Algorithms in Genomic and Structural Bioinformatics
The main activity of my group is in developing fast computational algorithms for large-scale analysis of biological sequences and structures. Two major algorithms have been developed, each for the bioinformatics of genomics and structural biology, respectively. The one for genomics, called the UniMarker (UM) method, allows one to compare the human genome with the mouse genome, to cross-reference all the human SNP and EST sequences in the public domain, and to locate their genomic position, all in just hours or few days of the CPU time of one Pentium IV personal computer. The one for structural biology, called FLASH or OPAAS, is a fast algorithm for comparing protein structures. Besides being very fast, OPAAS (the improved version of FLASH) distinguishes itself from many existing structure comparison methods with the capability to identify viable alternative alignments including those exhibiting permutation at all levels of permutation complexity. I will present an application of the UM method for detecting orthologous genes.
Research Fellow, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
I received a Ph.D. degree in Chemical Engineering from University of Pittsburgh (Pittsburgh, PA) in 1989. I then worked for Biosym Technologies Inc. (San Diego, CA) for five years. At Biosym, I helped lead a team funded by a consortium of pharmaceutical and chemical companies to develop a suite of new-generation molecular energy functions for the simulation and modeling of biological and chemical molecules. Since 1994 I have been a Principal Investigator for the Laboratory for Bioinformatics and Biomolecule Modeling at the Institute of Biomedical Sciences at the Academia Sinica. My laboratory has produced a number of bioinformatics databases and software tools (http://gln.ibms.sinica.edu.tw/software.php).