List of works by Nicholas J Croucher

A high-resolution view of genome-wide pneumococcal transformation

scientific article

A simple method for directional transcriptome sequencing using Illumina technology

scientific article

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

scientific article

Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom

scientific article published in 2021

Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates

scientific article published on 17 February 2022

Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts

scientific article published on 29 June 2009

Bacterial genomes in epidemiology--present and future.

scientific article published on 04 February 2013

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes

scientific article

Correction: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species.

scientific article published on 20 October 2011

Dense genomic sampling identifies highways of pneumococcal recombination

scientific article published on 09 February 2014

Designing ecologically optimized pneumococcal vaccines using population genomics

scientific article published on 03 February 2020

Detection of recombination events in bacterial genomes from large population samples

scientific article

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening

scientific article published on 04 January 2017

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

scientific article published on 23 April 2019

Diversification of bacterial genome content through distinct mechanisms over different timescales.

scientific article

Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection

scientific article (publication date: 2013)

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

scientific article published in January 2018

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.

scientific article published on 11 February 2017

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

scientific article

Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape

scientific article

Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition

article

Fast and flexible bacterial genomic epidemiology with PopPUNK

scientific article published on 24 January 2019

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae

scientific article published on 22 October 2020

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

scientific article published on 16 October 2017

Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach

scientific article published on 10 September 2012

Genome-wide association, prediction and heritability in bacteria with application to <i>Streptococcus pneumoniae</i>

scientific article published on 22 February 2022

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

scientific article

Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae

scientific article published on 14 October 2019

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution

scientific article

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.

scientific article

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

scientific article published on 20 May 2020

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.

scientific article published on 9 May 2015

Identification, variation and transcription of pneumococcal repeat sequences

scientific article

Impact of 13-Valent Pneumococcal Conjugate Vaccination on Streptococcus pneumoniae Carriage in Young Children in Massachusetts.

scientific article published on 03 October 2013

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

scientific article

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

scientific article published on 16 April 2019

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

scholarly article

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

scientific article published on 15 May 2019

Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

scientific article published on 31 January 2017

Large scale genomic analysis shows no evidence for repeated pathogen adaptation during the invasive phase of bacterial meningitis in humans

Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius

scientific article published in March 2012

Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination

article

Phandango: an interactive viewer for bacterial population genomics.

scientific article published on 25 September 2017

Phase-variable methylation and epigenetic regulation by type I restriction-modification systems

scientific article

Pneumococcal Vaccines: Host Interactions, Population Dynamics, and Design Principles

scientific article published on 01 September 2018

Pneumococcal capsular switching: a historical perspective

scientific article published on 21 November 2012

Pneumococcal capsule synthesis locus cps as evolutionary hotspot with potential to generate novel serotypes by recombination.

scientific article published on 08 June 2017

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

scientific article

Population genomics of post-vaccine changes in pneumococcal epidemiology.

scientific article published on 05 May 2013

Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies

article

Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores

scientific article published on 19 June 2009

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

scientific article

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis

scientific article

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

scientific article

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak

scientific article published on June 2012

Recombination of the Phase-Variable spnIII Locus Is Independent of All Known Pneumococcal Site-Specific Recombinases

scientific article published on 10 July 2019

Recombination produces coherent bacterial species clusters in both core and accessory genomes.

scientific article published on 5 November 2015

Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81

scientific article

Selective and genetic constraints on pneumococcal serotype switching

scientific article published on 31 March 2015

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

scientific article published on 16 September 2016

Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis

scientific article

SuperDCA for genome-wide epistasis analysis

scientific article published on 29 May 2018

Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae

scientific article published on 13 September 2019

The application of genomics to tracing bacterial pathogen transmission.

scientific article published on 22 November 2014

The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success

scientific article published on 16 November 2012

The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci

scientific article published on 14 July 2021

Transformation asymmetry and the evolution of the bacterial accessory genome.

scientific article published in December 2017

Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone

scientific article published on 23 June 2014

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates

scientific article published on 30 April 2020

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