Hui-Hsien Chou

Associate Professor
Hui-Hsien Chou image

Dr. Chou, Associate Professor, received a B.S. in Chemical Engineering from the Ming-Chih Institute of Technology in 1984, and an additional B.S. in Computer Science from the National Taiwan University. He went on to receive his Ph.D. in computer Science from the University of Maryland, College Park, MD in 1996. Dr. Chou served as a Lecturer in the Department of Computer Science at the University of Maryland, College Park, from 1996 to 1997. He was also named a Postdoctoral Fellow for The Institute of Genomic Research, Rockville, MD from 1996 to 1998. At that time, he became a Research Scientist for Celera Genomics Corporation in Rockville. Dr. Chou came to Iowa State University in 1999 with a joint appointment in both the Departments of Computer Science, and in Genetics, Development and Cell Biology.

Research Description

My research interest has been the development of sophisticated computer science algorithms for efficiently solving large scale biological research problems, e.g., the automatic DNA sequence clean up programs (LUCY1 & 2), an efficient whole-genome oligo microarray design tool (PICKY), and an automatic Perl programming tool (VECT) for biologists. My software tools employ novel approaches to computing and generally provide better results than previous methods. For example, while most microarray design tools are still based on the sequence level comparison to screen out nontargets, my PICKY program has embedded a complete suite of thermodynamic equations in its calculations to infer the best oligo candidates based on the whole genome, and it does so orders of magnitude faster than any other comparable microarray design tools with the same computation depth. My recent focus is on the whole-genome siRNA design using a similar thermodynamic calculation approach.


  • Hui-Hsien Chou. Shared probe design and existing microarray reanalysis using PICKY. BMC Bioinformatics, 11:196, April 20, 2010.
  • Hui-Hsien Chou, Arunee Trisiriroj, Sunyoung Park, Yue-Ie C. Hsing, Pamela C. Ronald and Patrick S. Schnable. Direct calibration of PICKY-designed microarrays. BMC Bioinformatics, 10:347, Oct. 23, 2009.
  • Ki-Hong Jung, Christopher Dardick, Laura E. Bartley, Peijian Cao, Jirapa Phetsom, Patrick Canlas, Young-Su Seo, Michael Shultz, Shu Ouyang, Qiaoping Yuan, Bryan C. Frank, Eugene Ly, Li Zheng, Yi Jia, An-Ping Hsia, Kyungsook An, Hui-Hsien Chou, David Rocke, Geun Cheol Lee, Patrick S. Schnable, Gynheung An, C. Robin Buell, and Pamela C. Ronald. Refinement of Light-responsive Candidate Genes using Rice Oligonucleotide Arrays: Evaluation of Gene-redundancy. PLoS ONE, 3(10), Oct 6, 2008.
  • Young-Su Seo, Malinee Sriariyanun, Li Wang, Janice Pfeiff, Jirapa Phetsom, Ye Lin, Ki-Hong Jung, Hui-Hsien Chou, Adam J Bogdanove and Pamela C Ronald. A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes. BMC Microbiology, 8(1):99, 2008.
  • Scott Emrich, Li Li, Tsui-Jung Wen, Marna Yandeau-Nelson, Yan Fu, Ling Guo, Hui-Hsien Chou, Srinivas Aluru, Daniel Ashlock, and Patrick Schnable. Nearly identical paralogs (NIPs): implications for maize (Zea mays L.) genome evolution. Genetics, 175(1): 429–439, Jan. 2007.
  • Philip M. Maher, Hui-Hsien Chou, Elizabeth Hahn, Tsui-Jung Wen, and Patrick S. Schnable. 2006. GRAMA: Genetic Mapping Analysis of Temperature Gradient Capillary Electrophoresis (TGCE) Data. Theoretical and Applied Genetics 113(1):156-162.
  • Song Li and Hui-Hsien Chou. 2005. UBViz: Explore Biochemical Pathways in 3-D Space. BioTechniques 38:540-542.
  • Hui-Hsien Chou. 2005. Vect: an automatic visual Perl programming tool for nonprogrammers. BioTechniques 38:615-621.
  • Hui-Hsien Chou. 2005. Computational Design of Whole Genome Microarrays. In Srinivas Aluru, editor, Handbook of Computational Molecular Biology. ISBN 1584884061. CRC Press, Boca Raton, FL .
  • Xiaoqiu Huang, Liang Ye, Hui-Hsien Chou, I-Hsuan Yang, and Kun-Mao Chao. 2004. Efficient Combination of Multiple Word Models for Improved Sequence Comparison. Bioinformatics 20:2529-2533.
  • Song Li and Hui-Hsien Chou. 2004. Lucy2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics 20:2865-2866.
  • Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, and Patrick S. Schnable. 2004. Picky: Oligo Microarray Design for Large Genomes. Bioinformatics 20:2893-2902.
  • Hui-Hsien Chou, Wei Huang and James A. Reggia. 2002. The Trend Cellular Automata Programming Environment. Simulations 78(2):59-75.
  • Eugene W. Myers, et al.. 2000. A Whole-Genome Assembly of Drosophila. Science 287(3/2000):2196-2204.
  • Hui-Hsien Chou and James A. Reggia. 1998. Problem Solving During Artificial Selection of Self-Replicating Loops. Physica D 115:293-312.
  • Hui-Hsien Chou and Michael H. Holmes. 12. DNA Sequence Quality Trimming and Vector Removal. Bioinformatics 17(2001):1093-1104.
  • Hui-Hsien Chou, Granger G. Sutton, Anna Glodek, and John Scott. Lucy – A Sequence Cleanup Program. Proceedings of the Tenth Annual Genome Sequencing and Annotation Conference (GSAC X) (Miami, Florida).
Area of Expertise: 
Computational Biology and Bioinformatics
B.S., Chemical Engineering, Ming-Chih Institute of Technology, 1984
B.S., Computer Science, National Taiwan University, 1989
Ph.D., Computer Science, University of Maryland, College Park, 1996
507 Science ll