• A joint matrix completion and filtering model for influenza serological data integration. 

      Yuan, Xiao-Tong; Zhang, Tong; Wan, Xiu-Feng (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 7/25/2013)
      Antigenic characterization based on serological data, such as Hemagglutination Inhibition (HI) assay, is one of the routine procedures for influenza vaccine strain selection. In many cases, it would be impossible to measure ...
    • A perspective on multiple waves of influenza pandemics. 

      Mummert, Anna; Weiss, Howard; Long, Li-Ping; Amigó, José M; Wan, Xiu-Feng (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 4/23/2013)
      BACKGROUND: A striking characteristic of the past four influenza pandemic outbreaks in the United States has been the multiple waves of infections. However, the mechanisms responsible for the multiple waves of influenza ...
    • Cross-Ontology multi-level association rule mining in the Gene Ontology. 

      Manda, Prashanti; Ozkan, Seval; Wang, Hui; McCarthy, Fiona M.; Bridges, Susan M. (Public Library of ScienceDepartment of Computer Sciences and EngineeringDepartment of Plant and Soil SciencesDepartment of Basic SciencesJames Worth Bagley College of EngineeringCollege of Agriculture and Life SciencesCollege of Veterinary MedicineInstitute for Genomics, Biocomputing and Biotechnology, 10/12/2012)
      The Gene Ontology (GO) has become the internationally accepted standard for representing function, process, and location aspects of gene products. The wealth of GO annotation data provides a valuable source of implicit ...
    • Evidence of positive selection in mitochondrial complexes I and V of the African elephant. 

      Finch, Tabitha M.; Zhao, Nan; Korkin, Dmitry; Frederick, Katy H.; Eggert, Lori S. (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 4/2/2014)
      As species evolve, they become adapted to their local environments. Detecting the genetic signature of selection and connecting that to the phenotype of the organism, however, is challenging. Here we report using an ...
    • Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome 

      Warren, Samantha; Wan, Xiu-Feng; Conant, Gavin; Korkin, Dmitry (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 11/25/2013)
    • Identifying blood biomarkers and physiological processes that distinguish humans with superior performance under psychological stress. 

      Cooksey, Amanda M.; Momen, Nausheen; Stocker, Russell; Burgess, Shane C. (Public Library of ScienceDepartment of Basic SciencesDepartment of Mathematics and StatisticsCollege of Veterinary MedicineCollege of Arts and Sciences, 12/18/2009)
      BACKGROUND: Attrition of students from aviation training is a serious financial and operational concern for the U.S. Navy. Each late stage navy aviator training failure costs the taxpayer over $1,000,000 and ultimately ...
    • Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish. 

      Hossain, Mohammad J.; Waldbieser, Geoffrey C.; Sun, Dawei; Capps, Nancy K.; Hemstreet, William B.; Carlisle, Kristen; Griffin, Matt J.; Khoo, Lester; Goodwin, Andrew E.; Sonstegard, Tad S.; Schroeder, Steven; Hayden, Karl; Newton, Joseph C.; Terhune, Jeffery S.; Liles, Mark R. (Public Library of ScienceCollege of Veterinary Medicine, 11/20/2013)
      To investigate the molecular basis of the emergence of Aeromonas hydrophila responsible for an epidemic outbreak of motile aeromonad septicemia of catfish in the Southeastern United States, we sequenced 11 A. hydrophila ...
    • Investigation of the role of TNF-? converting enzyme (TACE) in the inhibition of cell surface and soluble TNF-? production by acute ethanol exposure. 

      von Maltzan, Kristine; Tan, Wei; Pruett, Stephen B. (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 2/3/2012)
      Toll-like receptors (TLRs) play a fundamental role in the immune system by detecting pathogen associated molecular patterns (PAMPs) to sense host infection. Ethanol at doses relevant for humans inhibits the pathogen induced ...
    • Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions. 

      Paul, Debarati; Kumar, Ranjit; Nanduri, Bindu; French, Todd; Pendarvis, Ken; Brown, Ashli; Lawrence, Mark L.; Burgess, Shane C. (Public Library of ScienceDepartment of Chemical EngineeringDepartment of Biochemistry and Molecular BiologyCollege of Veterinary MedicineJames Worth Bagley College of EngineeringCollege of Agriculture and Life SciencesLife Sciences and Biotechnology Institute, 2/28/2011)
      Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium able to utilize CO and H(2) to derive energy for fixation of CO(2). Thus, it is capable of growth using syngas, which is a ...
    • Proteomics-based systems biology modeling of bovine germinal vesicle stage oocyte and cumulus cell interaction. 

      Peddinti, Divyaswetha; Memili, Erdogan; Burgess, Shane C. (Public Library of ScienceDepartment of Basic SciencesDepartment of Animal and Dairy SciencesCollege of Veterinary MedicineCollege of Agriculture and Life SciencesInstitute for Digital Biology, 6/21/2010)
      BACKGROUND: Oocytes are the female gametes which establish the program of life after fertilization. Interactions between oocyte and the surrounding cumulus cells at germinal vesicle (GV) stage are considered essential for ...
    • Rag1-/- mutant zebrafish demonstrate specific protection following bacterial re-exposure. 

      Hohn, Claudia; Petrie-Hanson, Lora (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 9/6/2012)
      BACKGROUND: Recombination activation gene 1 deficient (rag1(-/-)) mutant zebrafish have a reduced lymphocyte-like cell population that lacks functional B and T lymphocytes of the acquired immune system, but includes Natural ...
    • Re-annotation is an essential step in systems biology modeling of functional genomics data. 

      van den Berg, Bart H. J.; McCarthy, Fiona M.; Lamont, Susan J.; Burgess, Shane C. (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 5/14/2010)
      One motivation of systems biology research is to understand gene functions and interactions from functional genomics data such as that derived from microarrays. Up-to-date structural and functional annotations of genes are ...
    • RNA-seq based transcriptional map of bovine respiratory disease pathogen "Histophilus somni 2336". 

      Kumar, Ranjit; Lawrence, Mark L.; Watt, James; Cooksey, Amanda M.; Burgess, Shane C.; Nanduri, Bindu (Public Library of ScienceCollege of Veterinary Medicine, 1/20/2012)
      Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems ...
    • Role of an iron-dependent transcriptional regulator in the pathogenesis and host response to infection with Streptococcus pneumoniae. 

      Gupta, Radha; Bhatty, Minny; Swiatlo, Edwin; Nanduri, Bindu (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 2/20/2013)
      Iron is a critical cofactor for many enzymes and is known to regulate gene expression in many bacterial pathogens. Streptococcus pneumoniae normally inhabits the upper respiratory mucosa but can also invade and replicate ...
    • Salmonella in broiler litter and properties of soil at farm location. 

      Volkova, Victoriya V.; Bailey, R. Hartford; Wills, Robert W. (Public Library of ScienceDepartment of Pathobiology and Population MedicineCollege of Veterinary Medicine, 7/28/2009)
      Contamination of litter in a broiler grow-out house with Salmonella prior to placement of a new flock has been shown to be a precursor of the flock's Salmonella contamination further down the production continuum. In the ...
    • Sequence-based antigenic change prediction by a sparse learning method incorporating co-evolutionary information. 

      Yang, Jialiang; Zhang, Tong; Wan, Xiu-Feng (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 9/4/2014)
      Rapid identification of influenza antigenic variants will be critical in selecting optimal vaccine candidates and thus a key to developing an effective vaccination program. Recent studies suggest that multiple simultaneous ...
    • Spatiotemporal structure of molecular evolution of H5N1 highly pathogenic avian influenza viruses in Vietnam. 

      Carrel, Margaret A.; Emch, Michael; Jobe, R. Todd; Moody, Aaron; Wan, Xiu-Feng (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 1/8/2010)
      BACKGROUND: Vietnam is one of the countries most affected by outbreaks of H5N1 highly pathogenic avian influenza viruses. First identified in Vietnam in poultry in 2001 and in humans in 2004, the virus has since caused 111 ...
    • Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq. 

      Das, Pranab J.; McCarthy, Fiona M.; Vishnoi, Monika; Paria, Nandina; Gresham, Cathy; Li, Gang; Kachroo, Priyanka; Sudderth, A. Kendrick; Teague, Sheila; Love, Charles C.; Varner, Dickson D.; Chowdhary, Bhanu P.; Raudsepp, Terje (Public Library of ScienceDepartment of Basic SciencesDepartment of Computer Sciences and EngineeringCollege of Veterinary MedicineJames Worth Bagley College of Engineering, 2/11/2013)
      Mature mammalian sperm contain a complex population of RNAs some of which might regulate spermatogenesis while others probably play a role in fertilization and early development. Due to this limited knowledge, the biological ...
    • Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines 

      Chouvarine, Philippe; Cooksey, Amanda M.; McCarthy, Fiona M.; Ray, David A.; Baldwin, Brian S.; Burgess, Shane C.; Peterson, Daniel G. (Public Library of ScienceDepartment of Biochemistry, Molecular Biology, Entomology, and Plant PathologyDepartment of Plant and Soil SciencesDepartment of Biological SciencesCollege of Veterinary MedicineCollege of Agriculture and Life SciencesCollege of Arts and SciencesInstitute for Genomics, Biocomputing and BiotechnologyBost Extension Center, 1/10/2012)
    • Tricarboxylic acid cycle and one-carbon metabolism pathways are important in Edwardsiella ictaluri virulence. 

      Dahal, Neeti; Abdelhamed, Hossam; Lu, Jingjun; Karsi, Attila; Lawrence, Mark L. (Public Library of ScienceDepartment of Basic SciencesCollege of Veterinary Medicine, 6/7/2013)
      Edwardsiella ictaluri is a Gram-negative facultative intracellular pathogen causing enteric septicemia of channel catfish (ESC). The disease causes considerable economic losses in the commercial catfish industry in the ...