Published in J Bacteriol on March 05, 2010
PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res (2013) 7.63
The genome of woodland strawberry (Fragaria vesca). Nat Genet (2010) 5.86
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Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS One (2011) 3.01
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J (2011) 2.97
Phylogenomics of prokaryotic ribosomal proteins. PLoS One (2012) 1.82
The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS One (2011) 1.70
Evolutionary transitions in bacterial symbiosis. Proc Natl Acad Sci U S A (2011) 1.69
Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci U S A (2012) 1.40
The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Genome Biol Evol (2014) 1.33
Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence. J Bacteriol (2013) 1.25
A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle. J Bacteriol (2011) 1.23
Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One (2013) 1.23
Novel magnetite-producing magnetotactic bacteria belonging to the Gammaproteobacteria. ISME J (2011) 1.22
Isolation of an aerobic sulfur oxidizer from the SUP05/Arctic96BD-19 clade. ISME J (2012) 1.20
Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses. J Bacteriol (2010) 1.10
Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition. PLoS One (2013) 1.10
Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches. BMC Biol (2011) 1.09
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Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria. BMC Genomics (2015) 1.02
Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist. BMC Genomics (2010) 1.01
A Coxiella-like endosymbiont is a potential vitamin source for the Lone Star tick. Genome Biol Evol (2015) 1.00
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Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. J Bacteriol (2013) 0.95
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Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. PLoS One (2011) 0.90
Genomic features of a bumble bee symbiont reflect its host environment. Appl Environ Microbiol (2014) 0.88
Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase. PLoS One (2014) 0.87
Involvement of the GspAB complex in assembly of the type II secretion system secretin of Aeromonas and Vibrio species. J Bacteriol (2011) 0.86
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Evolutionary origins and diversification of proteobacterial mutualists. Proc Biol Sci (2013) 0.84
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Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species. Front Microbiol (2013) 0.82
Molecular evolution of cytochrome bd oxidases across proteobacterial genomes. Genome Biol Evol (2015) 0.82
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Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales. PLoS One (2013) 0.81
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An inter-order horizontal gene transfer event enables the catabolism of compatible solutes by Colwellia psychrerythraea 34H. Extremophiles (2013) 0.80
Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process. BMC Microbiol (2014) 0.80
Evolution of the methyl directed mismatch repair system in Escherichia coli. DNA Repair (Amst) (2015) 0.80
Horizontal transfers and gene losses in the phospholipid pathway of bartonella reveal clues about early ecological niches. Genome Biol Evol (2014) 0.80
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Horizontal gene acquisition of Liberibacter plant pathogens from a bacteriome-confined endosymbiont of their psyllid vector. PLoS One (2013) 0.79
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Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades. Front Microbiol (2015) 0.78
Functional Interaction between the Cytoplasmic ABC Protein LptB and the Inner Membrane LptC Protein, Components of the Lipopolysaccharide Transport Machinery in Escherichia coli. J Bacteriol (2016) 0.77
Endotoxin structures in the psychrophiles Psychromonas marina and Psychrobacter cryohalolentis contain distinctive acyl features. Mar Drugs (2014) 0.77
Toxin-antitoxin systems in the mobile genome of Acidithiobacillus ferrooxidans. PLoS One (2014) 0.77
Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean. Proc Natl Acad Sci U S A (2016) 0.76
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Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions. Mar Biotechnol (NY) (2015) 0.76
The pine bark Adelgid, Pineus strobi, contains two novel bacteriocyte-associated gammaproteobacterial symbionts. Appl Environ Microbiol (2013) 0.76
Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput Biol (2016) 0.76
Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae). ISME J (2011) 0.76
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol (2017) 0.76
The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity. PLoS One (2016) 0.75
Marine amoebae with cytoplasmic and perinuclear symbionts deeply branching in the Gammaproteobacteria. Sci Rep (2015) 0.75
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The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria. BMC Genomics (2015) 0.75
Composition and Functional Characterization of Microbiome Associated with Mucus of the Coral Fungia echinata Collected from Andaman Sea. Front Microbiol (2016) 0.75
Deterioration to extinction of wastewater bacteria by non-thermal atmospheric pressure air plasma as assessed by 16S rDNA-DGGE fingerprinting. Front Microbiol (2015) 0.75
High Prevalence of Gammaproteobacteria in the Sediments of Admiralty Bay and North Bransfield Basin, Northwestern Antarctic Peninsula. Front Microbiol (2017) 0.75
Ordered orthology as a tool in prokaryotic evolutionary inference. Mob Genet Elements (2015) 0.75
Ribosomal selection of mRNAs with degenerate initiation triplets. Nucleic Acids Res (2017) 0.75
Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc. Front Microbiol (2017) 0.75
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OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03
The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics (2002) 29.41
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics (2002) 19.27
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol (2007) 14.96
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
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An approximately unbiased test of phylogenetic tree selection. Syst Biol (2002) 11.00
An improved general amino acid replacement matrix. Mol Biol Evol (2008) 9.36
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A simple, fast, and accurate method of phylogenomic inference. Genome Biol (2008) 5.47
The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science (2006) 4.54
From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol (2003) 4.47
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Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol (2004) 3.58
Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science (1999) 3.34
Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol (1999) 2.72
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Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. Int J Syst Evol Microbiol (2000) 2.56
A robust species tree for the alphaproteobacteria. J Bacteriol (2007) 2.54
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol (2006) 2.43
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Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation. J Mol Evol (2005) 1.27
Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules. Mol Phylogenet Evol (2004) 1.16
The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evol Biol (2007) 1.09
Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. Int J Syst Evol Microbiol (2009) 1.07
Strong mimicry of an rRNA binding site for two proteins by the mRNA encoding both proteins. RNA Biol (2008) 0.80
PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res (2013) 7.63
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (2006) 6.74
The genome of woodland strawberry (Fragaria vesca). Nat Genet (2010) 5.86
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun (2011) 4.57
Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States. MBio (2013) 4.06
Melanocortin 4 receptor sequence variations are seldom a cause of human obesity: the Swedish Obese Subjects, the HERITAGE Family Study, and a Memphis cohort. J Clin Endocrinol Metab (2002) 3.04
A robust species tree for the alphaproteobacteria. J Bacteriol (2007) 2.54
The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl. Plant Physiol (2005) 2.13
A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework. OMICS (2003) 2.10
Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol (2009) 1.96
Plasmids and rickettsial evolution: insight from Rickettsia felis. PLoS One (2007) 1.85
Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol (2009) 1.76
Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS One (2008) 1.67
The human obesity gene map: the 2004 update. Obes Res (2005) 1.64
PIML: the Pathogen Information Markup Language. Bioinformatics (2004) 1.59
Serial analysis of gene expression in the skeletal muscle of endurance athletes compared to sedentary men. FASEB J (2003) 1.56
The S8 serine, C1A cysteine and A1 aspartic protease families in Arabidopsis. Phytochemistry (2004) 1.42
GeneTrees: a phylogenomics resource for prokaryotes. Nucleic Acids Res (2006) 1.34
The human obesity gene map: the 2001 update. Obes Res (2002) 1.32
Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence. J Bacteriol (2013) 1.25
Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont. Genome Biol Evol (2013) 1.24
Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondrion-associated gene expression in mouse macrophages. Infect Immun (2006) 1.20
Multigene phylogeny reveals eusociality evolved twice in vespid wasps. Proc Natl Acad Sci U S A (2007) 1.19
The human obesity gene map: the 2002 update. Obes Res (2003) 1.08
New tick defensin isoform and antimicrobial gene expression in response to Rickettsia montanensis challenge. Infect Immun (2007) 1.07
Anaplasma marginale type IV secretion system proteins VirB2, VirB7, VirB11, and VirD4 are immunogenic components of a protective bacterial membrane vaccine. Infect Immun (2010) 1.04
The pathogen resource integration center: implications for Rickettsial research. Ann N Y Acad Sci (2005) 1.03
Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection. Mol Plant Microbe Interact (2007) 1.02
Variations on the tmRNA gene. RNA Biol (2009) 1.00
Comparative genomic analysis and phylogenetic position of Theileria equi. BMC Genomics (2012) 0.97
TolC-dependent secretion of an ankyrin repeat-containing protein of Rickettsia typhi. J Bacteriol (2012) 0.94
Named entity recognition for bacterial Type IV secretion systems. PLoS One (2011) 0.93
Surface proteome analysis and characterization of surface cell antigen (Sca) or autotransporter family of Rickettsia typhi. PLoS Pathog (2012) 0.92
Influence of the poly-3-hydroxybutyrate (PHB) granule-associated proteins (PhaP1 and PhaP2) on PHB accumulation and symbiotic nitrogen fixation in Sinorhizobium meliloti Rm1021. J Bacteriol (2007) 0.92
Targets of the Entamoeba histolytica transcription factor URE3-BP. PLoS Negl Trop Dis (2008) 0.91
Roles of poly-3-hydroxybutyrate (PHB) and glycogen in symbiosis of Sinorhizobium meliloti with Medicago sp. Microbiology (2007) 0.91
Sinorhizobium meliloti 1021 loss-of-function deletion mutation in chvI and its phenotypic characteristics. Mol Plant Microbe Interact (2010) 0.90
Characterization of an Entamoeba histolytica high-mobility-group box protein induced during intestinal infection. Eukaryot Cell (2008) 0.90
A typhus group-specific protease defies reductive evolution in rickettsiae. J Bacteriol (2009) 0.89
Rickettsia typhi possesses phospholipase A2 enzymes that are involved in infection of host cells. PLoS Pathog (2013) 0.89
Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. MBio (2012) 0.88
Extensive diversity of Rickettsiales bacteria in two species of ticks from China and the evolution of the Rickettsiales. BMC Evol Biol (2014) 0.87
Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment. Syst Biol (2007) 0.87
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Characterization and RNA-seq analysis of underperformer, an activation-tagged potato mutant. Plant Mol Biol (2013) 0.83
Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. MBio (2012) 0.83
Decoding the ubiquitin-mediated pathway of arthropod disease vectors. PLoS One (2013) 0.79
Transposon tagging in diploid strawberry. Plant Biotechnol J (2012) 0.79
An active ac/ds transposon system for activation tagging in tomato cultivar m82 using clonal propagation. Plant Physiol (2013) 0.78
Detection of Blastocrithidia spp. (Kinetoplastida: Trypanosomatidae) in Chagas disease vectors from Texas, USA. Vector Borne Zoonotic Dis (2009) 0.76
Developing bioinformatic resources for coronaviruses. Adv Exp Med Biol (2006) 0.75
PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform (2017) 0.75