Research Topics
| Xiaoqiu HuangSummaryAffiliation: Iowa State University Country: USA Publications
Research Grants
| Collaborators
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Detail Information
Publications
MAP2: multiple alignment of syntenic genomic sequencesLiang 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...
Sequence alignment with an appropriate substitution matrixXiaoqiu 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...
A generalized global alignment algorithmXiaoqiu 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...
PCAP: a whole-genome assembly programXiaoqiu 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...- Efficient combination of multiple word models for improved sequence comparisonXiaoqiu 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... - Dynamic use of multiple parameter sets in sequence alignmentXiaoqiu 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... - Maximum similarity: a new formulation of phylogenetic reconstructionXiaoqiu 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... - Application of a superword array in genome assemblyXiaoqiu 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... - PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significanceAnkit 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... - Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matricesAnkit 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... - Generating a genome assembly with PCAPXiaoqiu 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... - Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penaltyAnkit 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... - Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignmentAnkit 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... - A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverageJianmin 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)... - Genome analysis of the platypus reveals unique signatures of evolutionWesley 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... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard 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... - Physical map-assisted whole-genome shotgun sequence assembliesRene 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... - Generation and annotation of the DNA sequences of human chromosomes 2 and 4Ladeana 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... - TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasetsGeo 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... - MAVG: locating non-overlapping maximum average segments in a given sequenceYaw-Ling Lin
Department of Computer Science and Information Management, Providence University, Shalu 433, Taiwan
Bioinformatics 19:151-2. 2003..AVAILABILITY: http://iubio.bio.indiana.edu/soft/molbio/pattern/cpg_islands/... - Evolution of alternative splicing after gene duplicationZhixi 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 Grants
- A DNA SEQUENCE ASSEMBLY PROGRAMXiaoqiu Huang; Fiscal Year: 2003..The investigators will also assist the integration of their assembly program into sequencing environments at other genome centers. ..