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List of works by Thomas R. Connor

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

scientific article

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

scientific article published on 05 October 2016

Assessing the reliability of eBURST using simulated populations with known ancestry

scientific article

Bayesian semi-supervised classification of bacterial samples using MLST databases

scientific article

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

scientific article

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

publication published on 01 July 2021

Characterization of plasmids in extensively drug-resistant acinetobacter strains isolated in India and Pakistan

scientific article

Correction: Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa

scientific article published on 15 June 2015

Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity

scientific article published on 03 August 2021

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts

scientific article

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

scientific article published on 9 December 2012

Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.

scientific article

Engineering of Isogenic Cells Deficient for MR1 with a CRISPR/Cas9 Lentiviral System: Tools To Study Microbial Antigen Processing and Presentation to Human MR1-Restricted T Cells

scientific article published on 15 June 2016

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

scientific article published on 08 January 2021

Evidence for several waves of global transmission in the seventh cholera pandemic

scientific article

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

scientific article published in 2022

Genome Sequence of Pluralibacter gergoviae ECO77, a Multireplicon Isolate of Industrial Origin

scientific article published on 27 February 2020

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar

scientific article published on 27 August 2013

Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria

article

Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer

scientific article published in February 2012

Genomic Assemblies of Members of and Related Genera as a Resource for Natural Product Discovery

scientific article published on 15 October 2020

Genomic Assemblies of Members of and Related Genera as a Resource for Natural Product Discovery

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

scientific article published on 22 June 2015

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

scientific article published on 20 July 2023

Genomics reveals the novel species placement of industrial contaminant isolates incorrectly identified as

scientific article published in 2021

Genomics reveals the novel species placement of industrial contaminant isolates incorrectly identified as

scientific article published in April 2021

Hierarchical and spatially explicit clustering of DNA sequences with BAPS software

scientific article published on 13 February 2013

Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset

scientific article

Hyper-recombination, diversity, and antibiotic resistance in pneumococcus

scientific article published in June 2009

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

scientific article

Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study

scientific article published on 27 April 2015

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

scientific article

Kill and cure: genomic phylogeny and bioactivity of bacteria capable of pathogenic and beneficial lifestyles

scientific article published in January 2021

Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.

scientific article published on April 2016

Novel R pipeline for analyzing Biolog Phenotypic MicroArray data

scientific article

Parallel independent evolution of pathogenicity within the genus Yersinia

scientific article

Patterns of genome evolution that have accompanied host adaptation in Salmonella

scientific article

Peptide-MHC Class I Tetramers Can Fail To Detect Relevant Functional T Cell Clonotypes and Underestimate Antigen-Reactive T Cell Populations.

scientific article published on 26 February 2018

Population structure in the Neisseria, and the biological significance of fuzzy species

scientific article

Population subdivision and the detection of recombination in non-typable Haemophilus influenzae

scientific article

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

scientific article

Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process

scientific article

Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK.

scientific article

Salmonella bongori provides insights into the evolution of the Salmonellae

scientific article published in August 2011

Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms

scientific article published on 28 December 2012

Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa.

scientific article

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

scientific article published on 4 August 2015

Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice

scientific article

The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential

scientific article published on 22 August 2019

The Type III Secretion System Effector SeoC of Salmonella enterica subsp. salamae and S. enterica subsp. arizonae ADP-Ribosylates Src and Inhibits Opsonophagocytosis

scientific article published on 10 October 2016

The consistent differential expression of genetic pathways following exposure of an industrial Pseudomonas aeruginosa strain to preservatives and a laundry detergent formulation.

scientific article

Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities

scientific article

Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels

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

Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses.

scientific article

Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011.

scientific article published on 13 November 2014

Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans.

scientific article

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