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Microbial genomic taxonomy.
This book chapter argues for an open-access catalogue of taxonomic descriptions with
prototypes; diagnostic tables; and links to culture collections, to genome and gene …
prototypes; diagnostic tables; and links to culture collections, to genome and gene …
Comparison of 61 Sequenced Escherichia coli Genomes
Escherichia coli is an important component of the biosphere and is an ideal model for
studies of processes involved in bacterial genome evolution. Sixty-one publically available …
studies of processes involved in bacterial genome evolution. Sixty-one publically available …
GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis
ABSTRACT GET_HOMOLOGUES is an open-source software package that builds on
popular orthology-calling approaches making highly customizable and detailed pangenome …
popular orthology-calling approaches making highly customizable and detailed pangenome …
Multilocus sequence ty** of total-genome-sequenced bacteria
Accurate strain identification is essential for anyone working with bacteria. For many
species, multilocus sequence ty** (MLST) is considered the “gold standard” of ty**, but …
species, multilocus sequence ty** (MLST) is considered the “gold standard” of ty**, but …
Genomic encyclopedia of type strains of the genus Bifidobacterium
Bifidobacteria represent one of the dominant microbial groups that are present in the gut of
various animals, being particularly prevalent during the suckling stage of life of humans and …
various animals, being particularly prevalent during the suckling stage of life of humans and …
Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
Salmonella enterica is a common cause of minor and large food borne outbreaks. To
achieve successful and nearly 'real-time'monitoring and identification of outbreaks, reliable …
achieve successful and nearly 'real-time'monitoring and identification of outbreaks, reliable …
micropan: an R-package for microbial pan-genomics
Background A pan-genome is defined as the set of all unique gene families found in one or
more strains of a prokaryotic species. Due to the extensive within-species diversity in the …
more strains of a prokaryotic species. Due to the extensive within-species diversity in the …
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes
Background Escherichia coli exists in commensal and pathogenic forms. By measuring the
variation of individual genes across more than a hundred sequenced genomes, gene …
variation of individual genes across more than a hundred sequenced genomes, gene …
The Salmonella enterica Pan-genome
Salmonella enterica is divided into four subspecies containing a large number of different
serovars, several of which are important zoonotic pathogens and some show a high degree …
serovars, several of which are important zoonotic pathogens and some show a high degree …
A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient
aquaculture must be emphasized. The knowledge obtained from available genome …
aquaculture must be emphasized. The knowledge obtained from available genome …