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List of works by Mark Achtman

A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?

scientific article published on 7 November 2006

A genomic overview of the population structure of Salmonella.

scientific article

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

scientific article

A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.

scientific article published on 28 May 2010

A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

scientific article published on 29 July 2020

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

Accurate reconstruction of bacterial pan- and core genomes with PEPPAN

scientific article published on 14 October 2020

CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections

scientific article (publication date: 2012)

Ceftriaxone-resistant salmonella enterica serotype Newport, France.

scientific article published on June 2008

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

scientific article

Correction: CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections.

scientific article

Correction: Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

scientific article published on 21 October 2020

Distinct clones of Yersinia pestis caused the black death

scientific article published in 2010

Distinct genealogies for plasmids and chromosome

scientific article published in December 2014

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

scientific article

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

scientific article published on 24 February 2020

EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations

scientific article published in 2022

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

scientific article published on 9 November 2009

Evolution and population structure of Salmonella enterica serovar Newport

scientific article

Evolutionary history of Salmonella typhi

scientific article

Fate of the H-NS-repressed bgl operon in evolution of Escherichia coli

scientific article

Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence.

scientific article published on 14 August 2015

Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus

scholarly article

Genetic variations of live attenuated plague vaccine strains (Yersinia pestis EV76 lineage) during laboratory passages in different countries

scientific article published on 4 June 2014

Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium

scientific article

Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections.

scientific article

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature

scientific article published on 27 September 2021

GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens

scholarly article published 9 November 2017

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

scientific article published on 26 July 2018

High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia

scientific article published on 5 March 2008

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

scientific article published on 27 July 2008

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

scientific article published on 27 December 2012

How old are bacterial pathogens?

scientific article

Identification of new epidemiological molecular markers by comparative proteomics of serogroup A meningococcal isolates from three pandemic waves

scholarly article by Giulia Bernardini et al published 4 August 2009 in Proteomics - Clinical Applications

Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

scientific article

Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus

scientific article published on 05 October 2020

Microevolution and history of the plague bacillus, Yersinia pestis

scientific article published on 21 December 2004

Millennia of genomic stability within the invasive Para C Lineage ofSalmonella enterica

article published in 2017

Mismatch induced speciation in Salmonella: model and data

scientific article

Molecular epidemiology of extraintestinal pathogenic Escherichia coli isolates from a regional cohort of elderly patients highlights the prevalence of ST131 strains with increased antimicrobial resistance in both community and hospital care settings

scientific article

Multilocus sequence typing as a replacement for serotyping in Salmonella enterica

scientific article published in 2012

Multiple time scales for dispersals of bacterial disease over human history

chapter published in 2017

Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona

scientific article

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

scientific article published on 19 July 2018

Parallel independent evolution of pathogenicity within the genus Yersinia

scientific article

Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar

scientific article published on 13 September 2011

Population genetic structure of 4,12:a:- Salmonella enterica strains from harbor porpoises

scientific article

Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing

scientific article published on 27 September 2011

Population structures in the SARA and SARB reference collections of Salmonella enterica according to MLST, MLEE and microarray hybridization.

scientific article published on 16 March 2013

Principles of Systems Biology, No. 31

scientific article published on 01 August 2018

Recombination and population structure in Salmonella enterica.

scientific article

Revival of Seeliger's historical ‘Special Listeria Culture Collection’ ⬇️

scientific article published on October 18, 2011

Salmonella enterica Serotype Typhi with nonclassical quinolone resistance phenotype.

scientific article

Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old.

scientific article published on October 2002

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

scientific article published on 06 December 2019

The role of China in the global spread of the current cholera pandemic.

scientific article

The ubiquitous nature of Listeria monocytogenes clones: a large-scale Multilocus Sequence Typing study

scientific article published on 16 December 2013

Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains

scientific article

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

scientific article

What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B ⬇️

scientific article

Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines

scientific article (publication date: July 2006)

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

scientific article published in December 2010

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