Xiaoqiu Huang

Summary

Affiliation: Iowa State University
Country: USA

Publications

  1. pmc MAP2: multiple alignment of syntenic genomic sequences
    Liang Ye
    Department of Computer Science, Iowa State University 226 Atanasoff Hall, Ames, IA 50011 1040, USA
    Nucleic Acids Res 33:162-70. 2005
  2. doi request reprint Sequence alignment with an appropriate substitution matrix
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, Iowa 50011 1040, USA
    J Comput Biol 15:129-38. 2008
  3. pmc Dynamic use of multiple parameter sets in sequence alignment
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, IA 50011 1040, USA
    Nucleic Acids Res 35:678-86. 2007
  4. doi request reprint Maximum similarity: a new formulation of phylogenetic reconstruction
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, Iowa 50011 1040, USA
    J Comput Biol 16:887-96. 2009
  5. pmc Application of a superword array in genome assembly
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, IA 50011 1040, USA
    Nucleic Acids Res 34:201-5. 2006
  6. ncbi request reprint Efficient combination of multiple word models for improved sequence comparison
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, IA 50011 1040, USA
    Bioinformatics 20:2529-33. 2004
  7. pmc PCAP: a whole-genome assembly program
    Xiaoqiu Huang
    Department of Computer Science Iowa State University, Ames, Iowa 50011 1040, USA
    Genome Res 13:2164-70. 2003
  8. ncbi request reprint A generalized global alignment algorithm
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011 1040, USA
    Bioinformatics 19:228-33. 2003
  9. doi request reprint PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance
    Ankit Agrawal
    Department of Computer Science, Iowa State University, Ames, IA 50011 1041, USA
    Bioinformatics 25:1082-3. 2009
  10. doi request reprint Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices
    Ankit Agrawal
    Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011 1041, USA
    IEEE/ACM Trans Comput Biol Bioinform 8:194-205. 2011

Research Grants

  1. A DNA SEQUENCE ASSEMBLY PROGRAM
    Xiaoqiu Huang; Fiscal Year: 2003

Detail Information

Publications21

  1. pmc MAP2: multiple alignment of syntenic genomic sequences
    Liang Ye
    Department of Computer Science, Iowa State University 226 Atanasoff Hall, Ames, IA 50011 1040, USA
    Nucleic Acids Res 33:162-70. 2005
    ..This feature is useful for finding conserved functional elements in genomic sequences. The MAP2 program is freely available in source code form at http://bioinformatics.iastate.edu/aat/sas.html for academic use...
  2. doi request reprint Sequence alignment with an appropriate substitution matrix
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, Iowa 50011 1040, USA
    J Comput Biol 15:129-38. 2008
    ..SimDist was also used to compare three types of substitution matrices in scoring 444,461 pairs of homologous sequences from the 100 families...
  3. pmc Dynamic use of multiple parameter sets in sequence alignment
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, IA 50011 1040, USA
    Nucleic Acids Res 35:678-86. 2007
    ..On 168,475 of the 257,716 pairs (a rate of 65.4%), alignments from GAP4 were more statistically significant than alignments from GAP3 and SIM...
  4. doi request reprint Maximum similarity: a new formulation of phylogenetic reconstruction
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, Iowa 50011 1040, USA
    J Comput Biol 16:887-96. 2009
    ..Experimental results show that incorporating the maximum similarity objective into existing methods leads to improvements both in topology and in branch length...
  5. pmc Application of a superword array in genome assembly
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, IA 50011 1040, USA
    Nucleic Acids Res 34:201-5. 2006
    ..REP for computation of overlaps between reads. Experimental results produced by PCAP.REP and PCAP on a whole-genome dataset show that PCAP.REP produced a more accurate and contiguous assembly than PCAP...
  6. ncbi request reprint Efficient combination of multiple word models for improved sequence comparison
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, Ames, IA 50011 1040, USA
    Bioinformatics 20:2529-33. 2004
    ..Studies of efficient and sensitive sequence comparison methods are driven by a need to find homologous regions of weak similarity between large genomes...
  7. pmc PCAP: a whole-genome assembly program
    Xiaoqiu Huang
    Department of Computer Science Iowa State University, Ames, Iowa 50011 1040, USA
    Genome Res 13:2164-70. 2003
    ..The PCAP program was tested on a mouse whole-genome data set of 30 million reads and a human Chromosome 20 data set of 1.7 million reads. The program is freely available for academic use...
  8. ncbi request reprint A generalized global alignment algorithm
    Xiaoqiu Huang
    Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011 1040, USA
    Bioinformatics 19:228-33. 2003
    ..Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions...
  9. doi request reprint PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance
    Ankit Agrawal
    Department of Computer Science, Iowa State University, Ames, IA 50011 1041, USA
    Bioinformatics 25:1082-3. 2009
    ..The obvious advantage of the approach is more accurate estimates of statistical significance because of pairwise statistical significance, along with the advantage of BLAST/PSI-BLAST in terms of speed...
  10. doi request reprint Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices
    Ankit Agrawal
    Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011 1041, USA
    IEEE/ACM Trans Comput Biol Bioinform 8:194-205. 2011
    ..Further, using position-specific substitution matrices for estimating pairwise statistical significance gives significantly better results even than PSI-BLAST using pretrained PSSMs...
  11. doi request reprint Generating a genome assembly with PCAP
    Xiaoqiu Huang
    Iowa State University, Ames, Iowa, USA
    Curr Protoc Bioinformatics . 2005
    ..Another basic protocol for using PCAP on a distributed cluster of computers in a 3-Gb genome assembly project is presented, in addition to suggestions for understanding results from PCAP...
  12. pmc Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty
    Ankit Agrawal
    Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011 1041, USA
    BMC Bioinformatics 10:S1. 2009
    ..In this paper, we extend the earlier work on pairwise statistical significance by incorporating with it the use of multiple parameter sets...
  13. ncbi request reprint Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment
    Ankit Agrawal
    Department of Computer Science, Iowa State University, Ames, IA 50011 1041, USA
    Int J Comput Biol Drug Des 1:347-67. 2008
    ..An application of pairwise statistical significance to empirically determine effective gap opening penalties for protein local sequence alignment using the widely used BLOSUM matrices is also presented...
  14. pmc A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage
    Jianmin Wang
    Department of Computer Science, Iowa State University, Ames, Iowa 50011, USA
    BMC Bioinformatics 6:220. 2005
    ..Sequence-based methods for finding SNPs with allele frequencies may need to handle thousands of sequences from the same genome location (sequences of deep coverage)...
  15. pmc Genome analysis of the platypus reveals unique signatures of evolution
    Wesley C Warren
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 453:175-83. 2008
    ..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation...
  16. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  17. pmc Physical map-assisted whole-genome shotgun sequence assemblies
    Rene L Warren
    British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
    Genome Res 16:768-75. 2006
    ..A 6.5-fold coverage draft DNA sequence of the Pan troglodytes (chimpanzee) genome was assembled using map-derived constraints and resulted in a 26.1% increase in scaffold contiguity...
  18. ncbi request reprint Generation and annotation of the DNA sequences of human chromosomes 2 and 4
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 434:724-31. 2005
    ..Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions...
  19. ncbi request reprint TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  20. ncbi request reprint MAVG: locating non-overlapping maximum average segments in a given sequence
    Yaw Ling Lin
    Department of Computer Science and Information Management, Providence University, Shalu 433, Taiwan
    Bioinformatics 19:151-2. 2003
    ..It has applications in several areas of biomolecular sequence analysis including locating GC-rich regions and CpG islands in a genomic sequence, and annotating multiple sequence alignments...
  21. pmc Evolution of alternative splicing after gene duplication
    Zhixi Su
    James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
    Genome Res 16:182-9. 2006
    ..In the late stage, the gain and loss of alternative splicing seem to be independent between duplicates...

Research Grants3

  1. A DNA SEQUENCE ASSEMBLY PROGRAM
    Xiaoqiu Huang; Fiscal Year: 2003
    ..The investigators will also assist the integration of their assembly program into sequencing environments at other genome centers. ..