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

Publications31

  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 Combining de novo and reference-guided assembly with scaffold_builder
    Genivaldo GZ Silva
    Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
    Source Code Biol Med 8:23. 2013
    ..Scaffold_builder is written in Python and is available at http://edwards.sdsu.edu/scaffold_builder. A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded. ..
  12. pmc Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
    Savannah E Sanchez
    Department of Biology, San Diego State University
    J Vis Exp . 2015
    ..In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented. ..
  13. doi request reprint Global microbialization of coral reefs
    Andreas F Haas
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nat Microbiol 1:16042. 2016
    ..This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC. ..
  14. pmc Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum
    T David Matthews
    Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
    PLoS ONE 10:e0126883. 2015
    ..The loss of genes necessary for a gastrointestinal lifestyle ultimately leads to a systemic lifestyle and niche exclusion in the host-specific serovars. ..
  15. 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...
  16. 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...
  17. pmc Using viromes to predict novel immune proteins in non-model organisms
    Steven D Quistad
    Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego 92182, USA
    Proc Biol Sci 283:. 2016
    ..The pipeline described here provides a novel method to rapidly predict host immune components that can be applied to virtually any system with the potential to discover novel immune proteins. ..
  18. pmc Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors
    Linda W Kelly
    Department of Biology, San Diego State University, San Diego, CA 92182
    Proc Natl Acad Sci U S A 111:10227-32. 2014
    ..These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes. ..
  19. 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...
  20. 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...
  21. 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...
  22. 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...
  23. doi request reprint Computational approaches to predict bacteriophage-host relationships
    Robert A Edwards
    Department of Computer Science, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941 902, Brazil Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S Cass Ave, Argonne, IL 60439, USA
    FEMS Microbiol Rev 40:258-72. 2016
    ....
  24. pmc Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions
    Bas E Dutilh
    Department of Biology, San Diego State University, San Diego, CA, USA
    BMC Genomics 15:654. 2014
    ..Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat...
  25. 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. ..
  26. 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...
  27. pmc From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model
    Daniel A Cuevas
    Computational Science Research Center, San Diego State University, San Diego CA, USA
    Front Microbiol 7:907. 2016
    ..The extensibility of PyFBA facilitates novel techniques in creating accurate genome-scale metabolic models. ..
  28. pmc Draft Genome Sequence of Cylindrospermopsis raciborskii (Cyanobacteria) Strain ITEP-A1 Isolated from a Brazilian Semiarid Freshwater Body: Evidence of Saxitoxin and Cylindrospermopsin Synthetase Genes
    Adriana Sturion Lorenzi
    Department of Biological Sciences, Laboratory of Cyanobacteria, Luiz de Queiroz College of Agriculture, University of Sao Paulo USP, Piracicaba, Sao Paulo, Brazil Computational Science Research Center, San Diego State University, San Diego, California, USA
    Genome Announc 4:. 2016
    ..The identified genome sequence had 3,605,836 bp, 40.1% G+C, and predicted 3,553 coding sequences (including the synthetase genes). ..
  29. pmc A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
    Bas E Dutilh
    1 Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands 2 Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA 3 Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA 4 Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av Carlos Chagas Fo 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundao, CEP 21941 902 Rio de Janeiro, Brazil
    Nat Commun 5:4498. 2014
    ..Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome...
  30. 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...
  31. 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...