Microbial genomic taxonomy.

CC Thompson, L Vidal, V Salazar… - Trends in the …, 2021‏ - cabidigitallibrary.org
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 …

Comparison of 61 Sequenced Escherichia coli Genomes

O Lukjancenko, TM Wassenaar, DW Ussery - Microbial ecology, 2010‏ - Springer
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 …

GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis

B Contreras-Moreira, P Vinuesa - Applied and environmental …, 2013‏ - journals.asm.org
ABSTRACT GET_HOMOLOGUES is an open-source software package that builds on
popular orthology-calling approaches making highly customizable and detailed pangenome …

Multilocus sequence ty** of total-genome-sequenced bacteria

MV Larsen, S Cosentino, S Rasmussen… - Journal of clinical …, 2012‏ - journals.asm.org
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 …

Genomic encyclopedia of type strains of the genus Bifidobacterium

C Milani, GA Lugli, S Duranti, F Turroni… - Applied and …, 2014‏ - journals.asm.org
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 …

Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

P Leekitcharoenphon, EM Nielsen, RS Kaas, O Lund… - PloS one, 2014‏ - journals.plos.org
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 …

micropan: an R-package for microbial pan-genomics

L Snipen, KH Liland - BMC bioinformatics, 2015‏ - Springer
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 …

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

RS Kaas, C Friis, DW Ussery, FM Aarestrup - BMC genomics, 2012‏ - Springer
Background Escherichia coli exists in commensal and pathogenic forms. By measuring the
variation of individual genes across more than a hundred sequenced genomes, gene …

The Salmonella enterica Pan-genome

A Jacobsen, RS Hendriksen, FM Aaresturp… - Microbial ecology, 2011‏ - Springer
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 …

A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes

T Uengwetwanit, W Pootakham… - Molecular Ecology …, 2021‏ - Wiley Online Library
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient
aquaculture must be emphasized. The knowledge obtained from available genome …