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research divisions
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Epidemiology & Genetics
Joint
Cross Div.
Neuroscience
Corresponding
Cross Div.

Cardiovascular Research
Joint
Cross Div.

Infectious Disease &
Immunology
Cross Div.
Cancer
Joint
Corresponding
Cross Div.

Structural Biology

Research Scientist
Adjunct / Emeritus
Research Divisions information
Hwang, Ming-Jing's picture

Hwang, Ming-Jing

Research Fellow

 

Specialty:

  1. Bioinformatics
  2. Computational Biology
  3. Systems Biology

Ph.D. University of Pittsburgh

TEL:   02-27899033

FAX:   02-27887641

E-mail:   mjhwang@ibms.sinica.edu.tw

PubMed | Recent Publication | Personal Homepage


Research Description

    The main focus of our research has been to develop fast computational algorithms for analysis, especially on large-scales, of biological sequences, structures, and other biological data. Along this line we have developed several bioinformatics tools, including UniMarker for mapping genomic sequences, HMDEG for identifying deferentially expressed human and mouse genes, and OPAAS for comparing protein structures in non-sequential orders. More recently, we have developed network-based approaches for protein docking and binding site prediction, and for studying the organizational principles of house-keeping and tissue-specific genes. We are also interested in understanding the design principles of biological circuits, and have developed a computational pipeline to mathematically model and simulate prototypical gene networks.


Selected Recent Publication

  1. Chuang HY, Suen CS, Hwang MJ, Roffler SR. Toward reducing immunogenicity of enzyme replacement therapy: altering the specificity of human β-glucuronidase to compensate for α-iduronidase deficiency. Protein Engineering, Design and Selection. 2015, doi: 10.1093/protein/gzv041
  2. Shih ES, Hwang MJ. NPPD: A Protein-Protein Docking Scoring Function Based on Dyadic Differences in Networks of Hydrophobic and Hydrophilic Amino Acid Residues. Biology. 2015, 4: 282-297.
  3. Cheng YC, Chen PH, Chiang HY, Suen CS, Hwang MJ, Lin TY, Yang HC, Lin WC, Lai PL, Shieh SY. Candidate tumor suppressor B-cell translocation gene 3 impedes neoplastic progression by suppression of AKT. Cell Death & Disease. 2015, 6: e1584.
  4. Xie ZR, Hwang MJ. Methods for predicting protein-ligand binding sites. Methods in Molecular Biology (Clifton, N.J.). 2015, 1215: 383-398.
  5. Shyu YC, Lee TL, Chen X, Hsu PH, Wen SC, Liaw YW, Lu CH, Hsu PY, Lu MJ, Hwang JL, Tsai MD, Hwang MJ, Chen JR, Shen CK. Tight Regulation of a Timed Nuclear Import Wave of EKLF by PKCθ and FOE during Pro-E to Baso-E Transition. Developmental Cell. 2014, 28: 409-422.
  6. Chiang AW, Liu WC, Charusanti P, Hwang MJ. Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters. BMC Systems Biology. 2014, 8: 4.
  7. Chiang AW, Shaw GT, Hwang MJ. Partitioning the human transcriptome using HKera, a novel classifier of housekeeping and tissue-specific genes. PLoS One. 2013, 8: e83040.
  8. Chiang AW, Hwang MJ. A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits. BMC Bioinformatics. 2013, 14: Suppl 12, S5.
  9. Hsu CH, Chen CK, Hwang MJ. The architectural design of networks of protein domain architectures. Biol. Lett. 2013, 9:20130268.
  10. Xie ZR, Liu CK. Hsiao FC, Yao A, Hwang MJ. LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites. Nucleic Acids Research. 2013, 41(W1): W292-W296.
  11. Shih ES, Hwang MJ. A critical assessment of information-guided protein-protein docking predictions. Mol. Cell. Proteomics. 2013, 12:679-686.
  12. Xie ZR, Hwang MJ. Ligand binding site prediction using ligand-interacting and binding site-enriched protein triangles. Bioinformatics. 2012, 28:1579-1585.
  13. Shih ES, Hwang MJ. On the use of distance constraints in protein-protein docking computations. Proteins: Structure, Function, and Bioinformatics. 2012, 80:194-205.
  14. Shaw GTW, Shih ES, Chen CC, Hwang MJ. Preservation of ranking order in the expression of human housekeeping genes. PloS ONE. 2011, 6:e29314.
  15. Shih ES, Hwang MJ. "Non-sequential protein structure comparisons." Chapter 8 In Sequence and Genome Analysis: Methods and Applications. 2010, edited by Zhongming Zhao, iConcept Press (invited review).
  16. Xie Z R, Hwang MJ. An interaction-motif-based scoring function for protein-ligand docking. BMC Bioinformatics. 2010, 11:298.
  17. Lin WH, Liu W., Hwang MJ. Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. BMC Systems Biology. 2009, 3:32.