Published in Appl Environ Microbiol on August 30, 2013
Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains. BMC Microbiol (2013) 0.80
Archaeal viruses multiply: temporal screening in a solar saltern. Viruses (2015) 0.78
Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME J (2015) 0.78
Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi. BMC Genomics (2015) 0.78
Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods. J Virol (2016) 0.78
Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses. Viruses (2016) 0.76
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. PLoS One (2016) 0.75
Putative archaeal viruses from the mesopelagic ocean. PeerJ (2017) 0.75
A novel Halomonas ventosae-specific virulent halovirus isolated from the Qiaohou salt mine in Yunnan, Southwest China. Extremophiles (2015) 0.75
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics (2010) 42.80
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics (2008) 29.20
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
InterProScan: protein domains identifier. Nucleic Acids Res (2005) 18.82
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
TM4 microarray software suite. Methods Enzymol (2006) 13.78
Functional metagenomic profiling of nine biomes. Nature (2008) 11.00
Marine viruses and their biogeochemical and ecological effects. Nature (1999) 10.77
Marine viruses--major players in the global ecosystem. Nat Rev Microbiol (2007) 10.14
Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A (2002) 9.21
Global patterns in bacterial diversity. Proc Natl Acad Sci U S A (2007) 8.00
Aligning amino acid sequences: comparison of commonly used methods. J Mol Evol (1985) 7.63
Virus population dynamics and acquired virus resistance in natural microbial communities. Science (2008) 5.54
Explaining microbial population genomics through phage predation. Nat Rev Microbiol (2009) 3.87
Metagenomics: read length matters. Appl Environ Microbiol (2008) 3.51
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science (2012) 3.39
Viral and microbial community dynamics in four aquatic environments. ISME J (2010) 2.95
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics (2005) 2.94
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol (2009) 2.61
It's all relative: ranking the diversity of aquatic bacterial communities. Environ Microbiol (2008) 2.61
The Western English Channel contains a persistent microbial seed bank. ISME J (2011) 2.37
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J (2011) 2.14
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A (2010) 2.09
Sequence assembly demystified. Nat Rev Genet (2013) 2.09
The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One (2013) 1.89
Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci U S A (2013) 1.78
Exploring the viral world through metagenomics. Curr Opin Virol (2011) 1.73
Lineages of acidophilic archaea revealed by community genomic analysis. Science (2006) 1.70
Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A (2007) 1.68
Genetic diversity and temporal variation in the cyanophage community infecting marine Synechococcus species in Rhode Island's coastal waters. Appl Environ Microbiol (2003) 1.66
The archeoviruses. FEMS Microbiol Rev (2011) 1.62
Hypervariable loci in the human gut virome. Proc Natl Acad Sci U S A (2012) 1.58
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environ Microbiol (2012) 1.52
Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean. ISME J (2010) 1.48
Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS One (2012) 1.44
Effects of sunlight on bacteriophage viability and structure. Appl Environ Microbiol (1996) 1.39
Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ Microbiol (2012) 1.36
Portal protein diversity and phage ecology. Environ Microbiol (2008) 1.33
Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One (2013) 1.32
Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology (2012) 1.24
Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. ISME J (2013) 1.20
Haloarchaeal viruses: how diverse are they? Res Microbiol (2003) 1.17
Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS One (2012) 1.10
Virus-host interactions in salt lakes. Curr Opin Microbiol (2007) 1.07
Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol (2012) 1.06
Viral decay and viral production rates in continental-shelf and deep-sea sediments of the Mediterranean Sea. FEMS Microbiol Ecol (2010) 1.06
Protein transport in the halophilic archaeon Halobacterium sp. NRC-1: a major role for the twin-arginine translocation pathway? Microbiology (2002) 1.03
Evaluation of short read metagenomic assembly. BMC Genomics (2011) 1.03
TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus. Environ Microbiol (2011) 1.02
The metavirome of a hypersaline environment. Environ Microbiol (2010) 1.02
Seasonality and monthly dynamics of marine myovirus communities. Environ Microbiol (2012) 0.99
Spatial and temporal scales of aquatic bacterial beta diversity. Front Microbiol (2012) 0.98
Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea (2013) 0.96
Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia. Front Microbiol (2013) 0.95
Virioplankton community structure along a salinity gradient in a solar saltern. Extremophiles (2003) 0.94
Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes. Appl Environ Microbiol (2012) 0.94
Ecological traits of planktonic viruses and prokaryotes along a full-salinity gradient. FEMS Microbiol Ecol (2011) 0.90
Microbiology. Variety--the splice of life--in microbial communities. Science (2009) 0.88
Structural organization of an encephalitic human isolate of Banna virus (genus Seadornavirus, family Reoviridae). J Gen Virol (2005) 0.87
Interannual dynamics of viriobenthos abundance and morphological diversity in Chesapeake Bay sediments. FEMS Microbiol Ecol (2011) 0.86
Culture-independent approaches for studying viruses from hypersaline environments. Appl Environ Microbiol (2012) 0.85
Isolation independent methods of characterizing phage communities 2: characterizing a metagenome. Methods Mol Biol (2009) 0.84
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Virus population dynamics and acquired virus resistance in natural microbial communities. Science (2008) 5.54
Community proteomics of a natural microbial biofilm. Science (2005) 3.97
Community-wide analysis of microbial genome sequence signatures. Genome Biol (2009) 3.96
Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol (2007) 3.89
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science (2012) 3.39
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res (2006) 3.33
Microbial communities in acid mine drainage. FEMS Microbiol Ecol (2003) 3.03
The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS One (2008) 2.91
Microbial polysaccharides template assembly of nanocrystal fibers. Science (2004) 2.88
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res (2012) 2.81
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature (2007) 2.53
Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science (2013) 2.51
Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res (2010) 2.46
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife (2013) 2.36
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol (2011) 2.33
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J (2011) 2.14
Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A (2010) 2.12
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A (2010) 2.09
Microscopic evidence for liquid-liquid separation in supersaturated CaCO3 solutions. Science (2013) 2.03
AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J (2010) 1.95
Conserved noncoding sequences in the grasses. Genome Res (2003) 1.88
Community genomics in microbial ecology and evolution. Nat Rev Microbiol (2005) 1.87
Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol (2009) 1.86
In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science (2012) 1.86
Environmental risks of nanotechnology: National Nanotechnology Initiative funding, 2000-2004. Environ Sci Technol (2006) 1.84
Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol (2009) 1.81
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol (2008) 1.80
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun (2013) 1.80
Lineages of acidophilic archaea revealed by community genomic analysis. Science (2006) 1.70
Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio (2013) 1.70
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome (2013) 1.69
Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A (2007) 1.68
Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J (2010) 1.68
Astrophysical ionizing radiation and Earth: a brief review and census of intermittent intense sources. Astrobiology (2011) 1.60
Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J (2008) 1.60
Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment. Appl Environ Microbiol (2003) 1.58
Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A (2010) 1.58
Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J (2009) 1.58
Protists are microbes too: a perspective. ISME J (2008) 1.57
Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems. Science (2002) 1.55
Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun (2013) 1.55
Nanometre-size products of uranium bioreduction. Nature (2002) 1.54
Direction-specific interactions control crystal growth by oriented attachment. Science (2012) 1.47
Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS One (2013) 1.47
Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol (2009) 1.45
Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome (2014) 1.45
Water-driven structure transformation in nanoparticles at room temperature. Nature (2003) 1.45
The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev (2008) 1.42
Microbiology. Genomes from metagenomics. Science (2013) 1.40
Extracellular proteins limit the dispersal of biogenic nanoparticles. Science (2007) 1.40
Causes of an ad 774-775 14C increase. Nature (2012) 1.35
Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol (2005) 1.35
Genetic exchange across a species boundary in the archaeal genus ferroplasma. Genetics (2007) 1.35
Population genomics in natural microbial communities. Trends Ecol Evol (2006) 1.34
Persisting viral sequences shape microbial CRISPR-based immunity. PLoS Comput Biol (2012) 1.32
Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One (2013) 1.32
Metabolically active eukaryotic communities in extremely acidic mine drainage. Appl Environ Microbiol (2004) 1.30
Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid. Extremophiles (2004) 1.30
Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J (2008) 1.29
Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME J (2008) 1.27
Glycogen-accumulating organisms in laboratory-scale and full-scale wastewater treatment processes. Microbiology (2002) 1.26
Nanoparticles: strained and stiff. Science (2004) 1.21
Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl Environ Microbiol (2003) 1.19
Strainer: software for analysis of population variation in community genomic datasets. BMC Bioinformatics (2007) 1.16
Phage mutations in response to CRISPR diversification in a bacterial population. Environ Microbiol (2012) 1.15
Cultivating the uncultivated: a community genomics perspective. Trends Microbiol (2005) 1.08
Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS One (2012) 1.07
Cultivation and quantitative proteomic analyses of acidophilic microbial communities. ISME J (2009) 1.07
Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J (2008) 1.07
Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments. PLoS One (2013) 1.06
Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol (2012) 1.06
Characterization of extracellular polymeric substances from acidophilic microbial biofilms. Appl Environ Microbiol (2010) 1.06
G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell (2007) 1.06
Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol (2008) 1.05
Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ Microbiol (2011) 1.04
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res (2011) 1.04
Characterization of titanium dioxide nanoparticles using molecular dynamics simulations. J Phys Chem B (2005) 1.04