Robert A Edwards

Summary

Publications

  1. pmc Using pyrosequencing to shed light on deep mine microbial ecology
    Robert A Edwards
    Department of Biology, San Diego State University, San Diego, USA
    BMC Genomics 7:57. 2006
  2. doi request reprint Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
  3. doi request reprint Biodiversity and biogeography of phages in modern stromatolites and thrombolites
    Christelle Desnues
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:340-3. 2008
  4. pmc Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa
    Rebecca L Vega Thurber
    Department of Biology, Computational Sciences Research Center, and Center for Microbial Sciences, San Diego State University, San Diego, CA 92182, USA
    Proc Natl Acad Sci U S A 105:18413-8. 2008
  5. pmc Applying Shannon's information theory to bacterial and phage genomes and metagenomes
    Sajia Akhter
    Computational Science Research Center, San Diego State University, San Diego, CA, USA
    Sci Rep 3:1033. 2013
  6. pmc Viral communities associated with healthy and bleaching corals
    Kristen L Marhaver
    Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0202, USA
    Environ Microbiol 10:2277-86. 2008
  7. pmc The marine viromes of four oceanic regions
    Florent E Angly
    Department of Biology, San Diego State University, San Diego, California, USA
    PLoS Biol 4:e368. 2006
  8. doi request reprint Metagenomic analysis of stressed coral holobionts
    Rebecca Vega Thurber
    Department of Biology, San Diego State University, San Diego, CA, USA
    Environ Microbiol 11:2148-63. 2009
  9. pmc Multivariate analysis of functional metagenomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University San Diego, CA, USA
    Front Genet 4:41. 2013
  10. pmc The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes
    Florent E Angly
    Biology Department, San Diego State University, San Diego, California, United States of America
    PLoS Comput Biol 5:e1000593. 2009

Collaborators

Detail Information

Publications20

  1. pmc Using pyrosequencing to shed light on deep mine microbial ecology
    Robert A Edwards
    Department of Biology, San Diego State University, San Diego, USA
    BMC Genomics 7:57. 2006
    ..These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology...
  2. doi request reprint Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
    ....
  3. doi request reprint Biodiversity and biogeography of phages in modern stromatolites and thrombolites
    Christelle Desnues
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:340-3. 2008
    ..Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community...
  4. pmc Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa
    Rebecca L Vega Thurber
    Department of Biology, Computational Sciences Research Center, and Center for Microbial Sciences, San Diego State University, San Diego, CA 92182, USA
    Proc Natl Acad Sci U S A 105:18413-8. 2008
    ..These data support the hypotheses that corals experience viral infections, which are exacerbated by stress, and that herpes-like viruses are common in Cnidarians...
  5. pmc Applying Shannon's information theory to bacterial and phage genomes and metagenomes
    Sajia Akhter
    Computational Science Research Center, San Diego State University, San Diego, CA, USA
    Sci Rep 3:1033. 2013
    ....
  6. pmc Viral communities associated with healthy and bleaching corals
    Kristen L Marhaver
    Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0202, USA
    Environ Microbiol 10:2277-86. 2008
    ..Therefore, coral-associated viruses could potentially infect all components of the holobiont--coral, algal and microbial. Thus, we expect viruses to figure prominently in the preservation and breakdown of coral health...
  7. pmc The marine viromes of four oceanic regions
    Florent E Angly
    Department of Biology, San Diego State University, San Diego, California, USA
    PLoS Biol 4:e368. 2006
    ..These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure...
  8. doi request reprint Metagenomic analysis of stressed coral holobionts
    Rebecca Vega Thurber
    Department of Biology, San Diego State University, San Diego, CA, USA
    Environ Microbiol 11:2148-63. 2009
    ..Additionally, low-abundance Vibrio spp. were found to significantly alter microbiome metabolism, suggesting that the contribution of a just a few members of a community can profoundly shift the health status of the coral holobiont...
  9. pmc Multivariate analysis of functional metagenomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University San Diego, CA, USA
    Front Genet 4:41. 2013
    ..Several analyses identified the subtle differences that occur with environments, such as those seen in different regions of the marine environment...
  10. pmc The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes
    Florent E Angly
    Biology Department, San Diego State University, San Diego, California, United States of America
    PLoS Comput Biol 5:e1000593. 2009
    ....
  11. pmc PHACTS, a computational approach to classifying the lifestyle of phages
    Katelyn McNair
    Computational Science Research Center, Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
    Bioinformatics 28:614-8. 2012
    ..Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed...
  12. pmc Microbial ecology of four coral atolls in the Northern Line Islands
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California, USA
    PLoS ONE 3:e1584. 2008
    ..Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide...
  13. pmc Structure and function of a cyanophage-encoded peptide deformylase
    Jeremy A Frank
    Department of Biology, San Diego State University, San Diego, CA 92182 7720, USA
    ISME J 7:1150-60. 2013
    ..Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities...
  14. pmc Real time metagenomics: using k-mers to annotate metagenomes
    Robert A Edwards
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
    Bioinformatics 28:3316-7. 2012
    ..A last-common ancestor approach was also developed to describe the members of the community...
  15. pmc Reference-independent comparative metagenomics using cross-assembly: crAss
    Bas E Dutilh
    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
    Bioinformatics 28:3225-31. 2012
    ..Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences...
  16. pmc An application of statistics to comparative metagenomics
    Beltran Rodriguez-Brito
    Computational Science Research Center, San Diego State University, San Diego, USA
    BMC Bioinformatics 7:162. 2006
    ..Metagenomics also has the potential to identify significantly different metabolic potential in different environments...
  17. 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. ..
  18. ncbi request reprint Viral metagenomics
    Robert A Edwards
    Department of Biology, Center for Microbial Sciences, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
    Nat Rev Microbiol 3:504-10. 2005
    ..Metagenomic analyses of uncultured viral communities circumvent these limitations and can provide insights into the composition and structure of environmental viral communities...
  19. pmc SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
    Ramy K Aziz
    Computation Institute, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 7:e48053. 2012
    ..Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users...
  20. pmc PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
    Sajia Akhter
    Computational Science Research Center, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA
    Nucleic Acids Res 40:e126. 2012
    ..66% false-positive rate...