Xiaoqiu Huang

Xiaoqiu Huang, Professor
Department of Computer Science, Iowa State University
226 Atanasoff Hall, Ames, IA 50011
EM: xqhuang AT iastate DOT edu Phone: 515-294-2432 Fax: 515-294-0258
Google Scholar Citations: Profile


  1. Introduction to Data Structures: Com S 228
  2. Computational Techniques for Genome Assembly and Analysis: ComS/BCB 551


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

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

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

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

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

Ye L, 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, Wilson R. (2006)
Application of a Superword Array in Genome Assembly. Nucleic Acids Research 34: 201-205.

Huang X, Brutlag DL. (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, 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 BB, Srivastava SK, Leandro LF, O'Donnell K, Bhattacharyya MK. (2016) Identification of Highly Variable Supernumerary Chromosome Segments in an Asexual Pathogen. PLoS ONE 11: e0158183.

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).