Alice R Wattam

Summary

Affiliation: Virginia Polytechnic Institute and State University
Country: USA

Publications

  1. doi request reprint Comparative genomic analysis at the PATRIC, a bioinformatic resource center
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA
    Methods Mol Biol 1197:287-308. 2014
  2. pmc Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
    J Bacteriol 191:3569-79. 2009
  3. pmc Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
    MBio 3:e00246-11. 2012
  4. pmc PATRIC, the bacterial bioinformatics database and analysis resource
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60637, USA, Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA 24060, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, IL 60637, USA and Nestlé Institute of Health Sciences SA, Campus EPFL, Quartier de l Innovation, Lausanne, Switzerland
    Nucleic Acids Res 42:D581-91. 2014
  5. pmc Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
    MBio 3:e00246-12. 2012
  6. pmc Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
    J Bacteriol 196:920-30. 2014
  7. pmc Curation, integration and visualization of bacterial virulence factors in PATRIC
    Chunhong Mao
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
    Bioinformatics 31:252-8. 2015
  8. pmc The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
    Ross Overbeek
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
    Nucleic Acids Res 42:D206-14. 2014
  9. pmc PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species
    Joseph J Gillespie
    Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061, USA
    Infect Immun 79:4286-98. 2011

Collaborators

Detail Information

Publications9

  1. doi request reprint Comparative genomic analysis at the PATRIC, a bioinformatic resource center
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA
    Methods Mol Biol 1197:287-308. 2014
    ..While PATRIC contains many diverse tools and functionalities to explore both genome-scale and gene expression data, the main focus of this chapter is on comparative analysis of bacterial genomes. ..
  2. pmc Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
    J Bacteriol 191:3569-79. 2009
    ..The SARs contain many genes, including those involved in O-polysaccharide synthesis and type IV secretion, which if mutated or absent significantly affect the ability of Brucella to survive intracellularly in the infected host...
  3. pmc Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
    MBio 3:e00246-11. 2012
    ..The results demonstrate the existence of a group of early-diverging brucellae with traits that depart significantly from those of the Brucella species described thus far...
  4. pmc PATRIC, the bacterial bioinformatics database and analysis resource
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60637, USA, Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA 24060, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, IL 60637, USA and Nestlé Institute of Health Sciences SA, Campus EPFL, Quartier de l Innovation, Lausanne, Switzerland
    Nucleic Acids Res 42:D581-91. 2014
    ..All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue...
  5. pmc Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
    MBio 3:e00246-12. 2012
    ..The results demonstrate the existence of a group of early-diverging brucellae with traits that depart significantly from those of the Brucella species described thus far...
  6. pmc Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence
    Alice R Wattam
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
    J Bacteriol 196:920-30. 2014
    ....
  7. pmc Curation, integration and visualization of bacterial virulence factors in PATRIC
    Chunhong Mao
    Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
    Bioinformatics 31:252-8. 2015
    ..This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity...
  8. pmc The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
    Ross Overbeek
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
    Nucleic Acids Res 42:D206-14. 2014
    ..To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources. ..
  9. pmc PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species
    Joseph J Gillespie
    Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061, USA
    Infect Immun 79:4286-98. 2011
    ..Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided...