Xiaoqiu Huang
Professor

Office: 205 Atanasoff Phone: (515) 294-2432 Fax: (515) 294-0258 Email: xqhuang@cs.iastate.edu Homepage: http://www.cs.iastate.edu/~xqhuang/

Research Interests

Computational Problems in Genome Sequencing and Analysis

Research Areas

Bioinformatics and Computational Biology

Research Statement

My research in bioinformatics focuses on three computational problems in
genome sequencing and analysis.

Assembly of DNA fragments into longer sequences.

Identification of genes in genomic DNA sequences.

Comparison of genomic DNA sequences.

An assembly of the chimpanee genome has been produced with the PCAP program
by Washington University Genome Sequencing Center.

Education

Ph.D.   The Pennsylvania State University   1990
M.S.   The Pennsylvania State University   1989
B.S.   Changsha Institute of Technology, P. R. China   1982

Honors and Awards

2006 Iowa State University Inventor  "Honored as the developer of the PCAP program", Iowa State University, 2006

Current Grants

Making Improvements to the PCAP Genome Assembly Program. Xiaoqiu Huang. Washington University (2006-2010). $428,716.

Sequencing the Fusarium Virguliformae Genome. Xiaoqiu Huang. Soybean Research and Development Council (2009-2010). $107,780.

Representative Publications

Refereed Journal and Conference Publications

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

Xiaoqiu Huang. Sequence Alignment with an Appropriate Substitution Matrix. Journal of Computational Biology. Vol. 15. No. 2. pp. 129-138, 2008.

Huang, X. and Brutlag, D.L. Dynamic Use of Multiple Parameter Sets in Sequence Alignment. Nucleic Acids Research, Oxford University Press. Vol. 35. No. 2. pp. 678-686, 2007.

Huang, X., Yang, S.-P., Chinwalla, A., Hillier, L., Minx, P., Mardis, E. and Wilson, R. Application of a Superword Array in Genome Assembly. Nucleic Acids Research, Oxford University Press. Vol. 34. No. 1. pp. 201-205, 2006.

Wang, J. and Huang, X. A Method for Finding Single-Nucleotide Polymorphisms with Allele Frequencies in Sequences of Deep Coverage. BMC Bioinformatics, BioMedical Central. Vol. 6. pp. 220, 2005.

Ye, L. and Huang, X. MAP2: Multiple alignment of syntenic genomic sequences. Nucleic Acids Research, Oxford University Press. Vol. 33. No. 1. pp. 162-170, 2005.

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

Huang, X. and Chao, K.-M. A Generalized Global Alignment Algorithm. Bioinformatics. Vol. 19. pp. 228-233, 2003.

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

Huang, X., Adams, M.D., Zhou, H. and Kerlavage, A.R. A Tool for Analysis and Annotating Genomic Sequences. Genomics. Vol. 46. pp. 37-45, 1997.

Huang, X. and Miller, W. A Time-Efficient, Linear-Space Local Similarity Algorithm. Advances in Applied Mathematics. Vol. 12. pp. 337-357, 1991.