Core and periphery structures in protein interaction networks (2009)
Luo, Feng, Li, Bo, Wan, Xiu-Feng, Scheuermann, Richard H
Abstract Background Characterizing the structural properties of protein interaction networks will help illuminate the organizational and functional relationships among elements in biological systems....
Chourey, Karuna, Wei, Wei, Wan, Xiu-Feng, Thompson, Dorothea K
Abstract Background Shewanella oneidensis MR-1 exhibits diverse metal ion-reducing capabilities and thus is of potential utility as a bioremediation agent. Knowledge of the molecular components and...
Lin, Guohui, Cai, Zhipeng, Wu, Junfeng, Wan, Xiu-Feng, Xu, Lizhe, Goebel, Randy
Abstract Background Serotypes of the Foot-and-Mouth disease viruses (FMDVs) were generally determined by biological experiments. The computational genotyping is not well studied even with the...
Xiu-feng Wan, Guorong Chen, Feng Luo, Michael Emch, Ruben Donis
A quantitative genotype algorithm reflecting H5N1 Avian influenza niches
Intrinsic Terminator Prediction and Its Application in (2008)
Synechococcus Sp. Wh, Xiu-feng Wan, Dong Xu
¶ Corresponding author. We have developed a new method for intrinsic terminator prediction based on Rnall, an RNA local secondary structure prediction algorithm that we developed recently, and two...
Xiaomeng Wu, Zhipeng Cai, Xiu-feng Wan, Tin Hoang, Y Goebel, Guohui Lin
Motivation: The availability of the whole genomic sequences of HIV-1 viruses provides an excellent resource for studying the HIV-1 phylogenies using all the genetic materials. However, such huge...
Xiaomeng Wu, Xiu-feng Wan, Gang Wu, Dong Xu, Guohui Lin
§ To whom correspondence should be addressed. Abstract: The availability of complete genomic sequences allows us to infer the evolutionary footprints for species more precisely at a global scale....
Extremophiles (2004) 8:291–299 DOI 10.1007/s00792-004-0388-1 ORIGINAL PAPER (2008)
Xiu-feng Wan, Æ Susan, M. Bridges, Æ John, A. Boyle, Communicated K. Horikoshi, ...
Revealing gene transcription and translation initiation patterns in archaea, using an interactive clustering model
Kang, Cheol-Hee, Nam, Young-Do, Chung, Won-Hyong, Quan, Zhe-Xue, Park, Yong-Ha, Park, Soo-Je, ...
DNA-DNA hybridization has been established as an important technology in bacterial species taxonomy and phylogenetic analysis. In this study, we analyzed how the efficiency with which the genomic DNA...
A quantitative genotype algorithm reflecting H5N1 Avian influenza niches (2007)
Wan, Xiu-Feng, Chen, Guorong, Luo, Feng, Emch, Michael, Donis, Ruben
Motivation: Computational genotyping analyses are critical for characterizing molecular evolutionary footprints, thus providing important information for designing the strategies of influenza...
Nucleotide composition string selection in HIV-1 subtyping using whole genomes (2007)
Wu, Xiaomeng, Cai, Zhipeng, Wan, Xiu-Feng, Hoang, Tin, Goebel, Randy, Lin, Guohui
Motivation: The availability of the whole genomic sequences of HIV-1 viruses provides an excellent resource for studying the HIV-1 phylogenies using all the genetic materials. However, such huge...
CodonO: codon usage bias analysis within and across genomes (2007)
Angellotti, Michael C., Bhuiyan, Shafquat B., Chen, Guorong, Wan, Xiu-Feng
Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein...
Computational Identification of Reassortments in Avian Influenza Viruses (2007)
Xiu-Feng Wan, Xiaomeng Wu, Guohui Lin, Samuel B. Holton, Racheal A. Desmone, Chi-Ren Shyu, ...
Computational Identification of Reassortments in Avian Influenza Viruses (2007)
Xiu-Feng Wan, Xiaomeng Wu, Guohui Lin, Samuel B. Holton, Racheal A. Desmone, Chi-Ren Shyu, ...
Original Papers A Quantitative Genotype Algorithm Reflecting H5N1 Avian Influenza (2007)
Xiu-feng Wan, Guorong Chen, Feng Luo, Michael Emch, Ruben Donis
Motivation: Computational genotyping analyses are critical for characterizing molecular evolutionary footprints, thus providing important information for designing the strategies of influenza...
Running title: Hierarchical Probe Design (HPD) (2005)
Won-hyong Chung, Sung-keun Rhee, Xiu-feng Wan, Jin-woo Bae, These Contributed Equally
Motivation: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a...
Design of long oligonucleotide probes for functional gene detection in a microbial community (2005)
Chung, Won-Hyong, Rhee, Sung-Keun, Wan, Xiu-Feng, Bae, Jin-Woo, Quan, Zhe-Xue, Park, Yong-Ha
Motivation: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a...
Design of long oligonucleotide probes for functional gene detection in a microbial community (2005)
Chung, Won-Hyong, Rhee, Sung-Keun, Wan, Xiu-Feng, Bae, Jin-Woo, Quan, Zhe-Xue, Park, Yong-Ha
Motivation: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a...
Wan, Xiu-Feng, Xu, Dong, Kleinhofs, Andris, Zhou, Jizhong
Abstract Background Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has...
Whole Genome Phylogeny via Complete Composition Vectors (2004)
Xiaomeng Wu, Xiu-feng Wan, Gang Wu, Dong Xu, Guohui Lin
The availability of complete genomic sequences allows us to infer the evolutionary footprints between species in a global strategy. However, the length of these genomic sequences poses a challenge on...
Wan, Xiu-Feng, VerBerkmoes, Nathan C., McCue, Lee Ann, Stanek, Dawn, Connelly, Heather, Hauser, Loren J., ...
The availability of the complete genome sequence for Shewanella oneidensis MR-1 has permitted a comprehensive characterization of the ferric uptake regulator (Fur) modulon in this dissimilatory...
Leaphart, Adam B., Thompson, Dorothea K., Huang, Katherine, Alm, Eric, Wan, Xiu-Feng, Arkin, Adam, ...
The molecular response of Shewanella oneidensis MR-1 to variations in extracellular pH was investigated based on genomewide gene expression profiling. Microarray analysis revealed that cells elicited...
Shababi, Monir, Bourque, June, Palanichelvam, Karuppaiah, Cole, Anthony, Xu, Dong, Wan, Xiu-Feng, ...
We have screened portions of the large intergenic region of the Cauliflower mosaic virus (CaMV) genome for promoter activity in baker's yeast (Saccharomyces cerevisiae) and have identified an element...
Wan, Xiu-Feng, VerBerkmoes, Nathan C., McCue, Lee Ann, Stanek, Dawn, Connelly, Heather, Hauser, Loren J., ...
The availability of the complete genome sequence for Shewanella oneidensis MR-1 has permitted a comprehensive characterization of the ferric uptake regulator (Fur) modulon in this dissimilatory...
Leaphart, Adam B., Thompson, Dorothea K., Huang, Katherine, Alm, Eric, Wan, Xiu-Feng, Arkin, Adam, ...
The molecular response of Shewanella oneidensis MR-1 to variations in extracellular pH was investigated based on genomewide gene expression profiling. Microarray analysis revealed that cells elicited...
Shababi, Monir, Bourque, June, Palanichelvam, Karuppaiah, Cole, Anthony, Xu, Dong, Wan, Xiu-Feng, ...
We have screened portions of the large intergenic region of the Cauliflower mosaic virus (CaMV) genome for promoter activity in baker's yeast (Saccharomyces cerevisiae) and have identified an element...
CodonO: codon usage bias analysis within and across genomes
Angellotti, Michael C., Bhuiyan, Shafquat B., Chen, Guorong, Wan, Xiu-Feng
Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein...
Evolution of Highly Pathogenic H5N1 Avian Influenza Viruses in Vietnam between 2001 and 2007
Wan, Xiu-Feng, Nguyen, Tung, Davis, C. Todd, Smith, Catherine B., Zhao, Zi-Ming, Carrel, Margaret, ...
Highly pathogenic avian influenza (HPAI) H5N1 viruses have caused dramatic economic losses to the poultry industry of Vietnam and continue to pose a serious threat to public health. As of June 2008,...