Genome, Bacterial Concept

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• Chlamydophila pneumoniae PknD Exhibits Dual Amino Acid Specificity and Phosphorylates Cpn0712, a Putative Type III Secretion YscD Homolog  Academic Article
• Helicobacter pyloriPhysiology Predicted from Genomic Comparison of Two Strains  Academic Article
• oriT -Directed Cloning of Defined Large Regions from Bacterial Genomes: Identification of the Sinorhizobium meliloti pExo Megaplasmid Replicator Region  Academic Article
• A 16th century Escherichia coli draft genome associated with an opportunistic bile infection  Academic Article
• A Catalog of Reference Genomes from the Human Microbiome  Academic Article
• A draft genome of Yersinia pestis from victims of the Black Death  Academic Article
• A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history  Academic Article
• 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  Academic Article
• A shotgun lipidomics approach in Sinorhizobium meliloti as a tool in functional genomics  Academic Article
• An ancestral mitochondrial DNA resembling a eubacterial genome in miniature  Academic Article
• An assessment of genome annotation coverage across the bacterial tree of life  Academic Article
• An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products  Academic Article
• An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli  Academic Article
• AnnoTree: visualization and exploration of a functionally annotated microbial tree of life  Academic Article
• Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome  Academic Article
• Applications of CRISPR-Cas in its natural habitat  Academic Article
• Automated Identification of Depsipeptide Natural Products by an Informatic Search Algorithm  Academic Article
• Bacterial evolution: Making a host-adapted bacterium  Academic Article
• Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins  Academic Article
• Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes  Academic Article
• Characterization and complete genome analysis of the surfactin-producing, plant-protecting bacterium Bacillus velezensis 9D-6  Academic Article
• Characterization of a Rifampin-Inactivating Glycosyltransferase from a Screen of Environmental Actinomycetes  Academic Article
• Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting  Academic Article
• Clinically relevant mutations in core metabolic genes confer antibiotic resistance  Academic Article
• Coevolution of Codon Usage and tRNA Genes Leads to Alternative Stable States of Biased Codon Usage  Academic Article
• Comparative Genomics of Canadian Epidemic Lineages of Methicillin-Resistant Staphylococcus aureus  Academic Article
• Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica  Academic Article
• Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness  Academic Article
• Comparative genomics of metabolic pathways inMycobacteriumspecies: gene duplication, gene decay and lateral gene transfer  Academic Article
• Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools  Academic Article
• Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification  Academic Article
• Contributions of Speed and Accuracy to Translational Selection in Bacteria  Academic Article
• Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti  Academic Article
• Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing  Academic Article
• Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum  Academic Article
• Development and Validation of a PCR Assay To Detect the Prairie Epidemic Strain of Pseudomonas aeruginosa from Patients with Cystic Fibrosis  Academic Article
• Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids  Academic Article
• Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella  Academic Article
• Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?  Academic Article
• Drugs against superbugs: private lessons from bacteriophages  Academic Article
• Ecological Genomics of Marine Roseobacters  Academic Article
• Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus  Academic Article
• Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark  Academic Article
• Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks  Academic Article
• Estimating Selection Pressures from Limited Comparative Data  Academic Article
• Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss  Academic Article
• Estimation of Gene Insertion/Deletion Rates with Missing Data  Academic Article
• Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome  Academic Article
• Evolutionary and functional diversity of thePseudomonastype IVa pilin island  Academic Article
• Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction  Academic Article
• Extending CRISPR-Cas9 Technology from Genome Editing to Transcriptional Engineering in the Genus Clostridium  Academic Article
• Functional annotation of putative aminoglycoside antibiotic modifying proteins in Mycobacterium tuberculosis H37Rv  Academic Article
• GPAHex-A synthetic biology platform for Type IV–V glycopeptide antibiotic production and discovery  Academic Article
• Gene Gain and Gene Loss in Streptococcus: Is It Driven by Habitat?  Academic Article
• Gene amelioration demonstrated: the journey of nascent genes in bacteria  Academic Article
• Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome  Academic Article
• Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria  Academic Article
• Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A  Academic Article
• Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes  Academic Article
• Genome variation in the symbiotic nitrogen-fixing bacteriumSinorhizobium meliloti  Academic Article
• 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.  Academic Article
• Genomes of the Symbiotic Nitrogen-Fixing Bacteria of Legumes  Academic Article
• Genomes within genomes: nested symbiosis and its implications for plant evolution  Academic Article
• Genomic Instability in Regions Adjacent to a Highly Conserved pch Prophage in Escherichia coli O157:H7 Generates Diversity in Expression Patterns of the LEE Pathogenicity Island  Academic Article
• Genomic Profiling of Iron-Responsive Genes in Salmonella enterica Serovar Typhimurium by High-Throughput Screening of a Random Promoter Library  Academic Article
• Genomic insights into the evolution and ecology of botulinum neurotoxins  Academic Article
• Genomic inversions in Escherichia coli alter gene expression and are associated with nucleoid protein binding sites  Academic Article
• Genomic resources for identification of the minimal N₂‐fixing symbiotic genome  Academic Article
• Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori  Academic Article
• Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria  Academic Article
• Heterologous expression-facilitated natural products’ discovery in actinomycetes  Academic Article
• High rates of lateral gene transfer are not due to false diagnosis of gene absence  Academic Article
• Human symbionts inject and neutralize antibacterial toxins to persist in the gut  Academic Article
• Hybrids and hybridization in the Cryptococcus neoformans and Cryptococcus gattii species complexes  Academic Article
• Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis  Academic Article
• Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium  Academic Article
• Identification of distinctive molecular traits that are characteristic of the phylum “Deinococcus-Thermus” and distinguish its main constituent groups  Academic Article
• Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum.  Academic Article
• Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System  Academic Article
• Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification  Academic Article
• Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome  Academic Article
• IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.  Academic Article
• Isolation and characterization of Burkholderia cenocepacia CR318, a phosphate solubilizing bacterium promoting corn growth  Academic Article
• Lateral Transfers of Serine Hydroxymethyltransferase (glyA) and UDP-N-Acetylglucosamine Enolpyruvyl Transferase (murA) Genes from Free-living Actinobacteria to the Parasitic Chlamydiae  Academic Article
• Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis  Academic Article
• Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti  Academic Article
• Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades  Academic Article
• Molecular signatures for members of the genus Dehalococcoides and the class Dehalococcoidia  Academic Article
• Molecular signatures for the phylum Synergistetes and some of its subclades  Academic Article
• Molecular signatures in protein sequences that are characteristics of the phylum Aquificae  Academic Article
• Multicopy Suppressors for Novel Antibacterial Compounds Reveal Targets and Drug Efflux Susceptibility  Academic Article
• Novel DNA Sequences from Natural Strains of the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti  Academic Article
• Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of Pseudomonas aeruginosa  Academic Article
• Origin and evolution of gene families in Bacteria and Archaea  Academic Article
• PathFams: statistical detection of pathogen-associated protein domains  Academic Article
• Patterns of Bacterial Gene Movement  Academic Article
• Performance Characteristics of Next-Generation Sequencing for the Detection of Antimicrobial Resistance Determinants in Escherichia coli Genomes and Metagenomes  Academic Article
• Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria  Academic Article
• Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing  Academic Article
• 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  Academic Article
• Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation  Academic Article
• Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family  Academic Article
• Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria  Academic Article
• Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B  Academic Article
• Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species  Academic Article
• Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis  Academic Article
• Pollux: platform independent error correction of single and mixed genomes  Academic Article
• 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.  Academic Article
• Regulatory evolution at the host–pathogen interface  Academic Article
• Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures  Academic Article
• Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti  Academic Article
• Second-Pandemic Strain ofVibrio choleraefrom the Philadelphia Cholera Outbreak of 1849  Academic Article
• Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes  Academic Article
• Signature proteins for the major clades of Cyanobacteria  Academic Article
• Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups  Academic Article
• Signature proteins that are distinctive of alpha proteobacteria  Academic Article
• Spatial Patterns of Gene Expression in Bacterial Genomes  Academic Article
• Streptomyces Exploration: Competition, Volatile Communication and New Bacterial Behaviours  Academic Article
• Technical guide for genetic advancement of underdeveloped and intractable Clostridium  Academic Article
• Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions  Academic Article
• Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome  Academic Article
• The Composite Genome of the Legume Symbiont Sinorhizobium meliloti  Academic Article
• The Comprehensive Antibiotic Resistance Database  Academic Article
• The Divided Bacterial Genome: Structure, Function, and Evolution  Academic Article
• The Location of Substitutions and Bacterial Genome Arrangements  Academic Article
• The Recovery, Interpretation and Use of Ancient Pathogen Genomes  Academic Article
• The Therapeutic Pipeline for Pseudomonas aeruginosa Infections  Academic Article
• The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins  Academic Article
• The fate of laterally transferred genes: Life in the fast lane to adaptation or death  Academic Article
• The role of laterally transferred genes in adaptive evolution  Academic Article
• Uncovering rate variation of lateral gene transfer during bacterial genome evolution  Academic Article
• Use of genetic and chemical synthetic lethality as probes of complexity in bacterial cell systems  Academic Article
• Yersinia pestis: New Evidence for an Old Infection  Academic Article