Published in Proc Natl Acad Sci U S A on March 31, 2014
Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev (2015) 1.14
Structural basis for Na(+) transport mechanism by a light-driven Na(+) pump. Nature (2015) 1.05
Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom. ISME J (2014) 0.91
Characterization of a Cyanobacterial Chloride-pumping Rhodopsin and Its Conversion into a Proton Pump. J Biol Chem (2015) 0.87
Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. ISME J (2015) 0.86
In Vitro Demonstration of Dual Light-Driven Na(+)/H(+) Pumping by a Microbial Rhodopsin. Biophys J (2015) 0.85
Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology. Microbiol Mol Biol Rev (2016) 0.84
Nature's toolkit for microbial rhodopsin ion pumps. Proc Natl Acad Sci U S A (2014) 0.84
Ion-pumping microbial rhodopsins. Front Mol Biosci (2015) 0.84
From Gene to Function: Cell-free Electrophysiological and Optical Analysis of Ion Pumps in Nanodiscs. Biophys J (2017) 0.82
Winter diversity and expression of proteorhodopsin genes in a polar ocean. ISME J (2015) 0.80
Characterization of an Unconventional Rhodopsin from the Freshwater Actinobacterium Rhodoluna lacicola. J Bacteriol (2015) 0.80
Diversity and functional analysis of light-driven pumping rhodopsins in marine Flavobacteria. Microbiologyopen (2015) 0.80
Real-time kinetics of electrogenic Na(+) transport by rhodopsin from the marine flavobacterium Dokdonia sp. PRO95. Sci Rep (2016) 0.77
Using total internal reflection fluorescence microscopy to visualize rhodopsin-containing cells. Appl Environ Microbiol (2015) 0.77
Functional metagenomic screen reveals new and diverse microbial rhodopsins. ISME J (2016) 0.76
Asymmetric Functional Conversion of Eubacterial Light-driven Ion Pumps. J Biol Chem (2016) 0.76
Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif. Nat Commun (2016) 0.75
Molecular properties of a DTD channelrhodopsin from Guillardia theta. Biophys Physicobiol (2017) 0.75
Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium. Genome Announc (2014) 0.75
Draft Genome Sequences of Marine Flavobacterium Nonlabens Strains NR17, NR24, NR27, NR32, NR33, and Ara13. Genome Announc (2014) 0.75
Biochemical Analysis of Microbial Rhodopsins. Curr Protoc Microbiol (2016) 0.75
Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3. J Biol Chem (2016) 0.75
The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (2011) 220.97
The RAST Server: rapid annotations using subsystems technology. BMC Genomics (2008) 175.18
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci (1992) 44.38
Circos: an information aesthetic for comparative genomics. Genome Res (2009) 40.02
Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol (1971) 14.93
SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics (1998) 11.91
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science (2000) 10.82
IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics (2009) 5.69
Vibrational spectroscopy of bacteriorhodopsin mutants: light-driven proton transport involves protonation changes of aspartic acid residues 85, 96, and 212. Biochemistry (1988) 4.93
Identification of a third rhodopsin-like pigment in phototactic Halobacterium halobium. Proc Natl Acad Sci U S A (1982) 4.38
Control of transmembrane ion fluxes to select halorhodopsin-deficient and other energy-transduction mutants of Halobacterium halobium. Proc Natl Acad Sci U S A (1982) 4.31
Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol (2000) 4.01
Halorhodopsin is a light-driven chloride pump. J Biol Chem (1982) 3.24
Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature (2007) 3.20
Aspartic acid-96 is the internal proton donor in the reprotonation of the Schiff base of bacteriorhodopsin. Proc Natl Acad Sci U S A (1989) 3.06
Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature (2005) 2.59
Two possible roles of bacteriorhodopsin; a comparative study of strains of Halobacterium halobium differing in pigmentation. Biochem Biophys Res Commun (1977) 2.44
Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol (2008) 2.38
New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol (2005) 2.23
Xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna. Science (2005) 1.90
Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc Natl Acad Sci U S A (2007) 1.87
The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microbiol (2007) 1.79
The structure and mechanism of the family of retinal proteins from halophilic archaea. Curr Opin Struct Biol (1998) 1.73
Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci U S A (2007) 1.59
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. Nucleic Acids Res (2006) 1.51
The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol (2010) 1.43
A light-driven sodium ion pump in marine bacteria. Nat Commun (2013) 1.38
Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium. ISME J (2011) 1.27
Proton transport by proteorhodopsin requires that the retinal Schiff base counterion Asp-97 be anionic. Biochemistry (2003) 1.23
Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins. Genome Biol Evol (2013) 1.18
Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS One (2013) 1.14
Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PLoS One (2013) 1.08
Indibacter alkaliphilus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake. Int J Syst Evol Microbiol (2010) 1.05
Diversity and functional analysis of proteorhodopsin in marine Flavobacteria. Environ Microbiol (2012) 1.02
Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica. Int J Syst Evol Microbiol (2004) 0.97
Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics. PLoS One (2010) 0.96
Light-stimulated growth of proteorhodopsin-bearing sea-ice psychrophile Psychroflexus torquis is salinity dependent. ISME J (2013) 0.95
Complete genome sequence of Truepera radiovictrix type strain (RQ-24). Stand Genomic Sci (2011) 0.90
Gain and loss of phototrophic genes revealed by comparison of two Citromicrobium bacterial genomes. PLoS One (2012) 0.84
Genome sequence of Fulvimarina pelagi HTCC2506T, a Mn(II)-oxidizing alphaproteobacterium possessing an aerobic anoxygenic photosynthetic gene cluster and Xanthorhodopsin. J Bacteriol (2010) 0.84
Nonlabens marinus [corrected] sp. nov., a novel member of the Flavobacteriaceae isolated from the Pacific Ocean. Antonie Van Leeuwenhoek (2012) 0.83
Dead Sea rhodopsins revisited. Environ Microbiol Rep (2012) 0.80
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res (2007) 13.08
Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol (2006) 5.77
Retroperitoneal cystic masses: CT, clinical, and pathologic findings and literature review. Radiographics (2004) 5.24
Reverse methanogenesis: testing the hypothesis with environmental genomics. Science (2004) 4.42
Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature (2002) 4.14
An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc Natl Acad Sci U S A (2006) 3.89
Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A (2006) 3.85
A fourth IkappaB protein within the NF-kappaB signaling module. Cell (2007) 3.34
Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature (2006) 3.27
Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci U S A (2009) 3.17
Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science (2011) 3.12
Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol (2008) 3.10
Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol (2007) 3.10
Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci U S A (2002) 2.90
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci U S A (2010) 2.82
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature (2009) 2.72
Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA Res (2008) 2.72
Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning. Proc Natl Acad Sci U S A (2002) 2.70
Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J (2010) 2.54
Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc Natl Acad Sci U S A (2003) 2.53
Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc Natl Acad Sci U S A (2004) 2.38
Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre. Appl Environ Microbiol (2009) 2.35
Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol (2011) 2.28
Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology (2011) 2.27
Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol (2002) 2.24
Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol (2003) 2.15
The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants. PLoS Pathog (2009) 2.04
Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea. Appl Environ Microbiol (2002) 1.96
Different SAR86 subgroups harbour divergent proteorhodopsins. Environ Microbiol (2004) 1.93
Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J (2008) 1.92
Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ Microbiol (2009) 1.89
A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis. Proc Natl Acad Sci U S A (2009) 1.87
Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta. Appl Environ Microbiol (2005) 1.78
Active HSF1 significantly suppresses polyglutamine aggregate formation in cellular and mouse models. J Biol Chem (2005) 1.77
Core protein of hepatitis C virus induces cardiomyopathy. Circ Res (2004) 1.73
Vascular endothelial growth factor-expressing mesenchymal stem cell transplantation for the treatment of acute myocardial infarction. Arterioscler Thromb Vasc Biol (2005) 1.73
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J (2010) 1.72
Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res (2008) 1.71
Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ Microbiol (2008) 1.67
Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc Natl Acad Sci U S A (2012) 1.62
The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. DNA Res (2008) 1.59
Microbial oceanography of anoxic oxygen minimum zones. Proc Natl Acad Sci U S A (2012) 1.59
Clinical significance of Escherichia albertii. Emerg Infect Dis (2012) 1.57
ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorrhagic Escherichia coli through activation of two virulence regulatory genes. Mol Microbiol (2006) 1.53
Angiotensin II receptor blocker reduces oxidative stress and attenuates hypoxia-induced left ventricular remodeling in apolipoprotein E-knockout mice. Hypertens Res (2007) 1.51
Bacterial motility: links to the environment and a driving force for microbial physics. FEMS Microbiol Ecol (2006) 1.49
Pitavastatin reduces oxidative stress and attenuates intermittent hypoxia-induced left ventricular remodeling in lean mice. Hypertens Res (2010) 1.43
Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla. Environ Microbiol (2007) 1.41
Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor. Appl Environ Microbiol (2003) 1.40
Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc Natl Acad Sci U S A (2013) 1.39
A light-driven sodium ion pump in marine bacteria. Nat Commun (2013) 1.38
Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes. Genome Biol (2007) 1.37
Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2. J Bacteriol (2009) 1.37
Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method. DNA Res (2007) 1.37
NleC, a type III secretion protease, compromises NF-κB activation by targeting p65/RelA. PLoS Pathog (2010) 1.36
Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. Environ Microbiol (2008) 1.36
Evolutionary biology in biodiversity science, conservation, and policy: a call to action. Evolution (2010) 1.36
Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J (2011) 1.28
The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny. Proc Natl Acad Sci U S A (2005) 1.28
Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli. DNA Res (2008) 1.27
Comparative genomic analysis using microarray demonstrates a strong correlation between the presence of the 80-kilobase pathogenicity island and pathogenicity in Kanagawa phenomenon-positive Vibrio parahaemolyticus strains. Infect Immun (2008) 1.26
Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes. Genome Res (2009) 1.23
Isolation of Pseudomonas aeruginosa from open ocean and comparison with freshwater, clinical, and animal isolates. Microb Ecol (2007) 1.23
Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria. Appl Environ Microbiol (2006) 1.22
Clonal association of Staphylococcus aureus causing bullous impetigo and the emergence of new methicillin-resistant clonal groups in Kansai district in Japan. J Infect Dis (2002) 1.20
Recruitment and biological consequences of histone modification of H3K27me3 and H3K9me3. ILAR J (2012) 1.19
Imprinting control region (ICR) of the Peg3 domain. Hum Mol Genet (2012) 1.19
High-level fluoroquinolone resistance in ophthalmic clinical isolates belonging to the species Corynebacterium macginleyi. J Clin Microbiol (2007) 1.18
Complete nucleotide sequence of plasmid Rts1: implications for evolution of large plasmid genomes. J Bacteriol (2002) 1.18
The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing. DNA Res (2011) 1.18
Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. Environ Microbiol (2011) 1.16
Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor. Appl Environ Microbiol (2005) 1.15
DNA-binding motif and target genes of the imprinted transcription factor PEG3. Gene (2012) 1.15
ORF30 and ORF34 are essential for expression of late genes in murine gammaherpesvirus 68. J Virol (2008) 1.14
Multilocus sequence typing and phylogenetic analyses of Pseudomonas aeruginosa Isolates from the ocean. Appl Environ Microbiol (2008) 1.14
Colistin-Resistant mcr-1-Positive Pathogenic Escherichia coli in Swine, Japan, 2007-2014. Emerg Infect Dis (2016) 1.14
The genome of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas, reveals new insights into the evolution of firmicutes and the organism's intracellular adaptations. J Bacteriol (2011) 1.12
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics (2014) 1.12
Systematic identification and sequence analysis of the genomic islands of the enteropathogenic Escherichia coli strain B171-8 by the combined use of whole-genome PCR scanning and fosmid mapping. J Bacteriol (2008) 1.11
Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone. Ecology (2012) 1.10
TccP2 of O157:H7 and non-O157 enterohemorrhagic Escherichia coli (EHEC): challenging the dogma of EHEC-induced actin polymerization. Infect Immun (2006) 1.09
Development of a multiplex PCR-based rapid typing method for enterohemorrhagic Escherichia coli O157 strains. J Clin Microbiol (2009) 1.08