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All papers authored by Nicholas Croucher

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2022 Alessandra Løchen

ORCID

, James E. Truscott

ORCID

, Nicholas J. Croucher

ORCID

Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates

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2019 Tamsin C. M. Dewé

ORCID

, Joshua C. D’Aeth

ORCID

, Nicholas J. Croucher

ORCID

Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae

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Rebecca A. Gladstone

ORCID

, Stephanie W. Lo, John A. Lees, Nicholas J. Croucher

ORCID

, Andries J. van Tonder, Jukka Corander, Andrew J. Page, Pekka Marttinen, Leon J. Bentley, Theresa J. Ochoa, Pak Leung Ho, Mignon du Plessis, Jennifer E. Cornick, Brenda Kwambana-Adams, Rachel Benisty and 13 other authors

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

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Sonja Lehtinen, Paul Turner, Francois Blanquart, Marc Lipsitch, Stephen D. Bentley, Nicholas Croucher

ORCID

, Christophe Fraser, John Lees

On the evolutionary ecology of multidrug resistance in bacteria

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Alan McNally, Teemu Kallonen, Christopher Connor, Khalil Abudahab, David M. Aanensen, Carolyne Horner, Sharon J. Peacock, Julian Parkhill

ORCID

, Nicholas J. Croucher

ORCID

, Jukka Corander

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

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Patrick K. Mitchell, Taj Azarian, Nicholas J. Croucher

ORCID

, Alanna Callendrello, Claudette M. Thompson, Stephen I. Pelton, Marc Lipsitch, William P. Hanage

Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13

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2018 Khalil Abudahab, Joaquín M. Prada, Zhirong Yang, Stephen D. Bentley, Nicholas J. Croucher

ORCID

, Jukka Corander, David M. Aanensen

PANINI: Pangenome Neighbour Identification for Bacterial Populations

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Min Jung Kwun, Marco R. Oggioni, Megan De Ste Croix, Stephen D. Bentley, Nicholas J. Croucher

ORCID

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

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Taj Azarian, Pamela Martinez, Brian Arnold, Lindsay Grant, Jukka Corander, Christophe Fraser, Nicholas Croucher

ORCID

, Laura Hammitt, Raymond Reid, Mathuram Santosham, Robert Weatherholtz, Stephen Bentley, Katherine O’Brien, Marc Lipsitch, William Hanage

Predicting evolution using frequency-dependent selection in bacterial populations

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Nicholas J. Croucher

ORCID

, Alessandra Løchen

ORCID

, Stephen D. Bentley

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

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John A. Lees

ORCID

, Mercedes Valls Serón, Bart Ferwerda

ORCID

, Nicole E. Wheeler, Philip Hc C. Kremer, Mercedes Valls Serón, Nicholas J. Croucher

ORCID

, Rebecca A. Gladstone, Alienke J. Wijmega-Monsuur, Hester J. Bootsma, Nynke Y. Rots, Anne L. Wyllie, Krzysztof Trzciński, Leonard H. van den Berg, Aeilko H. Zwinderman

ORCID

and 42 other authors

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

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Xavier Didelot

ORCID

, Nicholas J. Croucher

ORCID

, Stephen D. Bentley, Simon R. Harris, Daniel J. Wilson

Bayesian inference of ancestral dates on bacterial phylogenetic trees

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Santeri Puranen, Maiju Pesonen, Johan Pensar, Ying Xu, John A. Lees, Stephen D. Bentley, Nicholas J. Croucher

ORCID

, Jukka Corander

SuperDCA for genome-wide epistasis analysis

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Chris Wymant, Francois Blanquart, Tanya Golubchik, Astrid Gall

ORCID

, Margreet Bakker, Nicholas J. Croucher

ORCID

, Daniela Bezemer, Matthew Hall, Swee Hoe Ong, Mariska Hillebregt, Croucher Nj, Oliver Ratmann, Katrien Fransen, M. Kate Grabowski, Jan Albert and 21 other authors

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

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2017 Katinka J. Apagyi, Christophe Fraser, Nicholas J. Croucher

ORCID

Transformation Asymmetry and the Evolution of the Bacterial Accessory Genome

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Joseph J. Campo, Nicholas Croucher

ORCID

, Paul Turner, Andrea Tate, Tim Le, Jozelyn Pablo, Chris Hung, Andy Teng, William P. Hanage, Marc Lipsitch, David Goldblatt, Mark Alderson, Xiaowu Liang

Understanding the Immune Response to Streptococcus Pneumoniae From Vaccination and Carriage on a Proteome Scale

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Megan De Ste Croix, Irene Vacca, Min Jung Kwun, Joseph D. Ralph, Stephen D. Bentley, Richard Haigh, Nicholas J. Croucher

ORCID

, Marco R. Oggioni

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

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Amelieke J. H. Cremers

ORCID

, Fredrick M. Mobegi

ORCID

, Christa van der Gaast-De Jongh, Michelle van Weert, Fred J. van Opzeeland, Minna Vehkala, Mirjam J. Knol, Hester J. Bootsma, Niko Välimäki, Niko Valimaki, Nicholas J. Croucher

ORCID

, Jacques F. Meis, Stephen Bentley, Sacha A. F. T. van Hijum, Jukka Corander and 3 other authors

The contribution of genetic variation of Streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease

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John A. Lees

ORCID

, Nicholas J. Croucher

ORCID

, David Goldblatt, François Nosten

ORCID

, Julian Parkhill, Claudia Turner, Paul Turner

ORCID

, Stephen D. Bentley

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

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Rafał J. Mostowy, Nicholas J. Croucher

ORCID

, Nicola De Maio, Claire Chewapreecha, Susannah J. Salter, Paul Turner, David M. Aanensen, Stephen D. Bentley, Xavier Didelot, Christophe Fraser

Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination

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