Dr. Xiaoqiu Huang

Photo of Xiaoqiu Huang

Xiaoqiu Huang is a professor in computer science at Iowa State University. He received his Ph.D. in computer science from Pennsylvania State University in 1990.


Assembly of DNA fragments into longer sequences, identification of genes in genomic DNA sequences, comparison of genomic DNA sequences.

Xiaoqiu Huang is interested in computational problems in genome sequencing and analysis.

He is the author of a widely used CAP3 assembly program. He and his colleagues have recently developed a whole-genome assembly program named PCAP. PCAP has been used by Washington University Genome Center in chimpanzee and chicken genome projects.



Huang, X. and Miller, W. (1991)
A Time-efficient, Linear-Space Local Similarity Algorithm. Advances in Applied Mathematics, 12:337-357.

Huang, X., Adams, M.D., Zhou, H. and Kerlavage, A.R. (1997)
A Tool for Analyzing and Annotating Genomic Sequences. Genomics, 46: 37-45.

Huang, X. and Madan, A. (1999)
CAP3: A DNA Sequence Assembly Program. Genome Research, 9: 868-877.

Huang, X. and Chao, K.-M. (2003)
A Generalized Global Alignment Algorithm. Bioinformatics, 19: 228-233.

Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)
PCAP: A Whole-Genome Assembly Program. Genome Research, 13: 2164-2170.

Ye, L. and Huang, X. (2005)
MAP2: Multiple Alignment of Syntenic Genomic Sequences. Nucleic Acids Research, 33: 162-170.

Huang, X., Yang, S.-P., Chinwalla, A., Hillier, L., Minx, P., Mardis, E. and Wilson, R. (2006)
Application of a Superword Array in Genome Assembly. Nucleic Acids Research, 34: 201-205.

Huang, X. and Brutlag, D.L. (2007)
Dynamic Use of Multiple Parameter Sets in Sequence Alignment. Nucleic Acids Research, 35: 678-686.

Huang, X. (2008)
Sequence Alignment with an Appropriate Substitution Matrix. Journal of Computational Biology, 15: 129-138.

Huang, X. and Vingron, M. (2009) Maximum Similarity: A New Formulation of Phylogenetic Reconstruction. Journal of Computational Biology, 16: 887-896.

Huang, X. (2014) Horizontal Transfer Generates Genetic Variation in an Asexual Pathogen. PeerJ 2: e650.

Huang, X., Das, A., Sahu, B.B., Srivastava, S.K., Leandro, L.F., O’Donnell, K. and Bhattachyrra, M.K. (2016) Identification of Highly Variable Supernumerary Chromosome Segments in an Asexual Pathogen. PLoS One, 11: e0158183.

Area of Expertise: 
Genome Assembly
B.S., Computer Science, Changsha Institute of Technology, 1982
M.S., Computer Science, Pennsylvania State University, 1989
Ph.D., Computer Science, Pennsylvania State University, 1990
226 Atanasoff Hall