DNA, Bacterial Concept

subject area of

• Molecular characterization of the Pseudomonas aeruginosa serotype O5 (PAO1) B‐band lipopolysaccharide gene cluster  Journal Articles
• Helicobacter apodemussp. nov., a newHelicobacterspecies identified from the gastrointestinal tract of striped field mice in Korea  Journal Articles
• oriT -Directed Cloning of Defined Large Regions from Bacterial Genomes: Identification of the Sinorhizobium meliloti pExo Megaplasmid Replicator Region  Journal Articles
• A Virulence and Antimicrobial Resistance DNA Microarray Detects a High Frequency of Virulence Genes in Escherichia coli Isolates from Great Lakes Recreational Waters  Journal Articles
• A molecular portrait of maternal sepsis from Byzantine Troy  Journal Articles
• A national investigation of the prevalence and diversity of thermophilic Campylobacter species in agricultural watersheds in Canada  Journal Articles
• A novel nucleoid-associated protein specific to the actinobacteria  Journal Articles
• A phosphate transport system is required for symbiotic nitrogen fixation by Rhizobium meliloti  Journal Articles
• A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history  Journal Articles
• A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.  Journal Articles
• A phylogenomic and molecular marker based proposal for the division of the genus Borrelia into two genera: the emended genus Borrelia containing only the members of the relapsing fever Borrelia, and the genus Borreliella gen. nov. containing the members of the Lyme disease Borrelia (Borrelia burgdorferi sensu lato complex)  Journal Articles
• A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives  Journal Articles
• A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia  Journal Articles
• A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera  Journal Articles
• A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades  Journal Articles
• A standardised method for interpreting the association between mutations and phenotypic drug resistance inMycobacterium tuberculosis  Journal Articles
• A synthetic luxCDABE gene cluster optimized for expression in high-GC bacteria  Journal Articles
• Accuracy of Results Obtained by Performing a Second Ligase Chain Reaction Assay and PCR Analysis on Urine Samples with Positive or Near-Cutoff Results in the LCx Test for Chlamydia trachomatis  Journal Articles
• Action of Nitrofurans on E. Coli  Journal Articles
• Action of some nitrofuran derivatives on glucose metabolism, ATP levels, and macromolecule synthesis in Escherichia coli  Journal Articles
• Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages  Journal Articles
• An Endemic Strain of Staphylococcus haemolyticus Colonizing and Causing Bacteremia in Neonatal Intensive Care Unit Patients  Journal Articles
• An anti-CRISPR from a virulent streptococcal phage inhibits Streptococcus pyogenes Cas9  Journal Articles
• An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli  Journal Articles
• Analysis of a 1600-kilobase Rhizobium meliloti megaplasmid using defined deletions generated in vivo.  Journal Articles
• Analysis of the legume-rhizobia symbiosis in shrubs from central western Spain  Journal Articles
• Analytical Sensitivity, Reproducibility of Results, and Clinical Performance of Five PCR Assays for Detecting Chlamydia pneumoniae DNA in Peripheral Blood Mononuclear Cells  Journal Articles
• Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array  Journal Articles
• AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species  Journal Articles
• Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of Bacteroidales and fecal source tracking markers  Journal Articles
• Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions  Journal Articles
• Association of circulating Chlamydia pneumoniaeDNA with cardiovascular disease: a systematic review  Journal Articles
• Bacillus DNA in fossil bees: an ancient symbiosis?  Journal Articles
• Bacterial DNA patterns identified using paired-end Illumina sequencing of 16S rRNA genes from whole blood samples of septic patients in the emergency room and intensive care unit  Journal Articles
• Bioinformatic evaluation of the secondary metabolism of antistaphylococcal environmental bacterial isolates  Journal Articles
• Biological effects of nitrofurans  Journal Articles
• BldD fromStreptomyces coelicoloris a non-essential global regulator that binds its own promoter as a dimer  Journal Articles
• BldD is a direct regulator of key developmental genes in Streptomyces coelicolor A3(2)  Journal Articles
• Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis  Journal Articles
• Breakage of bacterial DNA by nitrofuran derivatives.  Journal Articles
• Carbapenem-resistant Gram-negative bacilli in Canada 2009-10: results from the Canadian Nosocomial Infection Surveillance Program (CNISP)  Journal Articles
• Changes in the Ultraviolet Sensitivity of Escherichia coli During Growth in Batch Cultures  Journal Articles
• Characterization of Escherichia coli isolated from gut biopsies of newly diagnosed patients with inflammatory bowel disease  Journal Articles
• Characterization of a newly discovered Mu-like bacteriophage, RcapMu, in Rhodobacter capsulatus strain SB1003  Journal Articles
• Characterization of formulated microbial products by denaturing gradient gel electrophoresis, total cellular fatty acid analysis, and DNA microarray analysis  Journal Articles
• Characterization ofStreptococcus milleriGroup Isolates from Expectorated Sputum of Adult Patients with Cystic Fibrosis  Journal Articles
• Chlamydiae-specific proteins and indels: novel tools for studies  Journal Articles
• Chloramphenicol damages bacterial DNA  Journal Articles
• Circulating Nucleic Acids of Chlamydia pneumoniae and Cytomegalovirus in Patients Undergoing Coronary Angiography  Journal Articles
• Cloning and characterization of multiple groEL chaperonin-encoding genes in Rhizobium meliloti  Journal Articles
• Cloning and characterization of the pyruvate carboxylase from Sinorhizobium meliloti Rm1021  Journal Articles
• Cloning of HSP70 (dnaK) gene from Clostridium perfringens using a general polymerase chain reaction based approach  Journal Articles
• Cloning of a Chromosomal Region Responsible for Streptolysin S Production in Streptococcus pyogenes  Conferences
• Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform: Figure 1.  Journal Articles
• Colorimetric biosensing of pathogens using gold nanoparticles  Journal Articles
• Common biosynthetic origins for polycyclic tetramate macrolactams from phylogenetically diverse bacteria  Journal Articles
• Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica  Journal Articles
• Comparison of Gull Feces-Specific Assays Targeting the 16S rRNA Genes of Catellicoccus marimammalium and Streptococcus spp  Journal Articles
• Comparison of an Industry-Derived LCx Chlamydia pneumoniae PCR Research Kit to In-House Assays Performed in Five Laboratories  Journal Articles
• Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils  Journal Articles
• Comparison of plasmid- and chromosome-based polymerase chain reaction assays for detecting Chlamydia trachomatis nucleic acids  Journal Articles
• Comparison of ribotyping, arbitrarily primed PCR, and pulsed-field gel electrophoresis for molecular typing of Listeria monocytogenes  Journal Articles
• Comparison of the Proinflammatory and Procoagulant Properties of Nuclear, Mitochondrial, and Bacterial DNA  Journal Articles
• Complete sequences of a novel blaNDM-1-harbouring plasmid from Providencia rettgeri and an FII-type plasmid from Klebsiella pneumoniae identified in Canada  Journal Articles
• Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors  Journal Articles
• Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification  Journal Articles
• Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria  Journal Articles
• Controlled Expression of an rpoS Antisense RNA Can Inhibit RpoS Function in Escherichia coli  Journal Articles
• Crp Is a Global Regulator of Antibiotic Production in Streptomyces  Journal Articles
• Culture and Molecular Profiling of the Respiratory Tract Microbiota  Journal Articles
• Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age  Journal Articles
• DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA  Journal Articles
• DNA-based real-time detection and quantification of aeromonads from fresh water beaches on Lake Ontario  Journal Articles
• Defining Helicobacter pylori as a Pathogen: Strain Heterogeneity and Virulence  Conferences
• Desiccation as a suitable alternative to cold-storage of phyllosphere samples for DNA-based microbial community analyses.  Journal Articles
• Detection of high risk HPV and Chlamydia trachomatis in vaginal and cervical samples collected with flocked nylon and wrapped rayon dual swabs transported in dry tubes  Journal Articles
• Development of Real-Time PCR Assays for Detection of the Streptococcus milleri Group from Cystic Fibrosis Clinical Specimens by Targeting the cpn60 and 16S rRNA Genes  Journal Articles
• Development of a rapid quantitative PCR assay for direct detection and quantification of culturable and non-culturable Escherichia coli from agriculture watersheds  Journal Articles
• Diagnosis Of Chlamydia Trachomatis Urethral Infection In Symptomatic And Asymptomatic Men By Testing First-Void Urine In A Ligase Chain Reaction Assay  Journal Articles
• Diagnosis of Chlamydia trachomatis genitourinary infection in women by ligase chain reaction assay of urine  Journal Articles
• Distinction between Borrelia and Borreliella is more robustly supported by molecular and phenotypic characteristics than all other neighbouring prokaryotic genera: Response to Margos' et al. "The genus Borrelia reloaded" (PLoS ONE 13(12): e0208432)  Journal Articles
• Distribution and Diversity of Escherichia coli Populations in the South Nation River Drainage Basin, Eastern Ontario, Canada  Journal Articles
• Distribution and potential significance of a gull fecal marker in urban coastal and riverine areas of southern Ontario, Canada  Journal Articles
• Diversity and abundance of the bacterial 16S rRNA gene sequences in forestomach of alpacas (Lama pacos) and sheep (Ovis aries)  Journal Articles
• Diversity of Integron- and Culture-Associated Antibiotic Resistance Genes in Freshwater Floc  Journal Articles
• Division of the genus Borrelia into two genera (corresponding to Lyme disease and relapsing fever groups) reflects their genetic and phenotypic distinctiveness and will lead to a better understanding of these two groups of microbes (Margos et al. (2016) There is inadequate evidence to support the division of the genus Borrelia. Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijsem.0.001717)  Journal Articles
• Drosophila melanogaster as an Animal Model for the Study of Pseudomonas aeruginosa Biofilm Infections In Vivo  Journal Articles
• Dual Effects of MLS Antibiotics  Journal Articles
• EFFECTS OF SOME NITROFURANS ON DNA SYNTHESIS AND PROPHAGE INDUCTION.  Journal Articles
• Ecological Genomics of Marine Roseobacters  Journal Articles
• Endometrial microbiota is more diverse in people with endometriosis than symptomatic controls  Journal Articles
• Endonuclease III and endonuclease IV protect Escherichia coli from the lethal and mutagenic effects of near-UV irradiation  Journal Articles
• Evaluation of the NucliSens Basic Kit for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Genital Tract Specimens Using Nucleic Acid Sequence-Based Amplification of 16S rRNA  Journal Articles
• Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome  Journal Articles
• Evolutionary and functional diversity of the Pseudomonas type IVa pilin island  Journal Articles
• Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis  Journal Articles
• Experience with the antibiotic resistance analysis and DNA fingerprinting in tracking faecal pollution at two lake beaches  Journal Articles
• Exploring the Potential for Actinobacteria as Defensive Symbionts in Fungus-Growing Termites  Journal Articles
• Formation and excision of nitrofuran-DNA adducts in Escherichia coli  Journal Articles
• Functional analysis of genes responsible for the synthesis of the B-band O antigen of Pseudomonas aeruginosa serotype O6 lipopolysaccharide The GenBank accession number for the sequence reported in this paper is AF035937.  Journal Articles
• Functional annotation of putative aminoglycoside antibiotic modifying proteins in Mycobacterium tuberculosis H37Rv  Journal Articles
• Genetic Analysis of Mutations Affecting pckA Regulation in Rhizobium (Sinorhizobium) meliloti  Journal Articles
• Genetic and physical analyses of group E exo- mutants of Rhizobium meliloti  Journal Articles
• Genetic differentiation, recombination and clonal expansion in environmental populations of Cryptococcus gattii in India  Journal Articles
• Genome Sequence of Streptomyces griseus Strain XylebKG-1, an Ambrosia Beetle-Associated Actinomycete  Journal Articles
• Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.  Journal Articles
• Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.  Journal Articles
• Geographic Variation in Bacterial Communities Associated With the Red Turpentine Beetle (Coleoptera: Curculionidae)  Journal Articles
• Heterologous expression-facilitated natural products’ discovery in actinomycetes  Journal Articles
• Hidden antibiotics in actinomycetes can be identified by inactivation of gene clusters for common antibiotics  Journal Articles
• High-throughput DNA sequencing technologies for water and wastewater analysis  Journal Articles
• Hydrocarbon-related microbial processes in the deep sediments of the Eastern Mediterranean Levantine Basin  Journal Articles
• IS LEPROSY SPREADING AMONG NINE-BANDED ARMADILLOS IN THE SOUTHEASTERN UNITED STATES?  Journal Articles
• Identification of Conserved, RpoS-Dependent Stationary-Phase Genes of Escherichia coli  Journal Articles
• Identification of a Novel Group of Bacteria in Sludge from a Deteriorated Biological Phosphorus Removal Reactor  Journal Articles
• Identification of distinctive molecular traits that are characteristic of the phylum “Deinococcus-Thermus” and distinguish its main constituent groups  Journal Articles
• Identification of the DNA adduct formed by metabolism of 1,8-dinitropyrene in Salmonella typhimurium  Journal Articles
• Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System  Journal Articles
• Immunology: Chlamydial immunoglobulin IgG and IgA antibodies in serum and semen are not associated with the presence of Chlamydia trachomatis DNA or rRNA in semen from male partners of infertile couples  Journal Articles
• Incidence and Treatment Outcomes of PharyngealNeisseria gonorrhoeaeandChlamydia trachomatisInfections in Men Who Have Sex with Men: A 13‐Year Retrospective Cohort Study  Journal Articles
• Induction of antimicrobial activities in heterologous streptomycetes using alleles of the Streptomyces coelicolor gene absA1  Journal Articles
• Influences of non-selective interactions of nucleic acids on response rates of nucleic acid fiber optic biosensors  Conferences
• Inhibition of Transformation of Bacillus subtilis by Heavy Metals  Journal Articles
• Insertion/Deletion-Based Approach for the Detection of Escherichia coli O157:H7 in Freshwater Environments  Journal Articles
• Intergenic Sequence Comparison of Escherichia coli Isolates Reveals Lifestyle Adaptations but Not Host Specificity  Journal Articles
• Interspecific relationships of antibiotic resistance in Staphylococcus sp.: isolation and comparison of plasmids determining tetracycline resistance in S. aureus and S. epidermidis  Journal Articles
• Isolation and characterization of Burkholderia cenocepacia CR318, a phosphate solubilizing bacterium promoting corn growth  Journal Articles
• Kisameet Glacial Clay: an Unexpected Source of Bacterial Diversity  Journal Articles
• Laboratory Characterization of Methicillin‐ResistantStaphylococcus aureusin Canadian Hospitals: Results of 5 Years of National Surveillance, 1995–1999  Journal Articles
• Lateral Transfers of Serine Hydroxymethyltransferase (glyA) and UDP-N-Acetylglucosamine Enolpyruvyl Transferase (murA) Genes from Free-living Actinobacteria to the Parasitic Chlamydiae  Journal Articles
• Lipopolysaccharide core phosphates are required for viability and intrinsic drug resistance in Pseudomonas aeruginosa  Journal Articles
• Low-Virulence Citrobacter Species Encode Resistance to Multiple Antimicrobials  Journal Articles
• Mechanism of Mu DNA transposition  Journal Articles
• Mesalazine (5‐aminosalicylic acid) alters faecal bacterial profiles, but not mucosal proteolytic activity in diarrhoea‐predominant irritable bowel syndrome  Journal Articles
• Metabolism of 1-nitropyrene and formation of DNA adducts in Salmonella typhimurium  Journal Articles
• Microbial Diversity and Host-Specific Sequences of Canada Goose Feces  Journal Articles
• Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt  Journal Articles
• Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities  Journal Articles
• Molecular analysis of the leukotoxin determinants from Pasteurella haemolytica serotypes 1 to 16  Journal Articles
• Molecular epidemiology of vancomycin-resistant enterococcal bacteraemia: results from the Canadian Nosocomial Infection Surveillance Program, 1999-2009  Journal Articles
• Molecular mechanisms of cefoxitin resistance in Escherichia coli from the Toronto area hospitals  Journal Articles
• Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus  Journal Articles
• Molecular signatures for members of the genus Dehalococcoides and the class Dehalococcoidia  Journal Articles
• Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales , containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov.  Journal Articles
• Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae  Journal Articles
• Molecular signatures for the phylum Synergistetes and some of its subclades  Journal Articles
• Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment  Journal Articles
• Multiple lines of evidence to identify the sources of fecal pollution at a freshwater beach in Hamilton Harbour, Lake Ontario  Journal Articles
• Multiplex Polymerase Chain Reaction for the Diagnosis of Sexually Transmitted Diseases  Journal Articles
• Mutagen screening with bacteria: Niridazole and nitrofurans  Journal Articles
• NAD(P) ⁺ -Malic Enzyme Mutants of Sinorhizobium sp. Strain NGR234, but Not Azorhizobium caulinodans ORS571, Maintain Symbiotic N ₂ Fixation Capabilities  Journal Articles
• NITROFURAN DERIVATIVES AS RADIOMIMETIC AGENTS: CROSS-RESISTANCE STUDIES WITH ESCHERICHIA COLI.  Journal Articles
• Nitrofuran induced mutagenesis and error prone repair in Escherichia coli  Journal Articles
• Nitrofurazone-reducing enzymes in E. coli and their role in drug activation in vivo  Journal Articles
• Novel DNA Sequences from Natural Strains of the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti  Journal Articles
• On the Road to Bacterial Cell Death  Journal Articles
• Optimization and validation of rep-PCR genotypic libraries for microbial source tracking of environmental Escherichia coli isolates  Journal Articles
• Oral Treatment with Live Lactobacillus reuteri Inhibits the Allergic Airway Response in Mice  Journal Articles
• Overexpression of the dctA gene in Rhizobium meliloti: effect on transport of C₄ dicarboxylates and symbiotic nitrogen fixation  Conferences
• Overexpression, Purification, and Characterization of VanX, a D-, D-Dipeptidase which Is Essential for Vancomycin Resistance in Enterococcus faecium BM4147  Journal Articles
• Overproduction, solubilization, purification and DNA‐binding properties of AmpR from Citrobacter freundii  Journal Articles
• Phenotypic Diversity Caused by Differential RpoS Activity among Environmental Escherichia coli Isolates  Journal Articles
• Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces  Journal Articles
• Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives  Journal Articles
• Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov.  Journal Articles
• Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera  Journal Articles
• Phylogenomic Studies and Molecular Markers Studies Clarifying the Evolutionary Relationships and Classification of Pseudalkalibacillus species: Proposal for the family Guptaeabacillaceae fam. nov. harboring the genera Guptaeabacillus gen. nov. and Exobacillus gen. nov.  Journal Articles
• Phylogenomic and comparative genomic analyses of Leuconostocaceae species: identification of molecular signatures specific for the genera Leuconostoc, Fructobacillus and Oenococcus and proposal for a novel genus Periweissella gen. nov.  Journal Articles
• Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera  Journal Articles
• Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov.  Journal Articles
• Phylogenomic and molecular marker based studies to clarify the evolutionary relationships amongst Anoxybacillus species and demarcation of the family Anoxybacillaceae and some of its constituent genera.  Journal Articles
• Phylogenomic and molecular markers based studies on Staphylococcaceae and Gemella species. Proposals for an emended family Staphylococcaceae and three new families (Abyssicoccaceae fam. nov., Salinicoccaceae fam. nov. and Gemellaceae fam. nov.) harboring four new genera, Lacicoccus gen. nov., Macrococcoides gen. nov., Gemelliphila gen. nov., and Phocicoccus gen. nov.  Journal Articles
• Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus  Journal Articles
• Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov.  Journal Articles
• Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov.  Journal Articles
• Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades  Journal Articles
• Phylogeny of Helicobacter Isolates from Bird and Swine Feces and Description of Helicobacter pametensis sp. nov.  Journal Articles
• Pollux: platform independent error correction of single and mixed genomes  Journal Articles
• Polymorphism and selection of rpoS in pathogenic Escherichia coli  Journal Articles
• Predation in Homogeneous and Heterogeneous Phage Environments Affects Virulence Determinants of Pseudomonas aeruginosa  Journal Articles
• Programming a topologically constrained DNA nanostructure into a sensor  Journal Articles
• Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from archaea to chlamydiae and murA between chlamydiae and Streptomyces a aThe GenBank accession numbers for the sequences reported in this paper are indicated in the text.  Journal Articles
• Pyrosequencing reveals the complex polymicrobial nature of invasive pyogenic infections: microbial constituents of empyema, liver abscess, and intracerebral abscess  Journal Articles
• Rapidly prototyped multi-scale electrodes to minimize the voltage requirements for bacterial cell lysis  Journal Articles
• Recent Developments in the Molecular Biology of Extremely Halophilic Bacteria  Journal Articles
• Redesigned purification yields a fully functional PutA protein dimer from Escherichia coli.  Journal Articles
• Regulatory evolution at the host–pathogen interface  Journal Articles
• Replicate PCR Testing and Probit Analysis for Detection and Quantitation of Chlamydia pneumoniae in Clinical Specimens  Journal Articles
• Repression of Acinetobacter baumannii DNA damage response requires DdrR-assisted binding of UmuDAb dimers to atypical SOS box.  Journal Articles
• Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species  Journal Articles
• Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures  Journal Articles
• Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers  Journal Articles
• Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti  Journal Articles
• Role of intestinal microbiota and metabolites on gut homeostasis and human diseases  Journal Articles
• RpoS regulation of gene expression during exponential growth of Escherichia coli K12  Journal Articles
• Second-Pandemic Strain ofVibrio choleraefrom the Philadelphia Cholera Outbreak of 1849  Journal Articles
• Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes  Journal Articles
• Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes  Journal Articles
• Signals for local and systemic responses of plants to pathogen attack  Journal Articles
• Signature proteins for the major clades of Cyanobacteria  Journal Articles
• Site-directed mutagenesis and DNA sequence of pckA of Rhizobium NGR234, encoding phosphoenolpyruvate carboxykinase: gluconeogenesis and host-dependent symbiotic phenotype  Journal Articles
• Smoking, season, and detection of chlamydia pneumoniaeDNA in clinically stable COPD patients  Journal Articles
• Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation  Journal Articles
• Stability of Microbial Community Profiles Associated with Compacted Bentonite from the Grimsel Underground Research Laboratory  Journal Articles
• Stationary phase-induction of G→T mutations in Escherichia coli  Journal Articles
• Streptomyces IHF uses multiple interfaces to bind DNA  Journal Articles
• Structural Insights into the Regulation of Foreign Genes in Salmonella by the Hha/H-NS Complex  Journal Articles
• Targeted Mutagenesis of Burkholderia thailandensis and Burkholderia pseudomallei through Natural Transformation of PCR Fragments  Journal Articles
• Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid ofYersinia pestisfrom victims of the Black Death  Journal Articles
• The bldD Gene of Streptomyces coelicolor A3(2): a Regulatory Gene Involved in Morphogenesis and Antibiotic Production  Journal Articles
• The BldD Protein from Streptomyces coelicolor Is a DNA-Binding Protein  Journal Articles
• The Divided Bacterial Genome: Structure, Function, and Evolution  Journal Articles
• The Loss of Topography in the Microbial Communities of the Upper Respiratory Tract in the Elderly  Journal Articles
• The Recovery, Interpretation and Use of Ancient Pathogen Genomes  Journal Articles
• The Sinorhizobium meliloti chromosomal origin of replication  Journal Articles
• The action of 1-nitroso-8-nitroprene in Eachericia coli: DNA adduct formation and mutational consequeces in the absence of necleotide excision-repair  Journal Articles
• The complete sequence of the 1,683-kb pSymB megaplasmid from the N ₂ -fixing endosymbiont Sinorhizobium meliloti  Journal Articles
• The development and application of a molecular community profiling strategy to identify polymicrobial bacterial DNA in the whole blood of septic patients  Journal Articles
• The development of a DNA microarray-based assay for the characterization of commercially formulated microbial products  Journal Articles
• The effects of inhaled aztreonam on the cystic fibrosis lung microbiome  Journal Articles
• The genus Prevotella in cystic fibrosis airways  Journal Articles
• The influence of local DNA sequence and DNA repair background on the mutational specificity of 1-nitroso-8-nitropyrene in Escherichia coli: inferences for mutagenic mechanisms.  Journal Articles
• The mutational specificity of 2-(2-furyl)-3-(5-nitro-2-furyl)-acrylamide (AF2) in the lacI gene of Escherichia coli  Journal Articles
• The newly characterized colicin Y provides evidence of positive selection in pore-former colicin diversification During the time this manuscript was being prepared for publication, our colleague James V. Neel passed away. The other authors wish to dedicate this work to his memory. The GenBank accession number for the sequence reported in this paper is AF197335.  Journal Articles
• The relative contribution of methanotrophs to microbial communities and carbon cycling in soil overlying a coal-bed methane seep  Journal Articles
• The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus- Thermus group and cyanobacteria  Journal Articles
• The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator  Journal Articles
• The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga–Flavobacterium–Bacteroides division The GenBank accession numbers for the sequences reported in this paper are AY017380, AY017381, AY017382 and AY017383.  Journal Articles
• Transcriptional regulation of ACC deaminase gene expression inPseudomonas putidaUW4  Journal Articles
• Twenty-Five-Year Outbreak of Pseudomonas aeruginosa Infecting Individuals with Cystic Fibrosis: Identification of the Prairie Epidemic Strain  Journal Articles
• Type 2 diabetes influences bacterial tissue compartmentalisation in human obesity  Journal Articles
• Urine Specimens from Pregnant and Nonpregnant Women Inhibitory to Amplification of Chlamydia trachomatis Nucleic Acid by PCR, Ligase Chain Reaction, and Transcription-Mediated Amplification: Identification of Urinary Substances Associated with Inhibition and Removal of Inhibitory Activity  Journal Articles
• Use of Neonatal Fostering To Remove Helicobacter spp. from Deer Mice (Peromyscus maniculatus).  Journal Articles
• Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts  Journal Articles
• Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis  Journal Articles
• Yersinia pestis and the three plague pandemics–Authors' reply  Journal Articles
• “Colony Sequencing”: Direct Sequencing of Plasmid DNA from Bacterial Colonies  Journal Articles