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