Pan-genomics in the human genome era

RM Sherman, SL Salzberg - Nature Reviews Genetics, 2020 - nature.com
Since the early days of the genome era, the scientific community has relied on a single
'reference'genome for each species, which is used as the basis for a wide range of genetic …

Acinetobacter baumannii: evolution of a global pathogen

LCS Antunes, P Visca, KJ Towner - Pathogens and disease, 2014 - academic.oup.com
Acinetobacter baumannii is an opportunistic nosocomial pathogen and one of the six most
important multidrug resistant microorganisms in hospitals worldwide. This human pathogen …

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

L Pritchard, RH Glover, S Humphris… - Analytical …, 2016 - pubs.rsc.org
Soft rot Enterobacteriaceae (SRE) are bacterial plant pathogens that cause blackleg, wilt
and soft rot diseases on a broad range of important crop and ornamental plants worldwide …

Coagulase-negative staphylococci pathogenomics

X Argemi, Y Hansmann, K Prola, G Prévost - International journal of …, 2019 - mdpi.com
Coagulase-negative Staphylococci (CoNS) are skin commensal bacteria. Besides their role
in maintaining homeostasis, CoNS have emerged as major pathogens in nosocomial …

Performance comparison of benchtop high-throughput sequencing platforms

NJ Loman, RV Misra, TJ Dallman… - Nature …, 2012 - nature.com
Three benchtop high-throughput sequencing instruments are now available. The 454 GS
Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer …

Twenty years of bacterial genome sequencing

NJ Loman, MJ Pallen - Nature Reviews Microbiology, 2015 - nature.com
Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus
influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades …

PGAP: pan-genomes analysis pipeline

Y Zhao, J Wu, J Yang, S Sun, J Xiao, J Yu - Bioinformatics, 2012 - academic.oup.com
With the rapid development of DNA sequencing technology, increasing bacteria genome
data enable the biologists to dig the evolutionary and genetic information of prokaryotic …

Comparative genomics: the bacterial pan-genome

H Tettelin, D Riley, C Cattuto, D Medini - Current opinion in microbiology, 2008 - Elsevier
Bacterial genome sequencing has become so easy and accessible that the genomes of
multiple strains of more and more individual species have been and will be generated …

Conjugative plasmids: vessels of the communal gene pool

A Norman, LH Hansen… - … Transactions of the …, 2009 - royalsocietypublishing.org
Comparative whole-genome analyses have demonstrated that horizontal gene transfer
(HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of …

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

C Warinner, C Speller… - … Transactions of the …, 2015 - royalsocietypublishing.org
The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-
throughput biomolecular sequencing, which allows unprecedented access to the …