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
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.
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.
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.
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.
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.
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.
Xie Z R, Hwang MJ: An interaction-motif-based scoring function for protein-ligand docking. BMC Bioinformatics 2010, 11:298.
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).
Shih ES, Hwang MJ* (2011) “On the use of distance constraints in protein-protein docking computations”. Proteins: Structure, Function, and Bioinformatics. In press (DOI: 10.1002/prot.23179)