The microbial pan-genome.

By Duccio Medini, C. Donati, Herve Tettelin, V. Masignani, R. Rappuoli. 2005

1,226 citations recorded by the source corpus.

Subfields: Ecology, Food Science, Molecular Biology

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Citations in the corpus

UniProt: the universal protein knowledgebase (2016, methodology): “To complement the growing set of reference proteomes, UniProt has developed pan proteomes analogous to the pan genome concept (8).”
Bacterial insertion sequences: their genomic impact and diversity (2014, background): “The idea that many prokaryotic genomes are mosaic, composed of a 'central genome backbone' of essential and house-keeping genes (the core genome) interspersed with DNA segments constituting the 'mobilome' (a variety of accessory genes that form part of the pan genome), is now common currency (Medini”
Species-level functional profiling of metagenomes and metatranscriptomes (2018, neutral): “HUMAnN2 then constructs a sample-specific database by merging preconstructed, functionally annotated pangenomes of the identified species 23 .”
Blautia—a new functional genus with potential probiotic properties? (2021, background): “genome could reflect the species diversity in genetic composition.(37) As shown in Figure 3a, the number of pan-genome increased with the addition of Blautia genome, and the total number of pangenome reached 26,728 when the 74 genome was added to the calculations.”
Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health. (2013, background): “…pathogens, linking the aquatic and terrestrial resistomes and complicating the treatment of human infections (Sandaa et al., 1992; Furushita et al., 2003; Medini et al., 2005; Sørum, 2006; Sobecky and Hazen, 2009; Martinez, 2009a; Fondi and Fani, 2010; Erauso et al., 2011; Forsberg et al., 2012).”
The Pangenome: Diversity, Dynamics and Evolution of Genomes (2020, background): “The pangenome represents the total gene diversity of a given population: this comprises the total number of distinct orthologs, including core genes and accessory genes (Tettelin et al. 2005; Medini et al. 2005; Vernikos et al. 2015).”
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary (2016, background): “The full complement of all genes among a set of genomes is referred to as the pan-genome [11, 12].”
Size doesn’t matter: towards a more inclusive philosophy of biology (2007, background): “42Together, these categories of genes make up the ‘pan-genome’ of a species, sometimes called the ‘clade-specific metagenome’ (Lawrence and Hendrickson 2005; Medini et al. 2005).”
The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally (2017, background): “In the analysis that we have presented in this work we have discusses that in several cases CRP-orthologs regulate the expression of genes that are fundamental to the biology of a bacterial species, and that the CRP target-genes are inherited by HGT, and are thus part of the accessory genome.”
EDGAR: A software framework for the comparative analysis of prokaryotic genomes (2009, background): “Furthermore, a differentiation between open and closed pan-genomes has been introduced by Medini et al. [ 5 ].”
Explaining microbial population genomics through phage predation (2009, background): “However, with the advent of genomics, it has become apparent that the genomic diversity in prokaryotes arises more from having different sets of genes than from allelic differences at the same loc”