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research divisions
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Epidemiology & Genetics
Joint
Cross Div.
Cardiovascular Disease
Joint
Cross Div.

 

Cell & Developmental Biology/Regenerative Medicine
Joint
Cross Div.
Structural Biology

 

Infectious Disease &
Immunology
Cross Div.

 

Cancer
Joint
Corresponding
Cross Div.
Neuroscience
Corresponding
Cross Div.
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. Pao SY, Lin WL, and Hwang MJ: In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues. BMC Genomics 2006, 7:86.
  2. Shih ESC, Gan RC, Hwang MJ: OPAAS: a web server for Optimal, Permuted, and other Alternative Alignments of protein Structures. Nucleic Acids Research 2006, W95-W98.
  3. Liu WC, Lin WH, Davis AJ, Jorden F, Yang HT, and Hwang MJ: A network perspective on the topological importance of enzymes and their phylogenetic conservation. BMC Bioinformatics 2007, 8:121.
  4. Xie ZR, Yang HT, Liu WC, Hwang MJ: The role of microRNA in the delayed negative feedback regulation of gene expression. Biochemical and Biophysical Research Communications 2007, 358:722-726.
  5. Yang HT, Hsu CP, Hwang MJ: An analytical rate expression for the kinetics of gene transcription mediated by dimeric transcription factors. The Journal of Biochemistry (Tokyo) 2007, 142: 135-144.
  6. 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.
  7. Xie Z R, Hwang MJ: An interaction-motif-based scoring function for protein-ligand docking. BMC Bioinformatics 2010, 11:298.
  8. Shih ES, Hwang MJ (2010) "Non-sequential protein structure comparisons." Chapter 8 In Sequence and Genome Analysis: Methods and Applications, edited by Zhongming Zhao, iConcept Press (invited review).
  9. Shaw GTW, Shih ES, Chen CC, Hwang MJ (2011) Preservation of Ranking Order in the Expression of Human Housekeeping Genes. PloS ONE, 6(12):e29314.
  10. Shih ES, Hwang MJ (2012) On the use of distance constraints in protein-protein docking computations. Proteins: Structure, Function, and Bioinformatics, 80:194-205.
  11. Xie ZR, Hwang MJ (2012) Ligand binding site prediction using ligand-interacting and binding site-enriched protein triangles. Bioinformatics, 28:1579-1585.
  12. Shih ES, Hwang MJ (2013) A critical assessment of information-guided protein-protein docking predictions. Mol. Cell. Proteomics, 12(3):679-686.
  13. Xie ZR, Liu CK. Hsiao FC, Yao A, Hwang MJ (2013) LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites. Nucleic Acids Research, 41(W1): W292-W296.
  14. Hsu CH, Chen CK, Hwang MJ (2013) The architectural design of networks of protein domain architectures. Biol. Lett. 9(4):20130268.
  15. Chiang WT, Hwang MJ (2013) A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits. BMC Bioinformatics,14: Suppl 12, S5.