Shannon J Williamson
Affiliation: J. Craig Venter Institute
- The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samplesShannon J Williamson
J Craig Venter Institute, Rockville, Maryland, USA
PLoS ONE 3:e1456. 2008....
- From bacterial to microbial ecosystems (metagenomics)Shannon J Williamson
J Craig Venter Institute, San Diego, CA, USA
Methods Mol Biol 804:35-55. 2012..We highlight their issues and challenges, and review the solutions that are currently in use. We conclude with examples of metagenomic studies conducted on environments of varying complexities...
- Metagenomic exploration of viruses throughout the Indian OceanShannon J Williamson
Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, California, USA
PLoS ONE 7:e42047. 2012..This is the first study to holistically explore virioplankton dynamics across multiple size classes and provides unprecedented insight into virus diversity, metabolic potential and virus-host interactions...
- Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaicLisa Zeigler Allen
Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA, USA
ISME J 6:1403-14. 2012....
- The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein familiesShibu Yooseph
J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS Biol 5:e16. 2007..Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature...
- Genomic and functional adaptation in surface ocean planktonic prokaryotesShibu Yooseph
J Craig Venter Institute, Rockville, Maryland 20850, USA
Nature 468:60-6. 2010..Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass...
- Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environmentEmiley A Eloe
Center for Marine Biotechnology and Biomedicine, Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093 0202, USA Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 USA J Craig Venter Institute, Microbial and Environmental Genomics, La Jolla, CA, USA
Environ Microbiol Rep 3:449-58. 2011..The significance of these results to considerations of deep-sea microbial life and particle colonization is discussed in comparison to the few other deep-ocean phylogenetic surveys available...
- Hydroxyapatite-mediated separation of double-stranded DNA, single-stranded DNA, and RNA genomes from natural viral assemblagesCynthia Andrews-Pfannkoch
J Craig Venter Institute, 10355 Science Center Dr, San Diego, CA 92121, USA
Appl Environ Microbiol 76:5039-45. 2010..Taxonomic analysis demonstrated that the majority of environmental sequences, regardless of their source nucleic acid, were most similar to dsDNA viruses, reflecting the bias of viral metagenomic sequence databases...
- Single virus genomics: a new tool for virus discoveryLisa Zeigler Allen
Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, California, United States of America
PLoS ONE 6:e17722. 2011..The isolation and genome sequencing of uncultivated viruses using Single Virus Genomics approaches will enable researchers to address questions about viral diversity, evolution, adaptation and ecology that were previously unattainable...