Institute of Biomedical Sciences (IBMS), Academia Sinica,
Room N121,
128 Sec.2,
Yen-Chiu-Yuan Rd.,
Nangkang District,
Taipei, Taiwan 115

Tel: +886-2-27899033
Fax:+886-2-27887641

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Principal Investigator
Dr. Ming-Jing Hwang Research Specialty

 

Ph.D. Univ. of Pittsburgh

FAX : 02-27887641
TEL : 02-27899033
E-mail : mjhwang@ibms.sinica.edu.tw

  • Bioinformatics
  • Computational Biology
  • Systems Biology
  • Recent Publications
    Recent Journal Papers (1997-2001; all but #3 are SCI journals)

    1. Tzou, W.-S., Hwang, M.-J., (1997) ¡§A Model for Fis N-Terminus and Fis-Invertase Recognition,¡¨ FEBS Lett.  401:1-5. (NSC 85-2311-B-001-030-B16).

    2. Yang, P.-K., Lee, C.-Y., Hwang, M.-J., (1997) ¡§Shaker Pore Structure as Predicted by Annealed Atomic Simulation Using Symmetry and Novel Geometric Restraints,¡¨ Biophys. J. 72:2479-2489  (NSC 85-2113-M-001-011 & 86-2314-B-001-035).

    3. Tzou, W.-S., Hwang, M.-J., (1997) "Introduction to Protein Structure Predictions," (in Chinese) Chemistry (The Chinese Chem. Soc., Taiwan China), 55:101-109.

    4. Peng, Z., Ewig, C.S., Hwang, M.-J., Waldman, M., Hagler, A.T., (1997) ¡§Derivation of Clase II Force Fields. 4. van der Waals Parameters of Alkali Metal Cations and Halide Anions,¡¨ J. Phys. Chem., 101: 7243-7252.

    5. Maple, J.R., Hwang, M.-J., Jalkanen, K.J., Stockfisch, T.P., Hagler, A.T., (1998) ¡§Derivation of Class II Force Fields. 5. Quantum Force Field for Amides, Peptides, and Related Compounds,¡¨ J. Comput. Chem.,19:430-458.

    6. Hwang, M.-J., Ni, X., Waldman, M., Ewig, C.S., Hagler, A.T., (1998) ¡§Derivation of Class II Force Fields. 6. Carbohydrate Compounds and Anomeric Effects,¡¨ Biopolymers. 45:435-468.

    7. Chu, P.-Y., Hwang, M.-J., (1998) ¡§New Insights for Dinucleotide Backbone Binding in Conserved C5¡¦-H¡KO Hydrogen Bonds,¡¨ J. Mol. Biol. 279:695-701.

    8. Lee, C.-Y., Yang, P.-K., Tzou, W.-S., Hwang, M.-J., (1998) ¡§Estimates of Binding Free Energies for HIV Protease Inhibitors Using Different Levels of Approximations,¡¨ Protein Eng.11:429-437 (NSC86-2811-B-001-0029).

    9. Lin, W.-J., Hwang, M.-J. (1998¡§VHMPT: a graphical Viewer and editor for Helical Membrane Protein Topologies,¡¨ Bioinformatics, 14:866-868.

    10. Cheng, Y.-S., Tang, T.K., Hwang, M.-J. (1999¡§Amino Acid Conservation and Clinical Severity of Human Glucose-6-Phosphate Dehydrogenase Mutations,¡¨ J. Biomed. Sci. 6:106-114 (NSC87-2314-B-001-034).

    11. Tzou, W.-S., Hwang, M.-J. (1999)  ¡§Modeling Helix-Turn-Helix Protein-Induced DNA Bending with Knowledge-Based Distance Restraints,¡¨ Biophys. J., 77: 1191-1205.

    12. Lai, H.-L., Lin, T.-H., Kao, Y.-Y., Lin, W.-J., Hwang, M.-J., Chern, Y. (1999)  ¡§The N-Terminal Domain of Type VI Adenylyl Cyclase Mediates Its Inhibition by Protein Kinase C,¡¨    Mol. Pharmacol., 56: 644-650.

    13. Yang, P.-K., Tzou, W.-S., Hwang, M.-J. (1999)  ¡§Restraint-Driven Formation of ƒÑ-Helical Coiled Coils in Molecular Dynamics Simulations,¡¨ Biopolymers, 50: 667-677 (NSC85-2113-M-001-011).

    14. Hwang, M.-J., Chu, P.-Y., Chen, J.-C., Chao, I. (1999)  ¡§Conformational Analysis of Three Pyrophosphate Model Species: Diphosphate, Methyl Diphosphate, and Triphosphate,¡¨ J. Comput. Chem., 20: 1702-1715 (NSC86-2811-B-001-022).

    15. Chen, J.-W., Luo, Y.-L., Hwang, M.-J.*, Peng, F.-C., Ling, K.-H.* (1999)  ¡§Territrem B, a tremorgenic mycotoxin that inhibits acetylcholinesterase with a non-covalent yet irreversible binding mechanism,¡¨ J. Biol. Chem., 274:34916-34923.(*corresponding authors)

    16. Liu, C.L., Tsai, C.C., Lin, S.C., Wang, L.I., Hsu, C.I., Hwang, M.-J., Lin, J.Y. (2000)  ¡§Primary Structure and Function Analysis of the Abrus precatorius Agglutinin A Chain by Site-directed Mutagenesis,¡¨ J. Biol. Chem., 275: 1897-1901.

    17. Yao, P.-L.; Hwang, M.-J.*; Chen, Y.-M.; Yeh, K.-W.* (2001)  ¡§Site-Directed Mutagenesis Evidence for a Negatively Charged Trypsin Inhibitory Loop in Sweet Potato Sporamin.¡¨ FEBS Lett., 496: 134-138 (*corresponding authors).

    18. Ewig, C. S., Berry, R., Dinur, U., Hill, J.R., Hwang, M.-J., Li, H., Liang, C., Maple, J., Peng, Z.W., Stockfisch, T.P., Thacher, T.S., Yan, L., Ni, X., Hagler, A.T. (2001)  ¡§Derivation of Class II Force Fields. VIII. Derivation of a General Quantum Mechanical Force Field for Organic Compounds.¡¨ J. Comput. Chem., 22:1782-1800.

    19. Lin, T.H., Lai, H.L., Kao, Y.Y., Sun, C.N., Hwang, M.-J., Chern, Y. (2002)  ¡§Protein Kinase C Inhibits Type VI Adenylyl Cyclase (ACVI) by Phosphorylating the Regulatory N Domain and Two Catalytic C1 and C2 Domains.¡¨ J. Biol. Chem.277: 15721-15728

    20. Chen, L.Y.Y., Lu, S.H., Shih, S.C., Hwang, M.-J. (2002)  ¡§Single Nucleotide Polymorphism Mapping Using Genome-wide Unique Sequences.¡¨ Genome Research 12: 1106-1111

    21.Yang, J.M.*, Tsai, C.H., Hwang, M.-J.*, Tsai, H.K., Hwang J.K., Kao, C.Y. (2002)  ¡§GEM: a Guassian Evolutionary Method for Predicting Protein Side-chain Conformations.¡¨ Protein Sci. 11: 1897-1907 (*corresponding authors)

    22.Shih, Edward S.C., Hwang, M.-J.  (2003) "Protein Structure Comparison by Probability-Based Matching of Secondary Structure Elements." Bioinformatics 19:735-741.

    23. Chen, M.-C., Hwang, M.-J., Chou, Y.-C., Chen, W.-H., Cheng, G.,Nakano, H., Luh, T.-Y., Mai, S.-C., Hsieh, S.-L. (2003) "The Role of ASK1 in Lymphotoxin-beta Receptor-Mediated Cell Death." J. Biol. Chem., 278:16073-16081.

    24. Yeh CS, Chen FM, Wang JY, Cheng TL, Hwang MJ, Tzou WS. (2003) "Directional Shape Complementarity at The Protein-DNA Interface." J. Mol. Recognit., 16(4): 213-222

    25. Shih SR, Chiang C, Chen TC, Wu CN, Hsu JT, Lee JC, Hwang MJ,Li ML, Chen GW, Ho MS (2004) "Mutations at KFRDI and VGK domains of enterovirus 71 3C protease affect its RNA binding and proteolytic activities." J Biomed Sci. 11(2):239-248

    26. Shih E. S, Hwang M.-J. (2004) "Alternative Alignments from Comparison of Protein Strutures." Proteins: Structure, Function and Bioinformatics 56: 519-527

    27. Lee I.-Y., Soong T.-T., Ho J.-M., Hwang M.-J. (2004) "Derivation and Analysis of Fragment Libraries of Protein Structures." Fourth IEEE Symposium on Bioinformatics and Bioengineering (BiBE'04), Taichung, Taiwan. May 19-21, pp516-521

    28. Kao Y.-Y., Lai H.-L., Hwang M.-J., Chern Y. (2004) "An Important functional role of the N terminus domain of type VI adenylyl cyclase (ACVI) in Gia-mediated inhibition." J Biol Chem. 279: 34440-34448

    29. Liao B.-Y., Chang Y.-J., Ho J.-M., Hwang M.-J. (2004) "The UniMarker (UM) Method for Synteny Mapping of Large Genomes." Bioinformatics 20: 3156-3165

    30. Soong, T.-T., Hwang M.-J., Chen, C.-M. (2004) "Discovery of Recurrent Structural Motifs for Approximating Three-Dimensional Protein Structures." J. Chin. Chem. Soc. 51: 1107-1114

    31. Wang, S.-L., Chen, C.-M., Hwang M.-J. (2005) "Classification of Protein 3D Folds by Hidden Markov Learning on Sequences of Structural Alphabets. " Proceedings of The Third Asia-Pacific Bioinformatics Conference, Singapore, January 17-21. pp65-72

    32. Xie, Z.-R., Hwang M.-J. (2006) "A New Neural Network for B-Turn Predictions: The Effect of Site-Specific Amino Acid Preference." Proceedings of The Fourth Asia-Pacific Bioinformatics Conference, Taipei, February 13-16. pp237-246

    33. Pao, S.-Y, Lin, W.-L, Hwang M.-J. (2006) "In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues. " BMC Genomics, 7:86

    34. Shih, E.S.C., Gan, R.-C., Hwang M.-J. (2006) "OPAAS: a web server for Optimal, Permuted, and other Alternative Alignments of protein Structures. " Nucleic Acids Research (web server issue) W95-W98

    35. Chang, D.T.H., Weng, Y.-Z., Lin, J.-H., Hwang M.-J., Oyang, Y.-J. (2006) "Protemot: prediction of protein-binding sites with automatically extracted geometrical templates. " Nucleic Acids Research (web server issue) W303-W309

    36. Liu W.C., Lin W.H., Davis A.J., Jordan F., Yang H.T. Hwang M.J. (2007) "A network perspective on the topological importance of enzymes and their phylogenetic conservation." BMC Bioinformatics 8:121

    37. Xie, Z.R., Yang, H.T., Liu, W.C., Hwang M.J. (2007) "The role of microRNA in the delayed negative feedback regulation of gene expression." BBRC 358:722-726

    38. Yang, H.-t., Hsu, C.-P., Hwang M.J. (2007) "An analytical rate expression for the kinetics of gene transcription mediated by dimeric transcription factors." The Journal of Biochemistry (Tokyo) 142: 135-144

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