Hui-Hsien Chou. Vect: An Automatic Visual Perl Programming Tool for Nonprogrammers. BioTechniques, Vol. 38, No. 4: pp 615-621, Apr 2005. [abstract]

Song Li and Hui-Hsien Chou. UBViz: a software tool for exploring metabolic pathways in 3-D space. BioTechniques, Vol. 38, No. 4: pp 540-542, Apr 2005. [abstract]

Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, and Patrick S. Schnable. Picky: Oligo Microarray Design for Large Genomes. Bioinformatics, 20: 2893 - 2902, Nov 2004. [abstract]

Song Li and Hui-Hsien Chou. Lucy2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics, 20: 2865-2866, Nov 2004. [abstract]

Hui-Hsien Chou, Wei Huang and James A. Reggia. The Trend Cellular Automata Programming Environment. Simulations, 78(2):59–75, 2002. [abstract]

Hui-Hsien Chou and Michael H. Holmes. DNA Sequence Quality Trimming and Vector Removal. Bioinformatics, 17(12):1093–1104, 2001. [abstract]

Eugene W. Myers, et al., A Whole-Genome Assembly of Drosophila. Science, 287:2196–2204, March 24, 2000.

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, September 1998.

Hui-Hsien Chou and James A. Reggia. Problem Solving During Artificial Selection of Self-Replicating Loops. Physica D 115, pp. 293-312, 1998. [abstract]

James A. Reggia, Hui-Hsien Chou and Jason Lohn. Cellular Automata Models of Self-replicating Systems. In Marvin Zelkowitz, editor, Advances in Computers. Vol. 47, Academic Press, New York, 1998. [abstract]

Hui-Hsien Chou and James A. Reggia. Emergence of Self-Replicating Structures in a Cellular Automata Space. Physica D 110, pp. 252-276, 1997. [abstract]

Hui-Hsien Chou, Anthony R. Kerlavage and Granger G. Sutton. YASAT: a Multiple Sequence Alignment Tool. Program and Abstract Book. First Annual Conference on Computational Genomics. Herndon, VA, Nov. 1997.

Hui-Hsien Chou. Self-Replicating Structures in a Cellular Automata Space. Ph.D. Dissertation, CS-TR-3715/UMIACS-TR-96-85, University of Maryland, 1996.

Hui-Hsien Chou, James A. Reggia, Rafael Navarro-González, and Jayoung Wu. An Extended Cellular Space Method for Simulating Autocatalytic Oligonucleotides. Computers & Chemistry, Vol. 18, No. 1, pp. 33–43, 1994.

James A. Reggia, Steven L. Armentrout, Hui-Hsien Chou, and Yun Peng. Simple Systems That Exhibit Self-Directed Replication. Science, 259:1282–1288, Feb. 26, 1993.

Rafael Navarro-González, James A. Reggia, Jayoung Wu, and Hui-Hsien Chou. A Novel Computational Method to Simulate Non-Enzymatic Self-Replication. Origins of Life, 24:170–171, 1994.

James A. Reggia, Hui-Hsien Chou, Steven L. Armentrout, and Yun Peng. Minimizing Complexity in Cellular Automata Models of Self-Replication. Proc. First Intl. Conf. Intelligent Systems for Molecular Biology, Washington D.C., July 1993. Published by AAAI.

Hui-Hsien Chou. Towards a Computational Model of Emergent Self-Replication. Technical Report, CS-TR-3091/UMIACS-TR-93-54, University of Maryland, 1993.

Hui-Hsien Chou, James A. Reggia and Rafael Navarro-González. A Software Environment for Simulating Self-Replicating Hexadeoxynucleotides. Technical Report, CS-TR-2939/UMIACS-TR-92-86, University of Maryland, 1992.

James A. Reggia, Hui-Hsien Chou, Steven L. Armentrout, and Yun Peng. Simple System Exhibiting Self-Directed Replication: Annex of Transition Functions and Software Documentation. Technical Report, CS-TR-2965/UMIACS-TR-92-104, University of Maryland, 1992.