Published in J Bacteriol on January 17, 2014
Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria. Front Microbiol (2017) 0.75
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature (2000) 32.30
Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01
The energy charge of the adenylate pool as a regulatory parameter. Interaction with feedback modifiers. Biochemistry (1968) 9.00
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol (2009) 8.36
Genome streamlining in a cosmopolitan oceanic bacterium. Science (2005) 8.11
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature (2004) 5.00
An antioxidant function for DMSP and DMS in marine algae. Nature (2002) 3.59
Thermodynamics-based metabolic flux analysis. Biophys J (2006) 3.35
Oxidative stress in marine environments: biochemistry and physiological ecology. Annu Rev Physiol (2006) 3.29
Transformation of sulfur compounds by an abundant lineage of marine bacteria in the alpha-subclass of the class Proteobacteria. Appl Environ Microbiol (1999) 3.25
Cellular concentrations of enzymes and their substrates. J Theor Biol (1990) 3.12
Bacterial taxa that limit sulfur flux from the ocean. Science (2006) 2.79
Characterization of nucleotide pools as a function of physiological state in Escherichia coli. J Bacteriol (2007) 2.47
Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies. BMC Genomics (2005) 2.34
Cloning, characterization, and functional expression of acs, the gene which encodes acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol (1995) 2.18
Dimethylsulfoniopropionate and methanethiol are important precursors of methionine and protein-sulfur in marine bacterioplankton. Appl Environ Microbiol (1999) 1.96
Dimethylthetin can substitute for glycine betaine as an osmoprotectant molecule for Escherichia coli. J Bacteriol (1987) 1.91
Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase. J Biol Chem (1992) 1.75
Bacterial variations on the methionine salvage pathway. BMC Microbiol (2004) 1.68
Mutational analysis of a fatty acyl-coenzyme A synthetase signature motif identifies seven amino acid residues that modulate fatty acid substrate specificity. J Biol Chem (1997) 1.61
Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol (1997) 1.56
Consequences of reduced intracellular coenzyme A content in Escherichia coli. J Bacteriol (1986) 1.46
Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J Bacteriol (2008) 1.33
Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine. IUBMB Life (2009) 1.32
Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae. Biochemistry (2001) 1.28
Enzymatic microdetermination of serum free fatty acids. Anal Biochem (1979) 1.27
Bacterial Catabolism of Dimethylsulfoniopropionate (DMSP). Front Microbiol (2011) 1.24
Biochemical and structural characterization of the paralogous benzoate CoA ligases from Burkholderia xenovorans LB400: defining the entry point into the novel benzoate oxidation (box) pathway. J Mol Biol (2007) 1.20
One protein, two enzymes. J Biol Chem (1999) 1.19
Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature (2011) 1.18
Disruption of the Saccharomyces cerevisiae FAT1 gene decreases very long-chain fatty acyl-CoA synthetase activity and elevates intracellular very long-chain fatty acid concentrations. J Biol Chem (1998) 1.14
Changes in the size and composition of intracellular pools of nonesterified coenzyme A and coenzyme A thioesters in aerobic and facultatively anaerobic bacteria. Appl Environ Microbiol (1997) 1.01
Formyltetrahydrofolate hydrolase, a regulatory enzyme that functions to balance pools of tetrahydrofolate and one-carbon tetrahydrofolate adducts in Escherichia coli. J Bacteriol (1995) 1.01
XAS investigation of the structure and function of Ni in acireductone dioxygenase. Biochemistry (2002) 0.98
Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999. Int J Syst Evol Microbiol (2007) 0.93
Rat long chain acyl-CoA synthetase 5, but not 1, 2, 3, or 4, complements Escherichia coli fadD. J Biol Chem (2004) 0.88
Characterization of two long-chain fatty acid CoA ligases in the Gram-positive bacterium Geobacillus thermodenitrificans NG80-2. Microbiol Res (2012) 0.83
Protein expression in response to folate stress in Escherichia coli. J Bacteriol (1997) 0.80
Prepublication data sharing. Nature (2009) 12.24
Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol (2002) 11.02
Functional metagenomic profiling of nine biomes. Nature (2008) 11.00
Overview of the marine roseobacter lineage. Appl Environ Microbiol (2005) 5.79
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature (2004) 5.00
Bacterial carbon processing by generalist species in the coastal ocean. Nature (2008) 3.37
Genome characteristics of a generalist marine bacterial lineage. ISME J (2010) 3.11
Molecular and culture-based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus. Appl Environ Microbiol (2002) 2.96
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol (2009) 2.93
The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol (2010) 2.80
Bacterial taxa that limit sulfur flux from the ocean. Science (2006) 2.79
Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci (2008) 2.67
RNA-dependent cysteine biosynthesis in archaea. Science (2005) 2.50
Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol (2005) 2.46
RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci U S A (2006) 2.34
Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc Natl Acad Sci U S A (2013) 2.27
Toward a standards-compliant genomic and metagenomic publication record. OMICS (2008) 2.11
Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME J (2010) 1.90
Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol (2003) 1.85
Abundant and diverse bacteria involved in DMSP degradation in marine surface waters. Environ Microbiol (2008) 1.63
Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon. Environ Microbiol (2009) 1.62
Disruption of the operon encoding Ehb hydrogenase limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. J Bacteriol (2006) 1.58
Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J (2012) 1.53
Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol Cell Proteomics (2006) 1.49
Use of microautoradiography combined with fluorescence in situ hybridization to determine dimethylsulfoniopropionate incorporation by marine bacterioplankton taxa. Appl Environ Microbiol (2004) 1.37
Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage. ISME J (2010) 1.33
Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J Bacteriol (2008) 1.33
Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea. Proc Natl Acad Sci U S A (2007) 1.29
Occurrence and expression of gene transfer agent genes in marine bacterioplankton. Appl Environ Microbiol (2008) 1.28
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J (2013) 1.28
Desulfonatronum thiodismutans sp. nov., a novel alkaliphilic, sulfate-reducing bacterium capable of lithoautotrophic growth. Int J Syst Evol Microbiol (2003) 1.26
Changes in the soil bacterial communities in a cedar plantation invaded by moso bamboo. Microb Ecol (2013) 1.25
Bacterial Catabolism of Dimethylsulfoniopropionate (DMSP). Front Microbiol (2011) 1.24
Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A (2013) 1.21
Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature (2011) 1.18
Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One (2009) 1.17
Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP). Environ Microbiol (2007) 1.17
Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate. ISME J (2010) 1.16
Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis. Proc Natl Acad Sci U S A (2012) 1.15
Formate-dependent H2 production by the mesophilic methanogen Methanococcus maripaludis. Appl Environ Microbiol (2008) 1.15
Genomic insights into bacterial DMSP transformations. Ann Rev Mar Sci (2012) 1.13
Continuous culture of Methanococcus maripaludis under defined nutrient conditions. FEMS Microbiol Lett (2004) 1.13
Bacterioplankton assemblages transforming dissolved organic compounds in coastal seawater. Environ Microbiol (2007) 1.12
In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii. ISME J (2009) 1.10
Cysteine is not the sulfur source for iron-sulfur cluster and methionine biosynthesis in the methanogenic archaeon Methanococcus maripaludis. J Biol Chem (2010) 1.10
Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol (2007) 1.09
Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J Bacteriol (2008) 1.09
Use of internal standards for quantitative metatranscriptome and metagenome analysis. Methods Enzymol (2013) 1.09
Two biosynthetic pathways for aromatic amino acids in the archaeon Methanococcus maripaludis. J Bacteriol (2004) 1.08
Deep sequencing of a dimethylsulfoniopropionate-degrading gene (dmdA) by using PCR primer pairs designed on the basis of marine metagenomic data. Appl Environ Microbiol (2009) 1.08
Analyzing gene expression from marine microbial communities using environmental transcriptomics. J Vis Exp (2009) 1.08
The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics (2009) 1.07
Dimethylsulfoniopropionate turnover is linked to the composition and dynamics of the bacterioplankton assemblage during a microcosm phytoplankton bloom. Appl Environ Microbiol (2005) 1.06
Community analysis of high- and low-nucleic acid-containing bacteria in NW Mediterranean coastal waters using 16S rDNA pyrosequencing. Environ Microbiol (2012) 1.04
Evolution of divergent life history strategies in marine alphaproteobacteria. MBio (2013) 1.04
Omics for understanding microbial functional dynamics. Environ Microbiol (2011) 1.04
Dynamics of bacterial and fungal communities on decaying salt marsh grass. Appl Environ Microbiol (2003) 1.03
Bacterial community transcription patterns during a marine phytoplankton bloom. Environ Microbiol (2011) 1.03
Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method. J Mol Evol (2004) 1.03
Solirubrobacter pauli gen. nov., sp. nov., a mesophilic bacterium within the Rubrobacteridae related to common soil clones. Int J Syst Evol Microbiol (2003) 1.02
Intracellular pyruvate flux in the methane-producing archaeon Methanococcus maripaludis. Arch Microbiol (2002) 1.01
Biosynthesis of 4-thiouridine in tRNA in the methanogenic archaeon Methanococcus maripaludis. J Biol Chem (2012) 1.01
A call to action for the International Committee on Systematics of Prokaryotes. Trends Microbiol (2012) 1.01
The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis. Arch Microbiol (2003) 1.00
Polycyclovorans algicola gen. nov., sp. nov., an aromatic-hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton. Appl Environ Microbiol (2012) 0.99
Diverse organization of genes of the beta-ketoadipate pathway in members of the marine Roseobacter lineage. Appl Environ Microbiol (2004) 0.98
Flow-cytometric cell sorting and subsequent molecular analyses for culture-independent identification of bacterioplankton involved in dimethylsulfoniopropionate transformations. Appl Environ Microbiol (2005) 0.97
Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. Mol Microbiol (2006) 0.97
Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray. Environ Microbiol (2010) 0.97
Comparison of chitinolytic enzymes from an alkaline, hypersaline lake and an estuary. Environ Microbiol (2007) 0.96
The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Arch Microbiol (2003) 0.96
Abundance of 4Fe-4S motifs in the genomes of methanogens and other prokaryotes. FEMS Microbiol Lett (2004) 0.96
Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1. Stand Genomic Sci (2009) 0.96
Characterization of energy-conserving hydrogenase B in Methanococcus maripaludis. J Bacteriol (2010) 0.95
Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol (2006) 0.95
Porticoccus hydrocarbonoclasticus sp. nov., an aromatic hydrocarbon-degrading bacterium identified in laboratory cultures of marine phytoplankton. Appl Environ Microbiol (2011) 0.95
Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development. FEMS Microbiol Ecol (2008) 0.94
Bacterial community diversity in undisturbed perhumid montane forest soils in Taiwan. Microb Ecol (2009) 0.93
SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature (2016) 0.92
Methanogens: a window into ancient sulfur metabolism. Trends Microbiol (2012) 0.92
Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp. and description of Arenibacter algicola sp. nov., an aromatic hydrocarbon-degrading bacterium. Appl Environ Microbiol (2013) 0.91
Bacterial dimethylsulfoniopropionate degradation genes in the oligotrophic north pacific subtropical gyre. Appl Environ Microbiol (2012) 0.91
Changes in dimethylsulfoniopropionate demethylase gene assemblages in response to an induced phytoplankton bloom. Appl Environ Microbiol (2010) 0.91
Anaerovirgula multivorans gen. nov., sp. nov., a novel spore-forming, alkaliphilic anaerobe isolated from Owens Lake, California, USA. Int J Syst Evol Microbiol (2006) 0.91
Genetic systems for hydrogenotrophic methanogens. Methods Enzymol (2011) 0.90
Genome content of uncultivated marine Roseobacters in the surface ocean. Environ Microbiol (2011) 0.90
Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835. Int J Syst Evol Microbiol (2009) 0.90
Environmental, biochemical and genetic drivers of DMSP degradation and DMS production in the Sargasso Sea. Environ Microbiol (2012) 0.90
Algiphilus aromaticivorans gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov. Int J Syst Evol Microbiol (2012) 0.89
Microbial community response to seawater amendment in low-salinity tidal sediments. Microb Ecol (2009) 0.89
Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano. Int J Syst Evol Microbiol (2009) 0.88
Methanococci use the diaminopimelate aminotransferase (DapL) pathway for lysine biosynthesis. J Bacteriol (2010) 0.87