Xiaoqiu Huang


Xiaoqiu Huang, Professor
Department of Computer Science, Iowa State University
226 Atanasoff Hall, Ames, IA 50011
Email: xqhuang@cs.iastate.edu Phone: 515-294-2432 Fax: 515-294-0258

Teaching

  1. Discrete Computational Structures: ComS 330
  2. Computational Techniques for Genome Assembly and Analysis: ComS/BCB 551

Research

My research in bioinformatics focuses on three computational problems in
genome sequencing and analysis.
  1. Assembly of DNA fragments into longer sequences.
  2. Identification of genes in genomic DNA sequences.
  3. Comparison of genomic DNA sequences.

Selected Publications

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.

Computer Programs

We have developed a number of computer programs for analysis of DNA and protein sequences.
The programs below are used by scientists around the world in their research.
SIM: A local sequence alignment program,
MAP: A multiple sequence alignment program,
CAP3 and PCAP: Sequence and genome assembly programs (downloading),
AAT: A set of programs for finding genes in DNA sequences (downloading).