Nicholas J Croucher

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 41

Top Venues

Nature communications

Genome medicine

Genome research

G3 (Bethesda, Md.)

Harvard University T H Chan School of Public Health

University of Cambridge (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Harvard University T H Chan School of Public Health

United States

AXA post-doctoral fellow :: Centre for Communicable Disease Dynamics

Education History

University of Cambridge

United Kingdom

PHD :: Wellcome Sanger Institute

Publications

Sudaraka Mallawaarachchi, Gerry Q Tonkin-Hill, Anna K Pöntinen, Jessica K Calland, Rebecca A Gladstone, Sergio Arredondo-Alonso, Neil MacAlasdair, Harry A Thorpe, Janetta Top, Samuel K Sheppard, David Balding, Nicholas J Croucher, Jukka Corander
Detecting co-selection through excess linkage disequilibrium in bacterial genomes. NAR genomics and bioinformatics 6 (2) (2024)
Sophie Belman, Henri Pesonen, Nicholas J Croucher, Stephen D Bentley, Jukka Corander
Estimating between-country migration in pneumococcal populations. G3 (Bethesda, Md.) 14 (6) (2024)
Sophie Belman, Henri Pesonen, Nicholas J Croucher, Stephen D Bentley, Jukka Corander
Estimating between-country migration in pneumococcal populations. G3 (Bethesda, Md.) 14 (6) (2024)
Nicholas J Croucher
Immune interface interference vaccines: An evolution-informed approach to anti-bacterial vaccine design. Microbial biotechnology 17 (3) (2024)
Juri Kuronen, Samuel T Horsfield, Anna Kaarina Pöntinen, Sudaraka Mallawaarachchi, Sergio Arredondo-Alonso, Harry A Thorpe, Rebecca A Gladstone, Rob J L Willems, Stephen D Bentley, Nicholas J Croucher, Johan Pensar, John A Lees, Gerry Q Tonkin-Hill, Jukka Corander
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Genome research 34 (7) (2024)
Janine Lux, Hannah Portmann, Lucía Sánchez García, Maria Erhardt, Lalaina Holivololona, Laura Laloli, Manon F Licheri, Clement Gallay, Robert Hoepner, Nicholas J Croucher, Daniel Straume, Jan-Willem van Groenigen, Ronald Dijkman, Manfred Heller, Denis Grandgirard, Stephen L Leib, Lucy J Hathaway
Klebsiella pneumoniae peptide hijacks a Streptococcus pneumoniae permease to subvert pneumococcal growth and colonization. Communications biology 7 (1) (2024)
Sophie Belman, Henri Pesonen, Nicholas J Croucher, Stephen D Bentley, Jukka Corander
Estimating between-country migration in pneumococcal populations. G3 (Bethesda, Md.) 14 (6) (2024)
Juri Kuronen, Samuel T Horsfield, Anna Kaarina Pöntinen, Sudaraka Mallawaarachchi, Sergio Arredondo-Alonso, Harry A Thorpe, Rebecca A Gladstone, Rob J L Willems, Stephen D Bentley, Nicholas J Croucher, Johan Pensar, John A Lees, Gerry Q Tonkin-Hill, Jukka Corander
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Genome research 34 (7) (2024)
Nicholas J Croucher, Joseph J Campo, Timothy Q Le, Jozelyn V Pablo, Christopher Hung, Andy A Teng, Claudia Turner, Francois H Nosten, Stephen D Bentley, Xiaowu Liang, Paul Turner, David Goldblatt
Genomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci. Nature communications 15 (1) (2024)
Ana Vieira, Yu Wan, Yan Ryan, Ho Kwong Li, Rebecca L Guy, Maria Papangeli, Kristin K Huse, Lucy C Reeves, Valerie W C Soo, Roger Daniel, Alessandra Harley, Karen Broughton, Chenchal Dhami, Mark Ganner, Marjorie A Ganner, Zaynab Mumin, Maryam Razaei, Emma Rundberg, Rufat Mammadov, Ewurabena A Mills, Vincenzo Sgro, Kai Yi Mok, Xavier Didelot, Nicholas J Croucher, Elita Jauneikaite, Theresa Lamagni, Colin Stewart Brown, Juliana Coelho, Shiranee Sriskandan
Rapid expansion and international spread of M1 UK in the post-pandemic UK upsurge of Streptococcus pyogenes. Nature communications 15 (1) (2024)
Nicholas J Croucher, Joseph J Campo, Timothy Q Le, Jozelyn V Pablo, Christopher Hung, Andy A Teng, Claudia Turner, Francois H Nosten, Stephen D Bentley, Xiaowu Liang, Paul Turner, David Goldblatt
Genomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci. Nature communications 15 (1) (2024)
Sophie Belman, Henri Pesonen, Nicholas J Croucher, Stephen D Bentley, Jukka Corander
Estimating between-country migration in pneumococcal populations. G3 (Bethesda, Md.) 14 (6) (2024)
Nicholas J Croucher, Joseph J Campo, Timothy Q Le, Jozelyn V Pablo, Christopher Hung, Andy A Teng, Claudia Turner, Francois H Nosten, Stephen D Bentley, Xiaowu Liang, Paul Turner, David Goldblatt
Genomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci. Nature communications 15 (1) (2024)
Nicholas J Croucher, Joseph J Campo, Timothy Q Le, Jozelyn V Pablo, Christopher Hung, Andy A Teng, Claudia Turner, Francois H Nosten, Stephen D Bentley, Xiaowu Liang, Paul Turner, David Goldblatt
Genomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci. Nature communications 15 (1) (2024)
Ana Vieira, Yu Wan, Yan Ryan, Ho Kwong Li, Rebecca L Guy, Maria Papangeli, Kristin K Huse, Lucy C Reeves, Valerie W C Soo, Roger Daniel, Alessandra Harley, Karen Broughton, Chenchal Dhami, Mark Ganner, Marjorie A Ganner, Zaynab Mumin, Maryam Razaei, Emma Rundberg, Rufat Mammadov, Ewurabena A Mills, Vincenzo Sgro, Kai Yi Mok, Xavier Didelot, Nicholas J Croucher, Elita Jauneikaite, Theresa Lamagni, Colin Stewart Brown, Juliana Coelho, Shiranee Sriskandan
Rapid expansion and international spread of M1 UK in the post-pandemic UK upsurge of Streptococcus pyogenes. Nature communications 15 (1) (2024)
Janine Lux, Hannah Portmann, Lucía Sánchez García, Maria Erhardt, Lalaina Holivololona, Laura Laloli, Manon F Licheri, Clement Gallay, Robert Hoepner, Nicholas J Croucher, Daniel Straume, Jan-Willem van Groenigen, Ronald Dijkman, Manfred Heller, Denis Grandgirard, Stephen L Leib, Lucy J Hathaway
Klebsiella pneumoniae peptide hijacks a Streptococcus pneumoniae permease to subvert pneumococcal growth and colonization. Communications biology 7 (1) (2024)
Juri Kuronen, Samuel T Horsfield, Anna Kaarina Pöntinen, Sudaraka Mallawaarachchi, Sergio Arredondo-Alonso, Harry A Thorpe, Rebecca A Gladstone, Rob J L Willems, Stephen D Bentley, Nicholas J Croucher, Johan Pensar, John A Lees, Gerry Q Tonkin-Hill, Jukka Corander
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Genome research (2024)
Nicholas J Croucher, Joseph J Campo, Timothy Q Le, Jozelyn V Pablo, Christopher Hung, Andy A Teng, Claudia Turner, Francois H Nosten, Stephen D Bentley, Xiaowu Liang, Paul Turner, David Goldblatt
Genomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci. Nature communications 15 (1) (2024)
Janine Lux, Hannah Portmann, Lucía Sánchez García, Maria Erhardt, Lalaina Holivololona, Laura Laloli, Manon F Licheri, Clement Gallay, Robert Hoepner, Nicholas J Croucher, Daniel Straume, Jan-Willem van Groenigen, Ronald Dijkman, Manfred Heller, Denis Grandgirard, Stephen L Leib, Lucy J Hathaway
Klebsiella pneumoniae peptide hijacks a Streptococcus pneumoniae permease to subvert pneumococcal growth and colonization. Communications biology 7 (1) (2024)
Sudaraka Mallawaarachchi, Gerry Q Tonkin-Hill, Anna K Pöntinen, Jessica K Calland, Rebecca A Gladstone, Sergio Arredondo-Alonso, Neil MacAlasdair, Harry A Thorpe, Janetta Top, Samuel K Sheppard, David Balding, Nicholas J Croucher, Jukka Corander
Detecting co-selection through excess linkage disequilibrium in bacterial genomes. NAR genomics and bioinformatics 6 (2) (2024)
Min Jung Kwun, Alexandru V Ion, Marco Rinaldo Oggioni, Stephen D Bentley, Nicholas J Croucher
Diverse regulatory pathways modulate bet hedging of competence induction in epigenetically-differentiated phase variants of Streptococcus pneumoniae. Nucleic acids research (2023)
Samuel T Horsfield, Gerry Q Tonkin-Hill, Nicholas J Croucher, John A Lees
Accurate and fast graph-based pangenome annotation and clustering with ggCaller. Genome research (2023)
Min Jung Kwun, Alexandru V Ion, Hsueh-Chien Cheng, Joshua C D'Aeth, Sam Dougan, Marco R Oggioni, David A Goulding, Stephen D Bentley, Nicholas J Croucher
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA. Genome medicine 14 (1) (2022)
Min Jung Kwun, Alexandru V Ion, Hsueh-Chien Cheng, Joshua C D'Aeth, Sam Dougan, Marco R Oggioni, David A Goulding, Stephen D Bentley, Nicholas J Croucher
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA. Genome medicine 14 (1) (2022)
Min Jung Kwun, Alexandru V Ion, Hsueh-Chien Cheng, Joshua C D'Aeth, Sam Dougan, Marco R Oggioni, David A Goulding, Stephen D Bentley, Nicholas J Croucher
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA. Genome medicine 14 (1) (2022)
Min Jung Kwun, Alexandru V Ion, Hsueh-Chien Cheng, Joshua C D'Aeth, Sam Dougan, Marco R Oggioni, David A Goulding, Stephen D Bentley, Nicholas J Croucher
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA. Genome medicine 14 (1) (2022)
Min Jung Kwun, Alexandru V Ion, Hsueh-Chien Cheng, Joshua C D'Aeth, Sam Dougan, Marco R Oggioni, David A Goulding, Stephen D Bentley, Nicholas J Croucher
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA. Genome medicine 14 (1) (2022)
Alessandra Lochen, James E Truscott, Nicholas J Croucher
Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates. PLoS computational biology 18 (2) (2022)
Gerry Q Tonkin-Hill, Clare Ling, Chrispin Chaguza, Susannah J Salter, Pattaraporn Hinfonthong, Elissavet Nikolaou, Natalie Tate, Andrzej Pastusiak, Claudia Turner, Claire Chewapreecha, Simon D W Frost, Jukka Corander, Nicholas J Croucher, Paul Turner, Stephen D Bentley
Pneumococcal within-host diversity during colonization, transmission and treatment. Nature microbiology 7 (11) (2022)
Joshua C D'Aeth, Mark Pg van der Linden, Lesley McGee, Herminia de Lencastre, Paul Turner, Jae-Hoon Song, Stephanie W Lo, Rebecca A Gladstone, Raquel Sá-Leão, Kwan Soo Ko, William P Hanage, Robert F Breiman, Bernard Beall, Stephen D Bentley, Nicholas J Croucher, null null
The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci. eLife 10 (2021)
Gabrielle L Harrow, John A Lees, William P Hanage, Marc Lipsitch, Jukka Corander, Caroline Colijn, Nicholas J Croucher
Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. The ISME journal 15 (5) (2021)
Sonja Lehtinen, Claire Chewapreecha, John A Lees, William P Hanage, Marc Lipsitch, Nicholas J Croucher, Stephen D Bentley, Paul Turner, Christophe Fraser, Rafal J Mostowy
Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. Science advances 6 (21) (2020)
Taj Azarian, Pamela P Martinez, Brian J Arnold, Xueting Qiu, Lindsay R Grant, Jukka Corander, Christophe Fraser, Nicholas J Croucher, Laura L Hammitt, Raymond Reid, Mathuram Santosham, Robert C Weatherholtz, Stephen D Bentley, Katherine L O'Brien, Marc Lipsitch, William P Hanage
Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS biology 18 (10) (2020)
Caroline Colijn, Jukka Corander, Nicholas J Croucher
Designing ecologically optimized pneumococcal vaccines using population genomics. Nature microbiology 5 (3) (2020)
Min Jung Kwun, Marco Rinaldo Oggioni, Stephen D Bentley, Christophe Fraser, Nicholas J Croucher
Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae. Genes 10 (9) (2019)
John A Lees, Bart Ferwerda, Philip H C Kremer, Nicole E Wheeler, Mercedes Valls Serón, Nicholas J Croucher, Rebecca A Gladstone, Hester J Bootsma, Nynke Y Rots, Alienke J Wijmega-Monsuur, Elisabeth A M Sanders, Krzysztof Trzciński, Anne L Wyllie, Aeilko H Zwinderman, Leonard H van den Berg, Wouter Van Rheenen, Jan H Veldink, Zitta B Harboe, Lene F Lundbo, Lisette C P G M de Groot, Natasja M van Schoor, Nathalie van der Velde, Lars H Ängquist, Thorkild I A Sørensen, Ellen A Nohr, Alexander J Mentzer, Tara C Mills, Julian C Knight, Mignon du Plessis, Susan Nzenze, Jeffrey N Weiser, Julian Parkhill, Shabir Madhi, Thomas Benfield, Anne von Gottberg, Arie van der Ende, Matthijs C Brouwer, Jeffrey C Barrett, Stephen D Bentley, Diederik van de Beek
Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nature communications 10 (1) (2019)
John A Lees, Simon R Harris, Gerry Q Tonkin-Hill, Rebecca A Gladstone, Stephanie W Lo, Jeffrey N Weiser, Jukka Corander, Stephen D Bentley, Nicholas J Croucher
Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome research 29 (2) (2019)
Joseph J Campo, Timothy Q Le, Jozelyn V Pablo, Christopher Hung, Andy A Teng, Hervé Tettelin, Andrea Tate, William P Hanage, Mark R Alderson, Xiaowu Liang, Richard Malley, Marc Lipsitch, Nicholas J Croucher
Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination. eLife 7 (2018)
Jukka Corander, Christophe Fraser, Michael U Gutmann, Brian Arnold, William P Hanage, Stephen D Bentley, Marc Lipsitch, Nicholas J Croucher
Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nature ecology & evolution 1 (12) (2017)
John A Lees, Nicholas J Croucher, David Goldblatt, Francois H Nosten, Julian Parkhill, Claudia Turner, Paul Turner, Stephen D Bentley
Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration. eLife 6 (2017)
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R Harris, Stephen B Beres, James M Musser, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. PLoS genetics 13 (2) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Nicholas J Croucher