Published in PLoS One on June 14, 2013
Draft Genome Sequence of Bacillus pumilus 7P, Isolated from the Soil of the Tatarstan Republic, Russia. Genome Announc (2014) 1.09
Genomic analysis of a ginger pathogen Bacillus pumilus providing the understanding to the pathogenesis and the novel control strategy. Sci Rep (2015) 0.93
Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation. PLoS One (2016) 0.82
Genome Sequence of Bacillus pumilus MTCC B6033. Genome Announc (2014) 0.79
Sterilization of hydrogen peroxide resistant bacterial spores with stabilized chlorine dioxide. AMB Express (2015) 0.77
An ICEBs1-like element may be associated with the extreme radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores. Extremophiles (2013) 0.76
Stratosphere Conditions Inactivate Bacterial Endospores from a Mars Spacecraft Assembly Facility. Astrobiology (2017) 0.75
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform (2004) 72.40
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
NCBI BLAST: a better web interface. Nucleic Acids Res (2008) 15.14
SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res (2011) 9.15
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res (2003) 4.25
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res (2005) 3.22
Non-classical protein secretion in bacteria. BMC Microbiol (2005) 3.17
InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol (2007) 3.05
The Bacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene. Genes Dev (1990) 2.44
Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev (2011) 2.41
Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One (2007) 1.71
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 1.69
Getting the most from PSI-BLAST. Trends Biochem Sci (2002) 1.59
Hierarchical evolution of the bacterial sporulation network. Curr Biol (2010) 1.50
Recurrent isolation of hydrogen peroxide-resistant spores of Bacillus pumilus from a spacecraft assembly facility. Astrobiology (2005) 1.46
Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces. Int J Syst Evol Microbiol (2006) 1.46
Control of bacterial spores. Br Med Bull (2000) 1.42
Survival of spacecraft-associated microorganisms under simulated martian UV irradiation. Appl Environ Microbiol (2005) 1.37
Role of DNA repair by nonhomologous-end joining in Bacillus subtilis spore resistance to extreme dryness, mono- and polychromatic UV, and ionizing radiation. J Bacteriol (2007) 1.33
Survival of endospores of Bacillus subtilis on spacecraft surfaces under simulated martian environments: implications for the forward contamination of Mars. Icarus (2003) 1.27
Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species. Proc Natl Acad Sci U S A (2008) 1.27
Extreme spore UV resistance of Bacillus pumilus isolates obtained from an ultraclean Spacecraft Assembly Facility. Microb Ecol (2003) 1.22
Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analyses. Gene (2004) 1.22
The role of laterally transferred genes in adaptive evolution. BMC Evol Biol (2007) 1.18
The two major spore DNA repair pathways, nucleotide excision repair and spore photoproduct lyase, are sufficient for the resistance of Bacillus subtilis spores to artificial UV-C and UV-B but not to solar radiation. Appl Environ Microbiol (1996) 1.17
Recurrent isolation of extremotolerant bacteria from the clean room where Phoenix spacecraft components were assembled. Astrobiology (2010) 1.16
Temporal regulation and forespore-specific expression of the spore photoproduct lyase gene by sigma-G RNA polymerase during Bacillus subtilis sporulation. J Bacteriol (1994) 1.12
Survival of Bacillus pumilus spores for a prolonged period of time in real space conditions. Astrobiology (2012) 1.10
Spore UV and acceleration resistance of endolithic Bacillus pumilus and Bacillus subtilis isolates obtained from Sonoran desert basalt: implications for lithopanspermia. Astrobiology (2003) 1.04
Bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the Mars Odyssey spacecraft. Int J Syst Evol Microbiol (2004) 1.03
Gene duplications in prokaryotes can be associated with environmental adaptation. BMC Genomics (2010) 1.01
Spx mediates oxidative stress regulation of the methionine sulfoxide reductases operon in Bacillus subtilis. BMC Microbiol (2008) 1.01
Resistance of bacterial endospores to outer space for planetary protection purposes--experiment PROTECT of the EXPOSE-E mission. Astrobiology (2012) 0.99
Planetary protection policy overview and application to future missions. Adv Space Res (1989) 0.98
DNA photolyase homologs are the major UV resistance factors in the cyanobacterium Synechocystis sp. PCC 6803. Mol Gen Genet (2001) 0.97
Planetary exploration in the time of astrobiology: protecting against biological contamination. Proc Natl Acad Sci U S A (2001) 0.97
Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria. BMC Genomics (2008) 0.93
Role of the Nfo and ExoA apurinic/apyrimidinic endonucleases in repair of DNA damage during outgrowth of Bacillus subtilis spores. J Bacteriol (2008) 0.92
Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room. Int J Syst Evol Microbiol (2009) 0.90
The Deinococcus radiodurans DR1245 protein, a DdrB partner homologous to YbjN proteins and reminiscent of type III secretion system chaperones. PLoS One (2013) 0.89
Evaluation of various cleaning methods to remove bacillus spores from spacecraft hardware materials. Astrobiology (2004) 0.88
Global analysis of genomic texts: the distribution of AGCT tetranucleotides in the Escherichia coli and Bacillus subtilis genomes predicts translational frameshifting and ribosomal hopping in several genes. Electrophoresis (1998) 0.87
Protective role of spore structural components in determining Bacillus subtilis spore resistance to simulated mars surface conditions. Appl Environ Microbiol (2012) 0.86
Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont. Genome Biol Evol (2011) 0.85
UV photochemistry of DNA in vitro and in Bacillus subtilis spores at earth-ambient and low atmospheric pressure: implications for spore survival on other planets or moons in the solar system. Astrobiology (2002) 0.83
A consensus approach to planetary protection requirements: recommendations for Mars lander missions. Adv Space Res (1996) 0.81
Genome display tool: visualizing features in complex data sets. Source Code Biol Med (2007) 0.81
Implementing planetary protection requirements for sample return missions. Adv Space Res (2000) 0.81
Ribosome hopping and translational frameshifting are inadequate alternatives to translational attenuation in cat-86 regulation. J Bacteriol (1991) 0.80
Protection of Bacillus pumilus spores by catalases. Appl Environ Microbiol (2012) 0.80
Multifactorial resistance of Bacillus subtilis spores to high-energy proton radiation: role of spore structural components and the homologous recombination and non-homologous end joining DNA repair pathways. Astrobiology (2012) 0.80
Deinococcus aetherius sp. nov., isolated from the stratosphere. Int J Syst Evol Microbiol (2009) 0.79
Planetary Protection Policy (U.S.A.). Adv Space Res (1992) 0.78
The Neisseria gonorrhoeae photolyase orthologue phrB is required for proper DNA supercoiling but does not function in photo-reactivation. Mol Microbiol (2010) 0.78
DNA cyclobutane pyrimidine dimers with a cleaved internal phosphodiester bond can be photoenzymatically reversed by Escherichia coli PhrB photolyase. Nucleic Acids Res (1988) 0.78
Deinococcus radiodurans YgjD and YeaZ are involved in the repair of DNA cross-links. Extremophiles (2012) 0.77
Involvement of recF in 254 nm ultraviolet radiation resistance in Deinococcus radiodurans and Escherichia coli. Curr Microbiol (2010) 0.77
[Comparison of susceptibility of spores of Bacillus subtilis and Czech strains of Clostridium difficile to disinfectants]. Epidemiol Mikrobiol Imunol (2009) 0.76
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature (2010) 19.68
Direct selection of human genomic loci by microarray hybridization. Nat Methods (2007) 17.73
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (2009) 16.04
The Atlas genome assembly system. Genome Res (2004) 9.78
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science (2009) 7.64
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res (2007) 6.42
The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41
Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol (2009) 6.10
A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res (2009) 4.78
Genomic variation landscape of the human gut microbiome. Nature (2012) 4.38
Creating a honey bee consensus gene set. Genome Biol (2007) 4.17
Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83
Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med (2013) 3.65
Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol (2013) 3.32
Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol (2007) 3.25
Genetic basis for in vivo daptomycin resistance in enterococci. N Engl J Med (2011) 3.20
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol (2008) 2.97
Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol (2008) 2.71
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A (2004) 2.60
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature (2013) 2.53
Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J Bacteriol (2004) 2.44
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res (2006) 2.42
Novel bacterial taxa in the human microbiome. PLoS One (2012) 2.35
The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet (2011) 2.16
Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PLoS One (2012) 2.09
Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLoS One (2010) 2.02
Community annotation: procedures, protocols, and supporting tools. Genome Res (2006) 1.91
Clinical isolates of Enterococcus faecium exhibit strain-specific collagen binding mediated by Acm, a new member of the MSCRAMM family. Mol Microbiol (2003) 1.85
Bos taurus genome assembly. BMC Genomics (2009) 1.83
NCIR: a database of non-canonical interactions in known RNA structures. Nucleic Acids Res (2002) 1.83
Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One (2012) 1.82
Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. PLoS One (2010) 1.81
An Enterococcus faecalis ABC homologue (Lsa) is required for the resistance of this species to clindamycin and quinupristin-dalfopristin. Antimicrob Agents Chemother (2002) 1.79
Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence. J Bacteriol (2006) 1.75
Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One (2007) 1.71
Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med (2013) 1.66
Molecular characterization of a widespread, pathogenic, and antibiotic resistance-receptive Enterococcus faecalis lineage and dissemination of its putative pathogenicity island. J Bacteriol (2005) 1.66
A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement. Eur J Hum Genet (2011) 1.66
Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing. Invest Ophthalmol Vis Sci (2011) 1.63
Targeted high-throughput DNA sequencing for gene discovery in retinitis pigmentosa. Adv Exp Med Biol (2010) 1.58
Sequence analysis of the human virome in febrile and afebrile children. PLoS One (2012) 1.56
The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny. J Bacteriol (2006) 1.55
Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. RNA (2002) 1.50
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. J Math Biol (2012) 1.49
Biogeography of the ecosystems of the healthy human body. Genome Biol (2013) 1.48
Identification and phenotypic characterization of a second collagen adhesin, Scm, and genome-based identification and analysis of 13 other predicted MSCRAMMs, including four distinct pilus loci, in Enterococcus faecium. Microbiology (2008) 1.47
Graph accordance of next-generation sequence assemblies. Bioinformatics (2011) 1.47
Involvement of PhoP-PhoS homologs in Enterococcus faecalis virulence. Infect Immun (2002) 1.46
Systematic cloning of Treponema pallidum open reading frames for protein expression and antigen discovery. Genome Res (2003) 1.44
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol (2012) 1.43
Macrolide treatment failure in a case of secondary syphilis: a novel A2059G mutation in the 23S rRNA gene of Treponema pallidum subsp. pallidum. J Med Microbiol (2009) 1.42
Pooled genomic indexing of rhesus macaque. Genome Res (2005) 1.41
Correlation between ankle-brachial index and microalbuminuria in type 2 diabetes mellitus. Iran J Kidney Dis (2013) 1.40
Evidence that the enterococcal polysaccharide antigen gene (epa) cluster is widespread in Enterococcus faecalis and influences resistance to phagocytic killing of E. faecalis. Infect Immun (2002) 1.39
Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project. Genome Res (2004) 1.36
Daptomycin-resistant Enterococcus faecalis diverts the antibiotic molecule from the division septum and remodels cell membrane phospholipids. MBio (2013) 1.35
Bacterial communities of the coronal sulcus and distal urethra of adolescent males. PLoS One (2012) 1.34
Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. MBio (2013) 1.33
The application of cluster analysis in the intercomparison of loop structures in RNA. RNA (2005) 1.32
Transcriptome of Treponema pallidum: gene expression profile during experimental rabbit infection. J Bacteriol (2005) 1.30
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol (2008) 1.29
A novel Treponema pallidum antigen, TP0136, is an outer membrane protein that binds human fibronectin. Infect Immun (2008) 1.28
Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence. PLoS Negl Trop Dis (2012) 1.27
Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy. Antimicrob Agents Chemother (2012) 1.25
The singular quest for a universal tree of life. Microbiol Mol Biol Rev (2013) 1.24
Detection of viruses in young children with fever without an apparent source. Pediatrics (2012) 1.23
Transferable vancomycin resistance in a community-associated MRSA lineage. N Engl J Med (2014) 1.23
A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol (2011) 1.22
Evolutionary Genomics of Salmonella enterica Subspecies. MBio (2013) 1.17
Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Res (2013) 1.17
Emerging view of the human virome. Transl Res (2012) 1.17
An Enterococcus faecium secreted antigen, SagA, exhibits broad-spectrum binding to extracellular matrix proteins and appears essential for E. faecium growth. Infect Immun (2003) 1.16
Identification of essential domains for Escherichia coli tRNA(leu) aminoacylation and amino acid editing using minimalist RNA molecules. Nucleic Acids Res (2002) 1.16
Survival of rock-colonizing organisms after 1.5 years in outer space. Astrobiology (2012) 1.15
Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. Infect Genet Evol (2011) 1.15
Genome scale identification of Treponema pallidum antigens. Infect Immun (2005) 1.14
Astrovirus MLB2 viremia in febrile child. Emerg Infect Dis (2011) 1.14
Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Clin Infect Dis (2014) 1.11