Principal Investigator

Arthur Chun-Chieh Shih

Principle Investigator

Research Fellow, Institute of Information Science, Academia Sinica

Joint Research Fellow, Research Center for Information Technology Innovation, Academia Sinica

Joint Professor, Department of Life Science, National Taiwan Normal University

Core Faculty in:

(a)	TIGP Biodiversity Program, Academia Sinica and National Taiwan Normal University
(b)	Graduate Program for Information and Network Systems, Academia Sinica and National Chiao Tung University
(c)	Graduate Program for multimedia systems and Intelligent Computing, Academia Sinica and National Cheng Kung University

Email: arthur{at}iis{dot}sinica{dot}edu{dot}tw

Phone: 886-2-27883799 ext.1719

Office: N719, IIS, Academia Sinica

Lab: N416, IIS, Academia Sinica

Research Description (2014)

My research interests focus on the development of bioinformatic tools and the study of issues related to molecular evolution. Bioinformatics is an interdisciplinary discipline that integrates computational sciences and biology to process and analyze large data for exploring biological unknowns. The major computational challenge is to design a useful method that can be executed efficiently and effectively solve biological problems. On the other hand, the challenge for biology is how to find out meaningfully patterns from large data before forming a hypothesis. My recent research findings and achievements can be divided into three catgories: tool development, interdisciplinary collaboration, and study of evolution subjects. As regards tool development, we have developed GR-Aligner and JR-Assembler which can identify the breakpoints of rearrangement events, and assemble a giga-base-pair genome using lllumina short reads, respectively. Our interdisciplinary collaborations have with biologists from various institutes and research centers in Academia Sinica; through these collaborations, we study gene regulation in C4 plant leaf development, and miRNA regulatory networks in B cell differentiation and cardiac hypertrophy. Finally, we have used computational approaches to study gene duplication in C4 plant photosynthesis evolution and the origin of human miRNA evolution.

My Research Career

My research career until now can be divided into three periods: 1994-2001,2002-2006, and from 2007 until now. Before I was promoted as an assistant research fellow, my major research focused on image and signal processing. At that period, I had published a few of journal papers and several ones in IEEE Transactions on Image Processing which is the top journal in that field. In the second period, I started to enter the field of bioinformatics and had developed several tools for sequence alignment and visualization. Although I am a computer scientist by training, I found that to study biological issues are much more interesting than to develop tools. So, I spent a lot of time to study biology and read many literatures during this period. Moreover, I also believe that studying biological problems and questions through collaboration with biologists can enhance my understanding of what problems and questions are important and interesting to the biology community. Thus, in the third period my major research topics focus on studying biological issues collaborated with biologists as well as developing bioinformatics tools.