Genome, Bacterial Concept

subject area of

• Chlamydophila pneumoniae PknD Exhibits Dual Amino Acid Specificity and Phosphorylates Cpn0712, a Putative Type III Secretion YscD Homolog  Journal Articles
• Helicobacter pyloriPhysiology Predicted from Genomic Comparison of Two Strains  Journal Articles
• oriT -Directed Cloning of Defined Large Regions from Bacterial Genomes: Identification of the Sinorhizobium meliloti pExo Megaplasmid Replicator Region  Journal Articles
• A 16th century Escherichia coli draft genome associated with an opportunistic bile infection  Journal Articles
• A Catalog of Reference Genomes from the Human Microbiome  Journal Articles
• A draft genome of Yersinia pestis from victims of the Black Death  Journal Articles
• A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history  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 shotgun lipidomics approach in Sinorhizobium meliloti as a tool in functional genomics  Journal Articles
• An ancestral mitochondrial DNA resembling a eubacterial genome in miniature  Journal Articles
• An assessment of genome annotation coverage across the bacterial tree of life  Journal Articles
• An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products  Journal Articles
• An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli  Journal Articles
• AnnoTree: visualization and exploration of a functionally annotated microbial tree of life  Journal Articles
• AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods  Journal Articles
• Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome  Journal Articles
• Applications of CRISPR-Cas in its natural habitat  Journal Articles
• Automated Identification of Depsipeptide Natural Products by an Informatic Search Algorithm  Journal Articles
• Bacterial evolution: Making a host-adapted bacterium  Journal Articles
• Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes  Journal Articles
• Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins  Journal Articles
• Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes  Journal Articles
• Characterization and complete genome analysis of the surfactin-producing, plant-protecting bacterium Bacillus velezensis 9D-6  Journal Articles
• Characterization of a Rifampin-Inactivating Glycosyltransferase from a Screen of Environmental Actinomycetes  Journal Articles
• Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting  Journal Articles
• Clinically relevant mutations in core metabolic genes confer antibiotic resistance  Journal Articles
• Coevolution of Codon Usage and tRNA Genes Leads to Alternative Stable States of Biased Codon Usage  Journal Articles
• Comparative Genomics of Canadian Epidemic Lineages of Methicillin-Resistant Staphylococcus aureus  Journal Articles
• Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica  Journal Articles
• 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  Journal Articles
• Comparative genomics of metabolic pathways inMycobacteriumspecies: gene duplication, gene decay and lateral gene transfer  Journal Articles
• Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities  Journal Articles
• Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum  Journal Articles
• Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools  Journal Articles
• Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification  Journal Articles
• Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.  Journal Articles
• Contributions of Speed and Accuracy to Translational Selection in Bacteria  Journal Articles
• Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti  Journal Articles
• Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing  Journal Articles
• Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum  Journal Articles
• Development and Validation of a PCR Assay To Detect the Prairie Epidemic Strain of Pseudomonas aeruginosa from Patients with Cystic Fibrosis  Journal Articles
• Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids  Journal Articles
• Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella  Journal Articles
• Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae.  Journal Articles
• Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?  Journal Articles
• Draft Genome Sequence of Streptomyces sp. Strain Wigar10, Isolated from a Surface-Sterilized Garlic Bulb  Journal Articles
• Drugs against superbugs: private lessons from bacteriophages  Journal Articles
• Ecological Genomics of Marine Roseobacters  Journal Articles
• Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus  Journal Articles
• Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark  Journal Articles
• Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks  Journal Articles
• Estimating Selection Pressures from Limited Comparative Data  Journal Articles
• Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss  Journal Articles
• Estimation of Gene Insertion/Deletion Rates with Missing Data  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
• Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction  Journal Articles
• Extending CRISPR-Cas9 Technology from Genome Editing to Transcriptional Engineering in the Genus Clostridium  Journal Articles
• Functional annotation of putative aminoglycoside antibiotic modifying proteins in Mycobacterium tuberculosis H37Rv  Journal Articles
• GPAHex-A synthetic biology platform for Type IV–V glycopeptide antibiotic production and discovery  Journal Articles
• Gene Gain and Gene Loss in Streptococcus: Is It Driven by Habitat?  Journal Articles
• Gene amelioration demonstrated: the journey of nascent genes in bacteria  Journal Articles
• Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation  Journal Articles
• Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome  Journal Articles
• Genome Sequence of Streptomyces griseus Strain XylebKG-1, an Ambrosia Beetle-Associated Actinomycete  Journal Articles
• Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria  Journal Articles
• Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A  Journal Articles
• Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes  Journal Articles
• Genome variation in the symbiotic nitrogen-fixing bacteriumSinorhizobium meliloti  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
• Genomes of the Symbiotic Nitrogen-Fixing Bacteria of Legumes  Journal Articles
• Genomes within genomes: nested symbiosis and its implications for plant evolution  Journal Articles
• Genomic Instability in Regions Adjacent to a Highly ConservedpchProphage inEscherichia coliO157:H7 Generates Diversity in Expression Patterns of the LEE Pathogenicity Island  Journal Articles
• Genomic Profiling of Iron-Responsive Genes in Salmonella enterica Serovar Typhimurium by High-Throughput Screening of a Random Promoter Library  Journal Articles
• Genomic insights into the evolution and ecology of botulinum neurotoxins  Journal Articles
• Genomic inversions in Escherichia coli alter gene expression and are associated with nucleoid protein binding sites  Journal Articles
• Genomic resources for identification of the minimal N₂‐fixing symbiotic genome  Journal Articles
• Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori  Journal Articles
• Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria  Journal Articles
• Heterologous expression-facilitated natural products’ discovery in actinomycetes  Journal Articles
• High rates of lateral gene transfer are not due to false diagnosis of gene absence  Journal Articles
• Human symbionts inject and neutralize antibacterial toxins to persist in the gut  Journal Articles
• Hybrids and hybridization in the Cryptococcus neoformans and Cryptococcus gattii species complexes  Journal Articles
• Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis  Journal Articles
• Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium  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 signature proteins that are distinctive of the Deinococcus-Thermus phylum.  Journal Articles
• Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System  Journal Articles
• Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification  Journal Articles
• Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome  Journal Articles
• IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.  Journal Articles
• Isolation and characterization of Burkholderia cenocepacia CR318, a phosphate solubilizing bacterium promoting corn growth  Journal Articles
• Lateral Gene Transfer Dynamics in the Ancient Bacterial GenusStreptomyces  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
• Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis  Journal Articles
• Madurastatin D1 and D2, Oxazoline Containing Siderophores Isolated from an Actinomadura sp.  Journal Articles
• Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti  Journal Articles
• Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades  Journal Articles
• Molecular signatures for members of the genus Dehalococcoides and the class Dehalococcoidia  Journal Articles
• Molecular signatures for the phylum Synergistetes and some of its subclades  Journal Articles
• Molecular signatures in protein sequences that are characteristics of the phylum Aquificae  Journal Articles
• Multicopy Suppressors for Novel Antibacterial Compounds Reveal Targets and Drug Efflux Susceptibility  Journal Articles
• Novel DNA Sequences from Natural Strains of the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti  Journal Articles
• Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of Pseudomonas aeruginosa  Journal Articles
• Origin and evolution of gene families in Bacteria and Archaea  Journal Articles
• PathFams: statistical detection of pathogen-associated protein domains  Journal Articles
• Patterns of Bacterial Gene Movement  Journal Articles
• Performance Characteristics of Next-Generation Sequencing for the Detection of Antimicrobial Resistance Determinants in Escherichia coli Genomes and Metagenomes  Journal Articles
• Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria  Journal Articles
• Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing  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
• Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation  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 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 comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family  Journal Articles
• Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria  Journal Articles
• Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B  Journal Articles
• Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species  Journal Articles
• Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis  Journal Articles
• Pollux: platform independent error correction of single and mixed genomes  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
• Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli  Journal Articles
• Regulatory evolution at the host–pathogen interface  Journal Articles
• Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures  Journal Articles
• Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti  Journal Articles
• Second-Pandemic Strain ofVibrio choleraefrom the Philadelphia Cholera Outbreak of 1849  Journal Articles
• Selvamicin, an atypical antifungal polyene from two alternative genomic contexts  Journal Articles
• Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes  Journal Articles
• Signature proteins for the major clades of Cyanobacteria  Journal Articles
• Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups  Journal Articles
• Signature proteins that are distinctive of alpha proteobacteria  Journal Articles
• Spatial Patterns of Gene Expression in Bacterial Genomes  Journal Articles
• Streptomyces Exploration: Competition, Volatile Communication and New Bacterial Behaviours  Journal Articles
• Technical guide for genetic advancement of underdeveloped and intractable Clostridium  Journal Articles
• Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions  Journal Articles
• Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome  Journal Articles
• The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist  Journal Articles
• The Composite Genome of the Legume Symbiont Sinorhizobium meliloti  Journal Articles
• The Comprehensive Antibiotic Resistance Database  Journal Articles
• The Divided Bacterial Genome: Structure, Function, and Evolution  Journal Articles
• The Location of Substitutions and Bacterial Genome Arrangements  Journal Articles
• The Recovery, Interpretation and Use of Ancient Pathogen Genomes  Journal Articles
• The Therapeutic Pipeline for Pseudomonas aeruginosa Infections  Journal Articles
• The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins  Journal Articles
• The fate of laterally transferred genes: Life in the fast lane to adaptation or death  Journal Articles
• The role of laterally transferred genes in adaptive evolution  Journal Articles
• Uncovering rate variation of lateral gene transfer during bacterial genome evolution  Journal Articles
• Use of genetic and chemical synthetic lethality as probes of complexity in bacterial cell systems  Journal Articles
• Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts  Journal Articles
• Yersinia pestis: New Evidence for an Old Infection  Journal Articles