Using pyrosequencing to shed light on deep mine microbial ecologyRobert 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...
Functional metagenomic profiling of nine biomesElizabeth A Dinsdale
Department of Biology, San Diego State University, San Diego, California 92182, USA
Nature 452:629-32. 2008
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- 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...
- 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...
- 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...
- 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...
- 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...
- 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
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- 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
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- 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...
- 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...
- 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...
- 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
..RESULTS: Here, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities...
- 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...
Viral metagenomicsRobert 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...
- 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...
- 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...
