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N. Croucher · SciRah

Researcher profile · Semantic Scholar

N. Croucher

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N. Croucher — researcher profile on SciRah

h-index: 56
Works: 161
Citations: 14K

Most-cited papers

Phandango: an interactive viewer for bacterial population genomics
J. Hadfield, N. Croucher, R. Goater, K. Abudahab +2 more
2017bioRxiv596 citations Open access
Semantic Scholar
Fast and flexible bacterial genomic epidemiology with PopPUNK
J. Lees, S. Harris, G. Tonkin-Hill, R. Gladstone +5 more
2018bioRxiv394 citations Open access
Semantic Scholar
Bayesian inference of ancestral dates on bacterial phylogenetic trees
X. Didelot, N. Croucher, S. Bentley, S. Harris +1 more
2018bioRxiv284 citations Open access
Semantic Scholar
Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study
Stephanie W. Lo, R. Gladstone, A. V. van Tonder, J. Lees +85 more
2019Lancet. Infectious Diseases (Print)263 citations Open access
Semantic Scholar
International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact
R. Gladstone, Stephanie W. Lo, John A. Lees, N. Croucher +23 more
2019EBioMedicine229 citations Open access
Semantic Scholar
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
J. Lees, Minna Vehkala, Niko Välimäki, S. Harris +10 more
2016Nature Communications192 citations Open access
Semantic Scholar
Divergent serotype replacement trends and increasing diversity in pneumococcal disease in high income settings reduce the benefit of expanding vaccine valency
A. Løchen, N. Croucher, Roy M. Anderson
2020Scientific Reports150 citations Open access
Semantic Scholar
Frequency-dependent selection in vaccine-associated pneumococcal population dynamics
J. Corander, C. Fraser, Michael U Gutmann, Brian J. Arnold +4 more
2017Nature Ecology & Evolution149 citations Open access
Semantic Scholar
Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection
A. McNally, T. Kallonen, Christopher Connor, K. Abudahab +6 more
2019mBio100 citations Open access
Semantic Scholar
Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis
J. Lees, B. Ferwerda, P. Kremer, N. Wheeler +36 more
2018Nature Communications99 citations Open access
Semantic Scholar
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver
C. Wymant, F. Blanquart, T. Golubchik, A. Gall +28 more
2018Virus Evolution96 citations Open access
Semantic Scholar
Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration
J. Lees, N. Croucher, Goldblatt David, Nosten Francois +4 more
2017bioRxiv95 citations Open access
Semantic Scholar
Phase-variable methylation and epigenetic regulation by type I restriction-modification systems.
M. De Ste Croix, I. Vacca, M. Kwun, Joseph D. Ralph +4 more
2017FEMS Microbiology Reviews94 citations Open access
Semantic Scholar
Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study
Stephanie W. Lo, Kate C. Mellor, Robert Cohen, A. Alonso +97 more
2022The Lancet Microbe91 citations Open access
Semantic Scholar
Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 648
K. Schaufler, T. Semmler, L. Wieler, D. Trott +15 more
2019Antimicrobial Agents and Chemotherapy86 citations Open access
Semantic Scholar
Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening
N. Croucher, J. Campo, T. Le, X. Liang +3 more
2017Proceedings of the National Academy of Sciences of the United States of America77 citations Open access
Semantic Scholar
Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination
R. Mostowy, N. Croucher, N. de Maio, C. Chewapreecha +6 more
2017Molecular biology and evolution76 citations Open access
Semantic Scholar
Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections: a nationwide longitudinal microbial population genomic study in Norway between 2002-2017
R. Gladstone, A. McNally, A. Pöntinen, G. Tonkin-Hill +25 more
2021The Lancet Microbe75 citations Open access
Semantic Scholar
Pneumococcal within-host diversity during colonization, transmission and treatment
G. Tonkin-Hill, C. Ling, C. Chaguza, S. Salter +11 more
2022bioRxiv68 citations Open access
Semantic Scholar
Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
Romain Derelle, Johanna von Wachsmann, T. Mäklin, J. Hellewell +6 more
2024bioRxiv60 citations Open access
Semantic Scholar
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates
R. Gladstone, Stephanie W. Lo, R. Goater, C. Yeats +38 more
2020Microbial Genomics59 citations Open access
Semantic Scholar
Designing ecologically-optimised pneumococcal vaccines using population genomics
C. Colijn, J. Corander, N. Croucher
2020Nature Microbiology58 citations Open access
Semantic Scholar
Pneumococcal Vaccines: Host Interactions, Population Dynamics, and Design Principles.
N. Croucher, A. Løchen, S. Bentley
2018Annual Review of Microbiology51 citations Open access
Semantic Scholar
Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis
J. Lees, P. Kremer, A. S. Manso, N. Croucher +8 more
2017Microbial Genomics49 citations Open access
Semantic Scholar
Genome-wide epistasis and co-selection study using mutual information
J. Pensar, S. Puranen, Brian J. Arnold, N. MacAlasdair +13 more
2019bioRxiv46 citations Open access
Semantic Scholar
PANINI: Pangenome Neighbour Identification for Bacterial Populations
K. Abudahab, J. Prada, Zhirong Yang, S. Bentley +3 more
2018Microbial Genomics38 citations Open access
Semantic Scholar
Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae
T. Dewé, Joshua C. D’Aeth, N. Croucher
2019Microbial Genomics36 citations Open access
Semantic Scholar
Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae
T. Azarian, P. Martinez, Brian J. Arnold, Xue-Ting Qiu +12 more
2020PLoS Biology35 citations Open access
Semantic Scholar
Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom
Yu Wan, E. Mills, Rhoda C. Y. Leung, Ana Vieira +6 more
2021Microbial Genomics32 citations Open access
Semantic Scholar
The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci
Joshua C. D’Aeth, M. V. D. van der Linden, L. McGee, H. de Lencastre +95 more
2021eLife32 citations Open access
Semantic Scholar
Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study.
A. Pöntinen, R. Gladstone, Henri Pesonen, M. Pesonen +10 more
2024The Lancet Microbe31 citations Open access
Semantic Scholar
Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures
Gabrielle L. Harrow, J. Lees, W. Hanage, M. Lipsitch +3 more
2020The ISME Journal31 citations Open access
Semantic Scholar
Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host
L. Furi, Liam A. Crawford, Guillermo Rangel-Pineros, A. S. Manso +9 more
2019Journal of Bacteriology31 citations Open access
Semantic Scholar
Geographical migration and fitness dynamics of Streptococcus pneumoniae
S. Belman, N. Lefrancq, S. Nzenze, Sarah Downs +93 more
2024Nature30 citations Open access
Semantic Scholar
SuperDCA for genome-wide epistasis analysis
S. Puranen, M. Pesonen, J. Pensar, Yingying Xu +5 more
2017bioRxiv29 citations Open access
Semantic Scholar
The contribution of genetic variation of Streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease
A. Cremers, F. Mobegi, C. E. van der Gaast-de Jongh, Michelle van Weert +13 more
2017bioRxiv28 citations Open access
Semantic Scholar
Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination
J. Campo, T. Le, Jozelyn V. Pablo, C. Hung +9 more
2018eLife27 citations Open access
Semantic Scholar
International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease
R. Gladstone, L. Siira, O. Brynildsrud, D. Vestrheim +98 more
2022Vaccine23 citations Open access
Semantic Scholar
Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition
M. Kwun, M. Oggioni, M. De Ste Croix, S. Bentley +1 more
2018Nucleic Acids Research23 citations Open access
Semantic Scholar
Transformation Asymmetry and the Evolution of the Bacterial Accessory Genome
Katinka J. Apagyi, C. Fraser, N. Croucher
2017Molecular biology and evolution22 citations Open access
Semantic Scholar
Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates
A. Løchen, J. Truscott, N. Croucher
2021bioRxiv21 citations Open access
Semantic Scholar
Pneumococcal capsule expression is controlled through a conserved, distal cis-regulatory element during infection
David G. Glanville, Ozcan Gazioglu, Michela Marra, V. Tokars +7 more
2023PLoS Pathogens19 citations Open access
Semantic Scholar
Accurate and fast graph-based pangenome annotation and clustering with ggCaller
Samuel T. Horsfield, N. Croucher, J. Lees
2023bioRxiv19 citations Open access
Semantic Scholar
Accurate and fast graph-based pangenome annotation and clustering with ggCaller
Samuel T. Horsfield, G. Tonkin-Hill, N. Croucher, J. Lees
2023Genome Research19 citations Open access
Semantic Scholar
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA
M. Kwun, Alexandru V. Ion, Hsueh-Chien Cheng, Joshua C. D’Aeth +5 more
2022bioRxiv19 citations Open access
Semantic Scholar
Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae
S. Lehtinen, C. Chewapreecha, J. Lees, W. Hanage +6 more
2019Science Advances18 citations Open access
Semantic Scholar
Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13
Patrick K. Mitchell, T. Azarian, N. Croucher, Alanna Callendrello +4 more
2019Microbial Genomics16 citations Open access
Semantic Scholar
Epidemiological dynamics of bacteriocin competition and antibiotic resistance
S. Lehtinen, N. Croucher, F. Blanquart, C. Fraser
2020bioRxiv14 citations Open access
Semantic Scholar
Predicting the future distribution of antibiotic resistance using time series forecasting and geospatial modelling
B. Jeffrey, D. Aanensen, N. Croucher, S. Bhatt
202012 citations Open access
Semantic Scholar
Diverse regulatory pathways modulate bet hedging of competence induction in epigenetically-differentiated phase variants of Streptococcus pneumoniae
M. Kwun, Alexandru V. Ion, M. Oggioni, Stephen D. Bentley +1 more
2023bioRxiv11 citations Open access
Semantic Scholar

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