eighth International Conference on Intelligent Systems Design and Applications.(EI)
  17. Yen-Wei Chu*, Chin-Sheng Yu., Chia-Hsiang Pai and You-Ting Wu (2007) Protein Phosphorylation Site Prediction Using Data Fusion Approach, National Computer Symposium, v1, pp. 1-8 (NSC 96-2218-E-468-001)
  18. Yen-Wei Chu*, Chin-Sheng Yu., Chih-Ying Chen and Kun-Chang Hsieh (2007) Applying Sequence Conservation Strategy to Predict Protein Phosphorylation Site, National Computer Symposium, v1, pp.9-15 (NSC 96-2218-E-468-001)
  19. Ting-Yi Chang*, Yi-Ting Chen, and Yen-Wei Chu (2007) ‘Develop the Peer Assessment of Cooperative Learning in e-Learning — Using Consistent Fuzzy Preference Relation, National Computer Symposium, pp. 554-561
  20. Hui-Fuang Ng*, Ding-Fu Wang and Yen-Wei Chu (2007) Illumination invariant color descriptors for image matching. The 20th IPPR Conference on Computer Vision, Graphics and Image Processing, Miaoli, Taiwan.
  21. Yen-Wei Chu* and Chuen-Tsai Sun (2006) A Hybrid Genetic Algorithm Approach for Protein Secondary Structures, Proceedings of the 6th IEEE World Congress on Intelligent Control and Automation (WCICA), v. 4, pp. 3320-3324. (EI)
  22. Yen-Wei Chu*, Chuen-Tsai Sun, and Chung-Yuan Huang (2005) Finding Regularity in Protein Secondary Structures using a Cluster-based Genetic Algorithm. In Proceedings of International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics (CIMMACS’05), Miami, Florida, USA, pp. 179-183. (IEE, EI)
  23. Chung-Yuan Huang*, Chuen-Tsai Sun, and Yen-Wei Chu (2005) Using a Coevolution Mechanism with a Dyna Architecture for Parameter Adaptation in XCS Classifier Systems. In Proceedings of International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics (CIMMACS’05), Miami, Florida, USA, pp. 173-178. (IEE, EI)
  24. Yen-Wei Chu* and Chuen-Tsai Sun (2004) Regularity of secondary protein structures: A genetic algorithm approach, Proceedings of the 5th IEEE World Congress on Intelligent Control and Automation (WCICA), v. 3, pp. 2104-2108.(EI)
  25. Chuen-Tsai Sun* and Yen-Wei Chu (1997) Hysteresis Behavior in Fuzzy Perception: A Preliminary Experiment. Second International ICSC Symposium on Intelligent Industrial Automation and Soft Computing, Nimes, France, Sep. 1997.
Books:
  1. Chu Y.W. (2006) Finding Protein Secondary Structure Regularity and Related Applications: National Chiao Tung University, Hsinchu, Taiwan. (Dissertation)
  2. Chu Y.W. (1998) Studies on Hysteresis: Human Perception and Time Series Prediction: National Chiao Tung University, Hsinchu, Taiwan. (Master Thesis)

Chen, Ying-Tsong

Lab: Microbial Genomics Core Laboratory

Experience

Title Department Period
Professor NCHU, Institute of Genomics and Bioinformatics 2022.08 –
Adjunct Associate Investigator National Health Research Institutes,  Institute of Molecular and Genomic Medicine 2019.08-
Joint Associate Investigator National Health Research Institutes,  Institute of Molecular and Genomic Medicine 2018 – 2019
Associate Professor NCHU, Institute of Genomics and Bioinformatics 2015.02 – 2022.08
Assistant Professor NCHU, Institute of Genomics and Bioinformatics 2010.08 – 2015.01
Joint Assistant Investigator National Health Research Institutes,  Institute of Molecular and Genomic Medicine 2011 – 2017
Assistant Professor NCHU, Institute of Genomics and Bioinformatics 2009 – 2010
Postdoctoral Fellow National Health Research Institutes,  The Division of Molecular and Genomic Medicine 2004~2009
PhD NCTU, Department of Biological Science & Technology

Research

Research Interests
  1. Bacterial Genomics
  2. Functional Genomics
  3. Comparative Genomics
  4. Plastid Research

Lectures:

Course

Biochemistry (University Department of Horticulture)
Cell Biology (University Biotechnology Program)
Bioinformatics and Internship (University Department of Life Sciences)
Interesting Talk on Life Science and Bioinformatics (University General Course)
Biochemistry (Department of Food and Biotechnology)
Shotgun Sequencing Principles and Practice (Fundamentals)
Functional Biology (Foundation Institute)
Special Discussion on Biomedical Big Data (1, 2) (Foundation Institute)
Microbial Genetics and Genomes (1, 2)
Applied Genomics and Bioinformatics cum Internship (GFSI)
Panel Discussion (GFSI)
Thematic Study E (Medical Courses)

Publications

Journal (∗Corresponding author)
  1. Lee YL, Liu KM, Chang HL, Liao YC, Lin JS, Kung FY, Ho CM, Lin KH, Chen YT*. The evolutionary trend and genomic features of an emerging lineage of Elizabethkingia anophelis strains in Taiwan. Microbiol Spectr. 2022 [online]
  2. Hong YP, Wang YW, Chen BH, Song HY, Chiou CS, Chen YT*. RamAp, an efflux pump regulator carried by an IncHI2 plasmid. Antimicrob Agents Chenother. 2021 [Epub ahead of print]
  3. Hong YP, Chen YT, Wang YW, Chen BH, Teng RH, Chen YS, Chiou CS*. Integrative and conjugative element-mediated azithromycin resistance in multi drug-resistant Salmonella enterica serovar Albany. Antimicrob Agents Chemother. 2021 [Epub ahead of print]
  4. Lee YL, Liu KM, Chang HL, Lin JS, Kung FY, Ho CM, Lin KS, Chen YT*. A dominant strain of Elizabethkingia anophelis emerged from hospital water system to cause a three-year outbreak in a respiratory care center. J Hosp Infect. 2021. 108:43-51. PubMed PMID33157171.
  5. Yao-Chen Wang, Hui-Ling Tang, Yu-Chieh Liao, Chien-Shun Chiou, Ying-Tsong Chen, Ming-Ko Chiang, Min-Chi Lu, and Yi-Chyi Lai :Co-carriage of distinct blaKPC-2and blaOXA-48 plasmids in a single ST11 carbapenem-resistant Klebsiella pneumoniae isolate. Antimicrobial Agents and Chemotherapy(2019)
  6. Dou HY, Lin CH, Chen YY, Yang SJ, Chang JR, Wu KM, Chen YT, Chin PJ, Liu YM, Su IJ, Tsai SF: Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates. Scientific Reports(2017)
  7. Chiou CS, Chen YT, Wang YW, Liu YY, Kuo HC, Tu YH, Lin AC, Liao YS, Hong YP :Dissemination of mcr-1-Carrying Plasmids among Colistin-Resistant Salmonella Strains from Humans and Food-Producing Animals in Taiwan. Antimicrobial Agents and Chemotherapy(2017)
  8. Lu MC, Chen YT, Chiang MK, Wang YC, Hsiao PY, Huang YJ, Lin CT, Cheng CC, Liang CL, Lai YC: Colibactin contributes to the hyper virulence of pks+ K1 CC23 Klebsiella pneumoniae in mouse meningitis infections. Frontiers in Cellular and Infection Microbiology(2017)
  9. Chen YT, Lai YC, Tan MC, Hsieh LY, Wang JT, Shiau YR, Wang HY, Lin AC, Lai JF, Huang IW, Lauderdale TL: Prevalence and characteristics of pks genotoxin gene cluster-positive clinical Klebsiella pneumoniae isolates in Taiwan. Scientific Reports(2017)
  10. Horng-Yunn Dou, Yih-Yuan Chen, Ying-Tsong Chen, Jia-Ru Chang, Chien- Hsing Lin, Keh-Ming Wu, Ming-Shian Lin, Ih-Jen Su and Shih-Feng Tsai: Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan. Evolutionary Bioinformatics(2016)
  11. Chen YT, Siu LK, Tsai YK, Lin FM, Koh TH, Chen JH: A Common Flanking Region in Promiscuous Plasmids Encoding blaNDM-1 in Klebsiella pneumoniae Isolated in Singapore. Microbial Drug Resistance(2016)
  12. Huang TW, Lauderdale TL, Liao TL, Hsu MC, Chang FY, Chang SC, Khong WX, Ng OT, Chen YT, Kuo SC, Chen TL, Mu JJ, Tsai SF: Effective transfer of a 47 kb NDM-1-positive plasmid among Acinetobacter species. Journal of Antimicrobial Chemotherapy(2015)
  13. Chang JW, Hou MM, Hsieh JJ, Cheung YC, Wang HM, Chen JS, Wang CH,Chen CH, Yeh KY, Ou LY, Hsieh CH, Wu HDI, Chen YT, Chang IC, Huang SF: Early radiographic response to epidermal growth factor receptor- tyrosine kinase inhibitor in non-small cell lung cancer patients with epidermal growth factor receptor mutations: A prospective study. Biomedical Journa(2015)
  14. Chen CJ, Wu TL, Chen YT, Fung CP, Chuang YC, Lin JC, and Siu LK: Closely related NDM-1-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. PlosONE(2014)
  15. Tang HJ, Chen YT, Chiang T, Fung CP, Chuang YC, Siu LK: Identification of the first imported KPC-3 Klebsiella pneumoniae from the USA to Taiwan. International Journal of Antimicrobial Agents(2014)
  16. Lai YC, Lin AC, Chiang MK, Dai YH, Hsu CC, Lu MC, Liau CY, and Chen YT: Genotoxic Klebsiella pneumoniae in Taiwan. PlosONE(2014)
  17. Chen YT, Lin JC, Fung CP, Lu PL, Chuang YC, Wu TL, Siu LK: KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. Journal of Antimicrobial Chemotherapy
  18. Lai YC, Lin AC, Chiang MK, Dai YH, Hsu CC, Lu MC, Liau CY, and Chen YT*. Genotoxic Klebsiella pneumoniae in Taiwan. PlosONE. 2014. 9:e96292.
  19. Chen YT*, Lin JC, Fung CP, Lu PL, Chuang YC, Wu TL, Siu LK*. KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. Journal of Antimicrobial Chemotherapy. 2013. 69:628-631.
  20. Huang TW, Wang JT, Lauderdale TL, Liao TL, Lai JF, Tan MJ, Lin AC, Chen YT*, Tsai SF, Chang SC*. Complete sequences of two plasmids in an NDM-1 positive Klebsiella oxytoca isolated from Taiwan. Antimicrobial Agents and Chemotherapy. 2013. 57:4072-4076.
  21. Huang TW, Chen TL, Chen YT*, Lauderdale TL, Liao TL, Lee YT, Chen CP, Liu YM, Lin AC, Chang YH, Wu KM, Kirby R, Lai JF, Tan, MC, Siu, LK, Chang CM, Fung CP, Tsai SF. Copy Number Change of the NDM-1 Sequence in a Multidrug-Resistant Klebsiella pneumoniae Clinical Isolate. PlosONE. 2013. 8:e62774.
  22. Chen YT*, Lin AC, Siu LK, Koh TH. Sequence of closely related plasmids encoding blaNDM-1 in two unrelated Klebsiella pneumoniae isolates in Singapore. PlosONE. 2012. 7:e48737.
  23. Lin AC, Liao TL, Lin YC, Lai YC, Lu MC, Chen YT*. Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-negative K1 Clinical Strain. Journal of Bacteriology. 2012. 194:6316.
  24. Liao TL, Chen SY, Lin AC, Huang TW, Lauderdale TL, Tsai SF, and Chen YT*. Complete genome sequence of Klebsiella oxytoca E718, a New Delhi Metallo-beta-lactamase-1-producing nosocomial strain. Journal of Bacteriology. 2012. 194:5454.
  25. Huang SH, Wang CK, Peng HL, Wu CC, Chen YT*, Hong YM, and Lin CT. Role of the small RNA RyhB in the Fur regulon in mediating the capsular polysaccharide biosynthesis and iron acquisition systems in Klebsiella pneumoniae. BMC Microbiology. 2012. 12:148.
  26. Huang TW, Chen FJ, Miu WC, Liao TL, Lin AC, Huang IW, Wu KM, Tsai SF, Chen YT*, and Lauderdale TL*. Complete Genome Sequence of Staphylococcus aureus M013, a pvl-positive ST59:SCCmec V Strain Isolated in Taiwan. Journal of Bacteriology. 2012. 194:1256-1257.
  27. Chen YT*, Chang WC J, Liu HP, Yu TF, Chiu YT, Hsieh JJ, Chen YT, Chen YR, Wu I HD, Huang SF*. Clinical implications of high MET gene dosage in non-small cell lung cancer patients without prior tyrosine kinase inhibitor treatment. Journal of Thoracic Oncology. 2011. 6:2027-2035.
  28. Chang JR, Lin CH, Tsai SF, Su IJ, Tseng FC, Chen YT*, Chiueh TS, Sun JR, Huang TS, Chen YS, and Dou HR*. Genotypic analysis of genes associated with transmission and drug resistance in the Beijing lineage of Mycobacterium tuberculosis. Clinical Microbiology and Infection. 2011. 17:1391-1396.
  29. Hoang KC, Lai TH, Lin CS, Chen YT*, and Liau CY*.The Chitinolytic Activities of Streptomyces sp. TH-11. International Journal of Molecular Sciences. 2011. 12:56-65.
  30. Liu HP, Wu HDI, Chang JWC, MD, Wu YC, Yang HY, Chen YT*, Hsieh WY, Chen YT, Chen YR, Huang SF*. Prognostic implications of EGFR and KRAS gene mutations, and EGFR gene copy numbers in Surgically Resectable Non-Small Cell Lung Cancer Patients in Taiwan. Journal of Thoracic Oncology. 2010. 5:1175-1184.
  31. Tang HL, Chiang MK, Liou WJ, Chen YT*, Peng HL, Chiou CS, Liu KS, Lu MC, Tung KC and Lai YC*. Correlation between Klebsiella pneumoniae carrying pLVPK-derived loci and abscess formation. European Journal of Clinical Microbiology & Infectious Diseases. 2010. 29:689-698.
  32. Shu HY, Fung CP, Liu, YM, Wu, KM, Chen YT*, Li LH, Liu TT, Kirby R, and Tsai SF*. Genetic diversity of capsular polysaccharide biosynthesis in Klebsiella pneumoniae clinical isolates. Microbiology. 2009. 155:4170-4183.
  33. Wu KM, Li LH, Yan JJ, Tsao N, Liao TL, Tsai HC, Fung CP, Chen HJ, Liu YM, Wang JT, Fang CT, Chang SC, Shu HY, Liu TT, Chen YT*, Shiau YR, Lauderdale TL, Su IJ, Kirby R* and Tsai SF. Genome Sequencing and Comparative Analysis of Klebsiella pneumoniae NTUH-K2044, a Strain Causing Liver Abscess and Meningitis. Journal of Bacteriology. 2009. 191:4492-4501.
  34. Chen YT*, Liao TL, Liu YM, Lauderdale TL, Yan JJ, and Tsai SF. Mobilization of qnrB2 and ISCR1 in Plasmids. Antimicrobial Agents and Chemotherapy. 2009. 53:1235-1237.

 

Conference (*Invited speaker)
  1. YT Chen, CA Liao, XY Huang, AC Lin, TL Lauderdale: Identification and genomic analyses of an emerging virulent Klebsiella pneumoniae K62 clone in Taiwan. The 41th Annual Meeting of the Molecular Biology Society of Japan Yokohama/Japan
  2. Ying-Tsong Chen, Tsai-Ling Lauderdale, Xin-Ying Huang, Ann-Chi Lin: Population genetics studies of Klebsiella pneumoniae genotoxic K62 type in Taiwan. 4th Annual Microbiology & Infectious Diseases Asia Congress 7th Annual Next Generation Sequencing & Clinical Diagnostics Asia Congress 5th Annual Single Cell Analysis Asia Congress Singapore
  3. Yu-Han Liu, Ann-Chi Li, Chun-Hong Chen, Ying-Tsong Chen: Genomics Studies on the Ae. albopictus mitochondria. IMGM Poster Day NHRI/Taiwan
  4. XY Huang, AC Lin, TL Lauderdale, YT Chen: Complete Sequencing and Analyses of a Genotoxic Klebsiella pneumoniae K62 strain. 3rd Annual Microbiology & Infectious Diseases Asia Congress / 6th Annual Next Generation Sequencing Asia CongressSingapore
  5. YT Chen: 克雷白氏肺炎菌的基因體學研究(invited speech). 2016農業暨生物資訊分析前瞻與新知研討會
  6. YT Chen: 基因毒性與台灣的克雷白氏肺炎菌(invited speech). 2015細菌學研討會
  7. 洪義閔，陳盈璁: 克雷白氏肺炎桿菌基因體小島模組間交互作用與功能之探討. 2015細菌學研討會
  8. YT Chen: Genotoxic Klebsiella pneumoniae in Taiwan (invited speech). International Symposium on Evolutionary Genomics and Bioinformatics
  9. YT Chen: Functional Genomics Studies on Genotoxic Klebsiella pneumoniae in Taiwan (invited speech). 2014 Life Taiwan User Conference -The future of laboratory developed testing – The total solution powered by Roche
  10. TL Liao; TW Huang; KM Wu; CT Lee; YM Liu; AC Lin; YT Chen; TT Liu; N Bisharat; LI Hor; SF Tsai: A single chromosome of 5.2 Mb in Vibrio vulnificus biotype 3 strain CECT7356. IMGM Poster Day NHRI/Taiwan
  11. YC Lai; AC Lin; YT Chen: Genotoxicity of Klebsiella pneumoniae in Taiwan. IMGM Poster Day NHRI/Taiwan
  12. 洪義閔，黃意真，張詠鈞，賴怡琪，林靖婷，陳盈璁: 克雷白氏肺炎桿菌基因體小島KPHPI208的功能性研究. 2014細菌學研討會
  13. Genotoxicity of Klebsiella pneumoniae in Taiwan (2014) 2014 IMGM Poster Party, IMGM, NHRI, Taiwan
  14. A single chromosome of 5.2 Mb in Vibrio vulnificus biotype 3 strain CECT7356 (2014) IMGM Poster Party, IMGM, NHRI, Taiwan
  15. Complete genome sequence of Klebsiella pneumoniae 1084 and the identification of a genotoxin-encoding virulence genomic island (2013) 2013 IMGM Poster Party, IMGM, NHRI, Taiwan
  16. Missing pieces in Klebsiella pneumoniae genomes (2012) 2012第廿八屆生物夏令營
  17. Towards a database of antimicrobial resistance genes (2012) 2012 UST-UCSD I-RICE Symposium and Joint Biomedical Informatics Symposium between National Yang-Ming University (NYMU), and University of California, San Diego (UCSD)
  18. Using nalidixic acid-susceptibility and borderline resistance to identify plasmid-mediated quinolone resistance (PMQR) in Salmonella in Taiwan. (2012) 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans and the Environment, France. June 26-30.
  19. Multiplex sequencing of antimicrobial resistance genes by PGM. (2012) 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans and the Environment, France. June 26-30.
  20. Application of 454 in Bacterial Genomics (2012) 生物資訊研究中心學術研討會 國立交通大學 (受邀演講)
  21. Complete Sequencing and Annotation of Klebsiella oxytoca E718. (2012) 轉譯醫學基因體蛋白質體之臨床應用學術研討, TaiChung, Taiwan. May 12.
  22. Missing Pieces in Klebsiella pneumoniae genomes. (2012) 轉譯醫學基因體蛋白質體之臨床應用學術研討, TaiChung, Taiwan. May 12.
  23. Complete Sequencing and Annotation of MRSA strain M013 from Taiwan. (2012) 轉譯醫學基因體蛋白質體之臨床應用學術研討, TaiChung, Taiwan. May 12.
  24. Comparative analysis of three NDM-1 positive plasmids using personal sequencers. (2012) 2012 NHRI Research Day, Zhunan, Taiwan. March 22.
  25. 遺失的克雷白氏桿菌DNA序列 (2011) 2011年克雷白氏桿菌學術研討會 國家衛生研究院感染症與疫苗研究所與國防醫學院 (受邀演講)
  26. PMQR in Taiwan (2010) 系統生物學研討會 國家衛生研究院 (專題演講)

Chen, Yu-Ting

Experience

Title Department Period
Associate Professor NCHU, Institute of Genomics and Bioinformatics 2019/08-present
Assistant Professor NCHU, Institute of Genomics and Bioinformatics 2013/03-2019-07
Section Director NCHU, Biotechnology Center Reference and Consultation Section 2008/08 – 2009-03
Assistant Professor NCHU, Biotechnology Center 2008/08 – 2009-03
Assistant Professor NCHU, Biotechnology Center 2006/08 – 2008/07
Adjunct Assistant Professor Hsing Wu University, General Education Center 2005/09 – 2006/06
Visiting Scholar United States Department of Agriculture 2005/03 – 2005/08
Postdoctoral Research Fellow Academia Sinica, Institute of Plant and Microbial Biology 2003/03 – 2006/07
PhD National Defense Medical Center, Graduate Institute of Life Sciences 1995/08 – 2003/02
M.S. TTU,  Department of Chemical Engineering 1993/09 – 1995/06
B.S. TTU, Department of Chemical Engineering and Biotechnology 1989/09 – 1993/06

Research

Research Interests
  1. Molecular biology
  2. Plant Transgenic
  3. Plant Functional Genomics
  4. Bioenergy

Lectures:

Course

Biochemistry, Experimental Biochemistry, Applied Genomics and Bioinformatics: Lecture and Experiment, Applied Genomics and Bioinformatics: Lecture and Experiment,Functional Biology
,Plant Gene Cloning Techniques Workshop, Special Topics in Plant Gene Transformation, To Construct and Analyze on Genomics Database,Special Topics in Lipid Biotechnology

Publications

Journal (*Corresponding author)
  1. Li JR, Liu CC, Sun CH, Chen YT*: Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells. BMC Genomics(2019)
  2. Chen YT†, Chang CC†, Chen CW, Chen KC, Chu YW: MADS-box gene classification in angiosperms by clustering and machine learning approaches. Front Genet(2019)
  3. Liu CH, Chen YT, Hou MH, Hu NJ, Chen CS*, Shaw JF*: Crystallographic analysis of the Staphylococcus epidermidis lipase involved in esterification in aqueous solution. Acta Cryst(2018)
  4. Chen YT†, Hong PF†, Wen L†, Lin CT*: Molecular cloning and characterization of a thioredoxin from Taiwanofungus camphorate. Bot Stud(2014)
  5. Huang CY†, Chen YT†, Wen L†, Sheu DC, Lin CT*: A peroxiredoxin cDNA from Taiwanofungus camphorata: role of Cys31 in dimerization. Mol Biol Reports(2014)
  6. Chuang HH, Cheng CY, Chen YT*, Shaw JF*: Novel highly active recombinant glutaredoxin from Chlorella sorokiniana T-89. J Agric Food Chem(2014)
  7. Chuang HH, Cheng CY, Chen YT, Shaw JF*. (2014) Novel Highly Active Recombinant Glutaredoxin from Chlorella sorokiniana T-89. J Agric Food Chem. 2014 Jan 14. J Agric Food Chem. 2014 Jan 29;62(4):927-933.
  8. Huang CY#,Chen YT, Wen L#, Sheu DC, Lin CT*. (2014) A peroxiredoxin cDNA from Taiwanofungus camphorata: role of Cys31 in dimerization. Mol Biol Rep. 41(1):155-164.
  9. Chen YT, Chin-Hui Shen, Wen-Dar Lin, Hsiu-An Chu, Bau-Lian Huang, Ching-I Kuo, Kai-Wun Yeh*, Li-Chun Huang*, and Ing-Feng Chang* (2013) Small RNAs of Sequoia sempervirens during rejuvenation and phase change. Plant Biology 15(1):27-36 (SCI)
  10. Ko CY, Lai YL, Liu WY, Lin CH, Chen YT, Chen LF, Lin TY*, Shaw JF*. (2012) Arabidopsis ENDO2: Its catalytic role and requirement of N-glycosylation for function. J Agric Food Chem. 60 (20), 5169–5179 (SCI)
  11. Chen PT, Chiang CJ, Chen YT, Lin HC, Liu CH, Chao YP*, Shaw JF*. (2012) Strategy for stable and high-level expression of recombinant trehalose synthase in Escherichia coli. J Agric Food Chem. 60 (23), 6063–6068 (SCI)
  12. Chu HA, Chang IF, Shen CH, Chen YT, Wang HT, Huang LC*, and Yeh KW* (2012) Photosynthetic properties and photosystem stoichiometry of in vitro-grown juvenile, adult, and rejuvenated Sequoia sempervirens (D. Don) Endl. Botanical Studies. 53:3.1 (SCI)
  13. Huang LC, Hsiao LJ, Pu SY, Kuo CI, Huang BL, Tseng TC, Huang HJ*, Chen YT(2012) DNA Methylation and genome rearrangement characteristics of Phase change in cultured shoots of Sequoia sempervirens. Physiola Planta 145: 360-368.(SCI)
  14. Chang PC, Pan WJ, Chen CW, Chen YT and Chu YW* (2012) DEsi: A design engine of siRNA that integrates SVMs prediction and feature filters. Biocat Agric Biotech 1: 129-134.
  15. Chuang HH, Chen PT, Wang WN, Chen YT*, Shaw JF* (2011) Functional proteomic analysis of rice bran esterases/lipases and characterization of a novel recombinant esterase. J Agric Food Chem. 2011 Mar 9;59(5):2019-25.
  16. Chang IF, Chen PJ, Shen CH, Hsieh TJ, Hsu YW, Huang BL, Kuo CI, Chen YT, Chu HA, Yeh KW, Huang LC (2010) Proteomic profiling of proteins associated with the rejuvenation of Sequoia sempervirens (D. Don) Endl. Proteome Science 8:64.
  17. Chen YT, Fang QS, Chiang CH, Yeh SD, Wu HW, Yu TA (2010) Transgenic Eustoma grandiflorum expressing the bar gene are resistant to herbicide Basta®. PCTOC: J Plant Biotech. 102 (3): 347-356. (SCI)
  18. Liau YJ, Chen YT, Lin CY, Huang JK, Lin CT (2010) Characterisation of 2-Cys peroxiredoxin isozyme (Prx1) from Taiwanofungus camphorata (Niu-chang-chih): Expression and enzyme properties. Food Chem. 119: 154-160. (SCI)
  19. Chen YT, Chen LFO, Shaw JF* (2008) Senescence associated genes in harvested broccoli florets, Plant Science 175, 137-144. (SCI)
  20. Chen YT, Chen HH, Uchimiya H, Chu MJ, Chiou YS, Shaw JF, Huang LC (2007) Prolonging the longevity of Cymbidium flowers through genetic transformation. Acta Horticulture. 738: 545-548.
  21. Lee, LC, Chen YT, Yen CC, Chiang TCY, Tang SJ, Lee GC* and Shaw JF* (2007) Altering the substrate specificity of Candida rugosa LIP4 by engineering the substrate binding sites. J. Agric. Food Chem. 55(13); 5103-5108. (SCI)
  22. Chen YT, Hsu LH, Huang IP, Tsai TC, Lee GC, and Shaw JF* (2007) Gene Cloning and Characterization of a Novel Recombinant Antifungal Chitinase from Papaya (Carica papaya) J. Agric. Food Chem. 55:714-722. (SCI)
  23. Wang YT, Yang CY, Chen YT, Lin Y and Shaw JF* (2004) Characterization of senescence-associated proteases in postharvest broccoli florets. Plant Physiol. Biochem. 42:663-670. (SCI)
  24. Chen LFO, Huang JY, Wang YH, Chen YT and Shaw JF* (2004) Ethylene insensitive and post-harvest yellowing retardation in mutant ethylene response sensor (boers) gene transformed broccoli (Brassica olercea var. italica) Mol. Breed. 14:199-213. (SCI)
  25. Yang CY, Chu FH, Wang YT, Chen YT, Yang SF, and Shaw JF* (2003) Novel broccoli 1-aminocyclopropane-1-carboxylate oxidase gene (Bo-ACO3) associated with the late stage of postharvest floret senescence. J. Agric. Food Chem. 51:2569-2575. (SCI)
  26. Chen YT, Lee IR, Yang CY, Wang YT, Yang SF, and Shaw JF* (2003) A novel papaya 1-aminocyclopropane-1-carboxylate oxidase gene (CP-ACO2) associated with late-stage senescence. Plant Science 164:531-540. (SCI)
  27. Lin CT, Lin MT, Chen YT and J.F. Shaw*. 1995. The gene structure of Cu/Zn-superoxide dismutase from sweet potato. Plant Physiol. 108: 827-828. (SCI)
  28. Lin CT, Lin MT, Chen YT and J.F. Shaw*. 1995. Subunit interaction enhances enzyme activity and stability of cytosolic Cu-Zn-superoxide dismutase. Plant Mol. Biol. 28: 303-311. (SCI)

 

Conference (*Invited speaker)
  1. Lin TW, Kou YT, Liu CH, Lin WT, Chen YT*: Build up the highest astaxanthin production platform by using optima cultural condition analysis of Chlorella. sp. DT and the tr ansgenic approach. 14th International Symposium on Agricultural Biocatalysis and Biotechnology
  2. Liu CH, Chen YT, Chen CS, Shaw JF: Lipase cloned from Staphylococcus epidermidis: crystallization and X-ray crystallographic analysis. 13th International Symposium on Agricultural Biocatalysis and Biotechnology
  3. Liu JH*, Nien CY, Chang CW, Hong CS, Chang SW, Chen YT and Shaw JF: Contribution of surface residues on the thermostability of the trehalose synthase from Picrophilus torridus. 13th International Symposium on Agricultural Biocatalysis and Biotechnology
  4. Liu CH, Chen PT, Hsu FY, Chen YT, Chen CS, Shaw JF: Thermal stable esterase (rGtEst1) of Geobacillus thermodnitrificans PS01.12th Cross-Strait International Conference on Symposium on Plant Molecular Biology and Biotechnology
  5. ZengWW, Chen TC, Wang SY, Liu CH, Chen YT*: Identification of an anti-proliferative 2,4-dimethoxy-6-methylbenzene- 1,3-diol from Antrodia cinnamomea. 12th Cross-Strait International Conference on Symposium on Plant Molecular Biology and Biotechnology
  6. Liu JH, Chuang HH, Chen TW, Shaw JF, and Chen YT*: Catalytic related amino acid of glutaredoxin from Chlorella sorokiniana 12th Cross-Strait International Conference on Symposium on Plant Molecular Biology and Biotechnology
  7. Zeng WW, Wang SY, Liu CH, Chen YT*: Identification of a dual-function phenolic compound with anti-oxidant and anti-proliferative activities in Antrodia cinnamome. 2016中草藥在抗老化植物新藥之應用趨勢研討會
  8. Chiu CM, Chao HY, Chen YT*: Physiological Function of GDSL-lipase in Rice (Oryza sativa). The 10th International Symposium on Agricultural Biocatalysis and Biotechnology
  9. Hsu FY, Liu CH, Chen YT, Chen PT, Chen CS, Shaw JF*: Gene analysis and Biochemical Characterization of a Novel Recombinant Lipase rGtLIP1 from Geobacillus thermodenitrificans PS01. The 10th International Symposium on Agricultural Biocatalysis and Biotechnology
  10. Chao HY, Chen YT*: Rice GDSL Lipase may Promote Grain Yield and Salt Resistance. The 10th International Symposium on Agricultural Biocatalysis and Biotechnology
  11. Huang YH, Zeng WW, Wang WN, Chen YT*: Improvement of the Antioxidant Activity of Antrodia cinnamomea by Medium Modification and Adding Methanolic Extract of Cinnamomum kanehirae The 10th International Symposium on Agricultural Biocatalysis and Biotechnology
  12. Kuo YT, Lee JH, Chen YT*: Beta-Carotene Ketolase of Chlorella. sp. DT Cloning and Overexpression for Astaxanthin Production in Transgenic Plant. The 10th International Symposium on Agricultural Biocatalysis and Biotechnology
  13.  Hsu-Han Chuang, Chen YT and Jei-Fu Shaw (2013) (Invited Lecture) Study the gene functions of rice lipases/esterases by using functional proteomics approaches. The 9th International Symposium on Agricultural Biocatalysis and Biotechnology. Piešťany, Slovak Republic, October 13 – 16, 2013.
  14.  Lee JH, Chen YT, Chuang HH, Chiu JM (2012) Cloning and characterization cinnamyl alcohol dehydrogenase from Chlorella sorokiniana T89. International Symposium on Oil Food Biotechnology. Kao-Hsiung, Taiwan, Dec 21-22. (Excellent Poster Award)
  15.  Zeng WW, Wang WN, Shaw JF*, and Chen YT (2012) Improvement of the antioxidant activity of Antrodia Cinnamomea by medium modification and adding methanolic extract of Cinnamomum kanehirae leaf. International Symposium on Oil Food Biotechnology. Kao-Hsiung, Taiwan, Dec 21-22. (Excellent Poster Award)
  16.  Cheng CY, Shaw JF*, Chen YT (2012) Cloning and characterization of glutaredoxin from Chlorella sorokiniana T89. International Symposium on Oil Food Biotechnology. Kao-Hsiung, Taiwan, Dec 21-22. (Excellent Poster Award)
  17.  Chen PT, Chiang CJ, Chen YT, Lin HC, Liu CH, Chao YP* and Shaw JF* (2012) Chromosome engineering Escherichia coli host for the efficient production of Picrophilus torridus trehalose synthase. International Symposium on Oil Food Biotechnology. Kao-Hsiung, Taiwan, Dec 21-22. (Best Poster Award)
  18.  Chuang HH, Liu CH, Chen YTand Shaw JF (2012) (Invited Lecture) Study rice estersaes/lipases by functional proteomics approach. International Symposium on Oil Food Biotechnology. Kao-Hsiung, Taiwan, Dec 21-22.
  19.  Jei-Fu Shaw* and Chen YT (2012) Biocatalysis in Agricultural Biotechnology. BIT’s 3rd Inaugural Symposium on Enzymes & Biocatalysis-2012 (SEB-2012), Xi’an, China. April, 25-28.
  20.  Chuang HH, Chen YT and Shaw JF (2011) (Invited lecture) Functional proteomic analysis and characterization of a novel rice bran esterases/lipases. The 7th International Symposium on Agricultural Biocatalysis and Biotechnology. Kyoto, Japan. Oct 10-13.
  21. Bezirganoglu I, Chen YT, Chuang HH, Hwang SY, Shaw JF* (2010) Improve the resistance to Rhizoctonia solani of transgenic melon (Cucumis melo silver light L.) plants with overexpressing chitinases. The 6th International Symposium on Biocatalysis and Biotechnology. Seoul, Korea. Nov 17-19.
  22. Yu TA, Chen YT*, Chiang CH, Wang PT, Chang YL, Shih HD, Yeh SD, Shaw JF* (2010) (Invited lecture) Transgenic melon plants expressing antifungal AFP3 protein develop resistance to fungal diseases. The 6th International Symposium on Biocatalysis and Biotechnology. Seoul, Korea. Nov 17-19.
  23. Chuang HH, Chen YT*, Shaw JF* (2010) (Invited lecture) Characterization and application of the recombinant rice bran lipase. 2010 Lipid Science Division Symposium at the Annual Meeting of Korean Society of Food Science and Technology. Inchon, Korea. Jun 16-18.
  24. Bezirganoglu I, Chen YT, Chang YL, Shaw JF* (2009) Melon transformation using antifungal protein & chitinase gene to against fungal disease Rhizoctania Solani. The 5th International Symposium on Biocatalysis and Biotechnology. Taiwan. Nov 18-20. (Excellent Poster Award)
  25. Chen YT and Shaw JF (2008) (Invited lecture) NCHU/CUHK Bilateral Symposium on Plant Biotechnology. Dec 17-23, Taichung, Taiwan.
  26. Chen YT and Shaw JF (2007) (Invited Speech) Functional genes and biotechenology. The Sixth Cross-Strait Symposium on Plant Molecular Biology and Biotechnology. Jul. 3-7, Hong Kong, China
  27. Chen YT and J.F. Shaw (2007) (Organizer and Invited Speech) Papaya functional genomics and biotechnological application. 3rd Internatrional Symposium on Biocatalysis amd Biotechnology. Nov. 28-30, Taichung, Taiwan
  28. Lee LC, Chen YT, Yen CC, Tang SJ, Lee GC and Shaw JF (2007) Altering the Substrate Specificity of Candida rugosa LIP4 by Engineering the Substrate-Binding Sites. 3rd Internatrional Symposium on Biocatalysis and Biotechnology. Nov. 28-30, Taichung, Taiwan.
  29. Chen YT, and Shaw JF (2007) (Organizer and Invited Speech) Papaya functional genomics and biotechnological application. 3rd Internatrional Symposium on Biocatalysis amd Biotechnology. Nov. 28-30, Taichung, Taiwan
  30. Chen YT and Shaw JF (2007) (Invited Speech) The Application of Functional Genomics Study on Papaya and Its Implication in Fruit Industry. The International Symposium on Bio-industry Development and Post-graduate Workshop, Dec. 4-7, Taichung, Taiwan.
  31. Chou YF, Chen HH, Chen YT, Shaw JF (2006) (Invited oral presentation) Molecular characterization of three broccoli chloropyllase genes, differentially regulated by ethylene. 7th International Symposium on the Plant Hormone Ethylene. June 18-22, Pisa, Italy.
  32. Chen YT, Huang IP, Shu LH, Shaw JF (2006) Cloning and characterization of ethylene-upregualted chitinase from papaya. 7th International Symposium on the Plant Hormone Ethylene. June 18-22, Pisa, Italy.
  33. Chen YT, Chen HH, Uchimiya H, Chu MJ, Chiou YS, Shaw JF, Huang LC (2005) (Invited oral presentation) Prolonging the longevity of Cymbidium flowers through genetic transformation. Proceeding of ISHS on the 3rd International Symposium on Biotechnology of Temperate Fruit Crops and Tropic species. October 10-14, USA.
  34. Chen YT (2005) (Invited speech) Papaya fruit maturation and ripening associated gene. April 19, USDA, Beltsville, USA.
  35. Chen YT, Chou TL, Yang CY, Kao CY, Lai HY, Jian WT, Shaw JF (2004) (Invited oral presentation) Papaya fruit maturation and ripening associated gene. International Symposium on Plant Functional Genomics. WA-06, June 6-11, Verona, Italy.
  36. Chen YT, Chou TL, Yang CY, Kao CY, Lai HY, Jian WT, Shaw JF (2003) Papaya fruit maturation and ripening associated gene. International Symposium on Plant Functional Genomics. A17, Nov 17-19, Taipei, Taiwan.
  37. Chen YT, Lee IR, Yang CY, Shaw JF (2001) Differential expression of the 1-aminocyclopropane-1-carboxylate oxidase gene family of papaya. 第十六屆生物醫學聯合年會生物化學及分子生物學學會壁報論文 P99, Mar, 24-25, Taipei, Taiwan。
  38. Chen YT and Shaw JF (2001) (Invited lecture) Papaya ACC oxidases. The 2nd Internationtional Symposium on Biotechnology of Tropical and Subtropical Species. Nov. 5-9.Taipei, Taiwan.
  39. Chen YT, Lee IR, Yang CY, Shaw JF (2000) Differential expression of the papaya 1-aminocyclopropane-1-carboxylate oxidase gene family. Symposium on Plant Sciences for 21st Century. C10. pp56. Nov. 9-10, Taipei, Taiwan.
  40. Yang CY, Lin Y, Chu FH, Chen YT, Lee YR, Shaw JF (2000) Senescemce associated genes of broccoli florets. Symposium on Plant Sciences for 21st Century. B5. pp34. Nov. 9-10, Taipei, Taiwan.
  41. Chen YT and Lin CT (1995) Purification and characterization of two isozymes of Cu/Zn-SOD from sweet potota tuberous root.農化學會第三十三次大會論文宣讀，1995。
  42. Chen YT and Lin CT (1995) Cloning and structure analysis of Cu/Zn-SOD gene from sweet potato. 農化學會第三十三次大會論文宣讀，1995。
  43. Chen YT and Lin CT (1995) Over expression of sweet potato cytosolic Cu/Zn-SOD in E. coli. 農化學會第三十三次大會論文宣讀，1995。
Books
  1. 陳玉婷、 陳榮芳、黃麗春、蕭介夫 (2004) 植物基因轉殖在植物保鮮儲運上之應用，教育部植物生物技術教學資源中心主編—植物基因轉殖之原理與應用，2004，p243-254。

 

Patent
  1. Shaw, J.F.,Y.T. Chen, L.H. Hus. Novel chitinase and use thereof. U.S.A patent US7670820, Jan 14, 2008-Jan 17, 2028 (March 2, 2010)

Liu, Jyung-Hurng

Lab: Structural Bioinformatics Lab

Honors:

Time Title
2006/07 “Glycosphingolipid-facilitated membrane insertion and internalization of cobra cardiotoxin: crystal structure of the cardiotoxin/sulfatide complex.”
中央研究院分子生物研究所 學生/助理/博士後申請出席國際學術會議獎助
2004/10 “Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli.”
國家同步輻射研究中心第十屆用戶年會暨研討會 學生口頭報告比賽第二名與壁報比賽佳作
2004/05 “Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli.”
第九屆生物物理新知研討會青年學子壁報論文獎第二名

Experience

Title Department Period
Joint Assistant Professor Graduate Institute of Biotechnology, NCHU 2008/08 – now
Assistant Professor Institute of Genomics and Bioinformatics 2009/02 – now
Assistant Professor Biophysics Society of R.O.C. 2007/05 –
Adjunct Assistant Professor Graduate Institute of Biotechnology, NCHU 2007/02 –
Joint Assistant Professor Department of Life Sciences, NCHU 2007/02 -now
Assistant Professor Biotechnology Center, NCHU 2008/08 -now
Postdoctoral Fellow Institute of Molecular Biology, Academia Sinica 2006/01 – 2007/01
Ph.D. Graduate Institute of Life Science, National Defense Medical Center and Academia Sinica 2001/08 – 2005/12
M.S. Institute of Genetics, National Yang Ming University 1995/09 to 1997/06
B.P. School of Pharmacy, Taipei Medical College 1991/09 to 1995/06

Professional

Content
  1. 美國結晶學會暑期訓練課程「Summer course in crystallography」蛋白質結構與功能(Structure and function of proteins) 美國喬治亞大學 (University of Georgia)(2001/06)

Speech

Content
  1. “Glycosphingolipid-facilitated membrane insertion and internalization of cobra cardiotoxin: crystal structure of the cardiotoxin/sulfatide complex.”美國結晶學會 2006 年年會「環太平洋地區X光與中子設施的科學研究」議程 (2006/07)

Lectures

Course [download course materials]
  • [Undergraduate courses] Biochemistry
  • [Undergraduate courses] Biotechnology
  • [Graduate courses] Seminar
  • [Graduate courses] Advanced Biochemistry
  • [Graduate courses] Applied Genomics and Bioinformatics: Lecture and Experiment
  • [Graduate courses] Protein Engineering
  • [Graduate courses] Protein Molecular Simulation & Rational Drug Design
  • [Grad. Inst. Biotech] Special Topics in Biochemistry
  • [Grad. Inst. Biotech] Special Topics in Biotechnology
  • [General education Lecture] Life Sciences & Life
  • [Summer Core Credit Course] Application and Experiment of Bioinformatics in Life Science
  • [Summer Core Credit Course] Functional Proteomics and Experiment
  • [Summer Core Credit Course] Genomics

 

Expertise
  1. Protein Structure Analyze
  2. Structural Bioinformatics
  3. X-ray Biomolecular Crystallography

Research

Lab research [details]

Research Interests:

 

My research interests are in the structure and function of a wide range of important biological macromolecules, including:

I. Chromatin structure remodeling mechanism in yeast

The eukaryotic genome is packaged into chromatin, which can inhibit the accessibility of certain DNA binding factors to their cognate sites in vivo. However, changes in chromatin structure play an important role in processes such as transcription, replication, DNA damage repair, and recombination. Two such ATP-dependent chromatin remodeling complexes in yeast Saccharomyces cerevisiae include the SWI/SNF complex and the RSC complex (Remodels the Structure of Chromatin). Of the two, only RSC is essential for viability, serving an important function in cell cycle progression from G2 to M. RSC is an abundant complex of at least 16 subunits, which was purified on the basis of homology of several of its subunits to those of the SWI/SNF complex.

 

II. JAK/STAT signaling pathway in fruitfly

The signal transduction pathway conducted by JAK (Janus Activated Kinases) and STAT(Signal Transducers and Activators of Transcription) plays a critical role in hematopoiesis and immune response, and mis-regulation of the pathways is associated with a wide range of immunologic diseases and to leukemia in humans. However, the structure/function relationship of the interaction between cytokine receptors, JAKs and STATs still remains largely elusive duo to the lack of structural information. In vertebrates, there are many ligands, receptors, JAKs and STATs making this signaling pathway very complex to be analyzed. By contrast, the JAK/STAT pathway in the fruitfly Drosophila melanogaster is less redundant offering a simpler model to study.

 

III. The telomere system of the Streptomyces linear plasmid SCP1

Linear plasmids and chromosomes of Streptomyces carry terminal proteins (TPs) covalently attached to the 5′ ends of the DNA. Most known telomeres are conserved in primary sequence and in the potential secondary structures formed during replication. The TP that caps these telomeres is also highly conserved and its coding gene, tpg, is present in most Streptomyces chromosomes and some linear plasmids. However, linear plasmid SCP1 of Streptomyces coelicolor contains atypical telomere sequences and no tpg homologue, and can replicate in the absence of tpg, suggesting that it carries a novel TP gene. A gene on SCP1 (designated tpc) encodes the TP that caps the SCP1 telomeres. The Tpc protein sequence does not resemble the Tpg proteins. A gene (designated tac) upstream of tpc was also required for replication of the SCP1 telomeres. These findings indicate that the Tac-Tpc system of SCP1 represents a novel telomere-capping system of Streptomyces linear replicons.

Publications

Journal (*Corresponding author)
  1. Liu, J.-H.*, Yang, J.-Y., Hsu, D.-W., Lai, Y.-H., Li, Y.-P., Tsai, Y.-R. and Hou, M.-H. (2019, Oct.) Crystal structure-based exploration of arginine-containing peptide binding in the ADP-ribosyltransferase domain of the type III effector XopAI protein(2019)
  2. Fang, Y.-T., Lai, W.-S., Liu, J.-H.*, Liu, Y.-C.*: Enhanced cecropin B2 production via chitin-binding domain and intein self-cleavage system. Biotechnology And Applied Biochemistry(2018)
  3. Shen, W.-F., Galula, J.U., Liu, J.-H., Liao, M.-Y., Huang, C.-H., Wang, Y.-C., Wu, H.-C., Liang, J.-J., Lin, Y.-L., Whitney, M.-T., Chang, G.-J., Chen, S.-R., Wu, S.-R., Chao, D.-Y.: Epitope resurfacing on dengue virus-like particle vaccine preparation to induce broad neutralizing antibody. Elife(2018)
  4. Chiu, H.-C., Huang, W.-R., Liao, T.-L., Chi, P.-I., Nielsen, B.L., Liu, J.-H., Liu, H.-J.: Mechanistic insights into avian reovirus p17-modulated suppression of cell cycle CDK-cyclin complexes and enhancement of p53 and cyclin H interaction. Journal Of Biological Chemistry(2018)
  5. Lee, C.-Y., Lin, C.-C., Liu, Y.-L., Liu, G.-Y.*, Liu, J.-H.*, Hung, H.-C.*: Molecular interplay between the dimer interface and the substrate-binding site of human peptidylarginine deiminase 4. Scientific Report(2017)
  6. Li, C., Bai, X., Meng, R., Shaozhou, W., Zhang, Q., Hua, R., Liu, J.-H., Liu, M., Zhang, Y.*: Identification of a new broadly cross-reactive epitope within domain III of the duck Tembusu virus E protein. Scientific Reports(2016)
  7. Li, C., Liu, J., Shaozhou, W., Bai, X., Zhang, Q., Hua, R., Liu, J.-H.*, Liu, M.*, Zhang, Y.*: Epitope identification and application for diagnosis of duck Tembusu virus infections in ducks. VIRUSES-BASEL(2016)
  8. Kuo, T.-C., Li, L.-W., Pan, S.-H.*, Fang, J.-M.*, Liu, J.-H., Cheng, T.-J., Wang, C.-J., Hung, P.-F., Chen, H.-Y., Hong, T.-M., Hsu, Y.-L., Wong, C.-H., Yang, P.-C.: Purine-type compounds induce microtubule fragmentation and lung cancer cell death through interaction with katanin. Journal of Medicinal Chemistry(2016)
  9. Chen, J.-C., Liu, J.-H., Hsu, D.-W., Shu, J.-C., Chen C.-Y., Chen, C.-C.*: Methylatable signaling helix coordinated inhibitory receiver domain in sensor kinase modulates environmental stress response in Bacillus cereus. PLoS One(2015)
  10. Hsieh, J.-Y., Li, S.-Y., Tsai, W.-C., Liu, J.-H., Lin, C.-L., Liu, G.-Y.*, Hung, H.-C.*: A small-molecule inhibitor suppresses the tumor-associated mitochondrial NAD(P)+-dependent malic enzyme (ME2) and induces cellular senescence. Oncotarget(2015)
  11. Lin, H.-Y., Liu, J.-H., Cheng, K.-L., Lin, J.-Y., Liu, N.-R., Meng, M.-H.*: A novel binding of GTP stabilizes the structure and modulates the activities of human phosphoglucose isomerase/autocrine motility factor. Biochemistry and Biophysics Reports(2015)
  12. Hsieh, J.-Y., Li, S.-Y., Chen, M.-C., Yang, P.-C., Chen, H.-Y., Chan, N.-L.*, Liu, J.-H.*, Hung, H.-C.*: Structural characteristics of the nonallosteric human cytosolic malic enzyme. BIOCHIMICA ET BIOPHYSICA ACTAPROTEINS AND PROTEOMICS(2014)
  13. Hsieh, J.-Y., Liu, J.-H., Yang, P.-C., Lin, C.-L., Liu, G.-Y.*, Hung, H.-C.* (2014, Jun). :Fumarate analogs act as allosteric inhibitors of the human mitochondrial NAD(P)+-dependent malic enzyme.PLoS One
  14. 1. Chepyshko, H., Lai, C.-P., Huang, L.-M., Liu, J.-H., and Shaw, J.-F. (2012, Jul.) Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. BMC Genomics 13, 309 doi:10.1186/1471-2164-13-309 (SCI, IF2011=4.073 Times cited :8)
  15. Hsieh, J.-Y., Liu, J.-H., Fang, Y.-W., Hung, H.-C. (2009, May.) Dual roles of Lys57 at the dimer interface of human mitochondrial NAD(P)+-dependent malic enzyme. Biochem. J. 402, 201-9. (SCI, IF2007=4.009 Times cited :0)
  16. Li, T.-N., Chin, K.-H., Liu, J.-H., Wang, A H.-J., Chou, S.-H. (2009, May.) XC1028 from Xanthomonas campestris adopts a PilZ domain-like structure without a c-di-GMP switch. Proteins. 75, 282-8. (SCI, IF2007=3.354 Times cited :0)
  17. Chou, C.-C., Chang, C.-W., Liu, J.-H., Chen, L.-F., Hsiao, C.-D., Chen, H.-W. (2007, Sep.) Small Ubiquitin-like Modifier Modification Regulates the DNA Binding Activity of Glial Cell Missing Drosophila Homolog a. J. Biol. Chem. 282, 27239-49. (SCI, IF2006=5.808 Times cited :3)
  18. Wang, C.-H.*, Liu, J.-H.*, Lee, S.-C., Wu, W.-g., and Hsiao, C.-D. (2006, Jan.) Glycosphingolipid-facilitated membrane insertion and internalization of cobra cardiotoxin: the sulfatide/cardiotoxin complex structure in a membrane-like environment suggests a lipid-dependent cell-penetrating mechanism for membrane binding polypeptides. J. Biol. Chem. 281, 656-77.(SCI, IF 2006=5.808; Times cited: 15) *These authors contributed equally to this work.
  19. Liu, J.-H., Chang, T.-W., Huang, C.-Y., Chen, S.-U., Wu, H.-N., Chang, M.-C., Hsiao, C.-D. (2004, Nov.) Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli. J. Biol. Chem. 279, 50465-71. (SCI, IF2006=5.808 Times cited : 5)
  20. Forouhar, F., Huang, W.-N., Liu, J.-H., Chien, K.-Y., Wu, W.-g. and Hsiao, C.-D. (2003, Jun.) Structural basis of the membrane-induced cardiotoxin A3 oligomerization. J. Biol. Chem. 278, 21980-8. (SCI, IF2006=5.808 Times cited :21)[PDB]
  21. Liu, J. H., Liao, Y. D., Sun Y. J. (2001, Nov.) Crystallization and preliminary X-ray diffraction analysis of cytotoxic ribonucleases from bullfrog Rana catesbeiana. Acta Crystallogr. D57, 1697-9. (SCI, IF2006=1.687 Times cited :0)

 

Conference (*Invited speaker)
  1. Liu, J.-H., Lee, Y.-P., Yang, J.-Y.: The Crystal Structure of the N-terminally Deleted Type III Effector protein XopAI. The 23th Biophysics Conference.
  2. Liu, J.-H., Lee, C.-Y., Lin, C.-C., Liu, Y.-L., Liu, G.-Y., Hung, H.-C.: Molecular Dynamics Study on the Interaction between Dimer Interface and Substrate-Binding Site of Human Peptidylarginine Deiminase 4. The 22th Biophysics Conference.
  3. Liu, J.-H.: Replica exchange molecular dynamics method for Trp-cage folding simulation in implicit solvent. The 20th Biophysics Conference.
  4. Peng, L.-W., Chen, Y.-T., and Liu, J.-H.: Crystallization of Dps protein from Klebsiella oxytoca The 20th NSRRC Users’ Meeting.
  5. Lin, C.-W., Hung, H.-C., and Liu, J.-H.: Crystallization of human cytosolic NADP+-dependent malic enzyme complexed with cofactor and substrates. The 20th NSRRC Users’ Meeting.
  6. Chen, C.-W., Shen, G.-H., Chen, J.-H., and Liu, J.-H.(2013, Nov) Virtual screening and experimental verification to identify potential inhibitors of the Erm(41) methyltransferase responsible for bacterial resistance against macrolide antibiotics. 台灣生物化學及分子生物學學會2013年冬令營. (Poster)
  7. Peng, L.-W., Chen, Y.-T. and Liu, J.-H.. (2013, Sep) Crystallization of β-lactamase like protein from Klebsiella oxytoca E718. The 19th NSRRC Users’ Meeting. (Poster)
  8. Liu, J.-H., Chen, C. K.-M., Chang, S.-W., Shaw, J.-F., Wang, A. H.-J., and Liu, J.-H. (2012, Oct.) Preliminary X-ray crystallographic analysis of trehalose synthase from Deinococcus radiodurans. The 18th NSRRC Users’ Meeting. (Poster)
  9. Chen, J.-W., Nien, C.-Y., Chen, C. K.-M., Chang, S.-W., Shaw, J.-F., Wang, A. H.-J., and Liu, J.-H.(2012, Oct.) Preliminary X-ray crystallographic analysis of trehalose synthase from Picrophilus torridus. The 18th NSRRC Users’ Meeting. (Poster)
  10. Nien, C.-Y., Cheng, C.-Y., Liu, J.-H., Shaw, J.-F., and Chen, Y.-T. (2012, May.) Crystal structure of glutaredoxin from Chlorella sorokiniana T-89. The 17th Biophysics Conference. (Poster)
  11. Hung, S.-J. and Liu, J.-H. (2012, May.) Design of an accurate predictor for the thermostable protein design in PERT server. The 17th Biophysics Conference. (Poster)
  12. Wu, J.-E., Chiu, S.-W., Yang, J.-Y., and Liu, J.-H. (2012, Mar.) Crystal structure of XopAI from Xanthomonas axonopodis pv. citri. 2012 International Conference on c-di-GMP and Xanthomonads. (Poster)
  13. Hung, S.-J. andLiu, J.-H. (2011, Dec.) PERT: an integrated informatics platform for thermostable protein design. 2011 Taiwan Enzyme Mechanism Conference. (Poster)
  14. Nien, C.-Y., Cheng, C.-Y., Shaw, J.-F., Chen, Y.-T., and Liu, J.-H. (2011, Oct.) Crystallization and preliminary X-ray crystallographic analysis of Chlorella glutaredoxin. The 17th NSRRC Users’ Meeting. (Poster)
  15. Wu, J.-E., Chiu, S.-W., Yang, J.-Y., and Liu, J.-H. (2010, Oct.) Crystallization and preliminary X-ray crystallographic analysis of XopAI from Xanthomonas axonopodis pv. citri. The 16th NSRRC Users’ Meeting. (Poster)
  16. Liu, J.-H., Hong, C.-S., Chang, S.-W., and Shaw, J.-F. (2009, Nov.) Investigation of the structural basis for thermostability of trehalose synthase from Picrophilus torridus. The 5th International Symposium on Biocatalysis and Biotechnology. (Poster)
  17. Hsu, Y.-J. and Liu, J.-H. (2009, Oct.) Effects of trimethylamine-N-oxide (TMAO) on the interactions of lysozyme in crystal. The 15th NSRRC Users’ Meeting. (Poster)