John A Lees (John Lees)

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 30

Top Venues

Nature communications

Genome research

Wellcome open research

eLife

Imperial College London

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

Affiliation History

Imperial College London

United Kingdom

MRC Research Fellow :: MRC Centre for Global Infectious Disease Analysis

Publications

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)
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)
Ouli Xie, Jacqueline M Morris, Andrew J Hayes, Rebecca J Towers, Magnus G Jespersen, John A Lees, Nouri L Ben Zakour, Olga Berking, Sarah L Baines, Glen P Carter, Gerry Tonkin-Hill, Layla Schrieber, Liam McIntyre, Jake A Lacey, Taylah B James, Kadaba S Sriprakash, Scott A Beatson, Tadao Hasegawa, Phil Giffard, Andrew C Steer, Michael R Batzloff, Bernard W Beall, Marcos D Pinho, Mario Ramirez, Debra E Bessen, Gordon Dougan, Stephen D Bentley, Mark J Walker, Bart J Currie, Steven Y C Tong, David J McMillan, Mark R Davies
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nature communications 15 (1) (2024)
Ouli Xie, Jacqueline M Morris, Andrew J Hayes, Rebecca J Towers, Magnus G Jespersen, John A Lees, Nouri L Ben Zakour, Olga Berking, Sarah L Baines, Glen P Carter, Gerry Tonkin-Hill, Layla Schrieber, Liam McIntyre, Jake A Lacey, Taylah B James, Kadaba S Sriprakash, Scott A Beatson, Tadao Hasegawa, Phil Giffard, Andrew C Steer, Michael R Batzloff, Bernard W Beall, Marcos D Pinho, Mario Ramirez, Debra E Bessen, Gordon Dougan, Stephen D Bentley, Mark J Walker, Bart J Currie, Steven Y C Tong, David J McMillan, Mark R Davies
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nature communications 15 (1) (2024)
Ouli Xie, Jacqueline M Morris, Andrew J Hayes, Rebecca J Towers, Magnus G Jespersen, John A Lees, Nouri L Ben Zakour, Olga Berking, Sarah L Baines, Glen P Carter, Gerry Tonkin-Hill, Layla Schrieber, Liam McIntyre, Jake A Lacey, Taylah B James, Kadaba S Sriprakash, Scott A Beatson, Tadao Hasegawa, Phil Giffard, Andrew C Steer, Michael R Batzloff, Bernard W Beall, Marcos D Pinho, Mario Ramirez, Debra E Bessen, Gordon Dougan, Stephen D Bentley, Mark J Walker, Bart J Currie, Steven Y C Tong, David J McMillan, Mark R Davies
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nature communications 15 (1) (2024)
Ouli Xie, Jacqueline M Morris, Andrew J Hayes, Rebecca J Towers, Magnus G Jespersen, John A Lees, Nouri L Ben Zakour, Olga Berking, Sarah L Baines, Glen P Carter, Gerry Tonkin-Hill, Layla Schrieber, Liam McIntyre, Jake A Lacey, Taylah B James, Kadaba S Sriprakash, Scott A Beatson, Tadao Hasegawa, Phil Giffard, Andrew C Steer, Michael R Batzloff, Bernard W Beall, Marcos D Pinho, Mario Ramirez, Debra E Bessen, Gordon Dougan, Stephen D Bentley, Mark J Walker, Bart J Currie, Steven Y C Tong, David J McMillan, Mark R Davies
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nature communications 15 (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)
Ouli Xie, Jacqueline M Morris, Andrew J Hayes, Rebecca J Towers, Magnus G Jespersen, John A Lees, Nouri L Ben Zakour, Olga Berking, Sarah L Baines, Glen P Carter, Gerry Tonkin-Hill, Layla Schrieber, Liam McIntyre, Jake A Lacey, Taylah B James, Kadaba S Sriprakash, Scott A Beatson, Tadao Hasegawa, Phil Giffard, Andrew C Steer, Michael R Batzloff, Bernard W Beall, Marcos D Pinho, Mario Ramirez, Debra E Bessen, Gordon Dougan, Stephen D Bentley, Mark J Walker, Bart J Currie, Steven Y C Tong, David J McMillan, Mark R Davies
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nature communications 15 (1) (2024)
The Tien Mai, John A Lees, Rebecca A Gladstone, Jukka Corander
Inferring the heritability of bacterial traits in the era of machine learning. Bioinformatics advances 3 (1) (2023)
The Tien Mai, John A Lees, Rebecca A Gladstone, Jukka Corander
Inferring the heritability of bacterial traits in the era of machine learning. Bioinformatics advances 3 (1) (2023)
Lloyd A C Chapman, Maite Aubry, Noémie Maset, Timothy W Russell, Edward S Knock, John A Lees, Henri-Pierre Mallet, Van-Mai Cao-Lormeau, Adam J Kucharski
Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia. Nature communications 14 (1) (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)
Philip H C Kremer, Bart Ferwerda, Hester J Bootsma, Nienke Y Rots, Alienke Jentien Wijmenga-Monsuur, Elisabeth A M Sanders, Krzysztof Trzciński, Chantal B F Vogels, Paul Turner, Arie van der Ende, Matthijs C Brouwer, Stephen D Bentley, Diederik van de Beek, John A Lees
Pneumococcal genetic variability in age-dependent bacterial carriage. eLife 11 (2022)
Anna Kaarina Pöntinen, Janetta Top, Sergio Arredondo-Alonso, Gerry Tonkin-Hill, Ana R Freitas, Carla Novais, Rebecca A Gladstone, Maiju E Pesonen, Rodrigo Meneses, Henri Pesonen, John A Lees, Dorota Jamrozy, Stephen D Bentley, Val F Lanza, Carmen Torres, Luisa Peixe, Teresa M Coque, Julian Parkhill, Anita C Schürch, Rob J L Willems, Jukka Corander
Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nature communications 12 (1) (2021)
Edward S Knock, Lilith K Whittles, John A Lees, Pablo Noel Perez-Guzman, Robert J Verity, Richard G FitzJohn, Katy A M Gaythorpe, Natsuko Imai, Wes Hinsley, Lucy C Okell, Alicia Roselló, Nikolas Kantas, Caroline E Walters, Sangeeta N Bhatia, Oliver John Watson, Charles Whittaker, Lorenzo Cattarino, Adhiratha Boonyasiri, Bimandra A Djafaara, Keith J Fraser, Han Fu, Haowei Wang, Xiaoyue Xi, Christl Ann Donnelly, Elita Jauneikaite, Daniel J Laydon, Peter J White, Azra C Ghani, Neil M Ferguson, Anne Cori, Marc Baguelin
Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England. Science translational medicine 13 (602) (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)
Pierre Nouvellet, Sangeeta N Bhatia, Anne Cori, Kylie E C Ainslie, Marc Baguelin, Samir Bhatt, Adhiratha Boonyasiri, Nicholas F Brazeau, Lorenzo Cattarino, Laura V Cooper, Helen Coupland, Zulma M Cucunubá, Gina Cuomo-Dannenburg, Amy Dighe, Bimandra A Djaafara, Ilaria Dorigatti, Oliver D Eales, Sabine L van Elsland, Fabricia F Nascimento, Richard G FitzJohn, Katy A M Gaythorpe, Lily Geidelberg, William D Green, Arran Hamlet, Katharina D Hauck, Wes Hinsley, Natsuko Imai, Benjamin Jeffrey, Edward Knock, Daniel J Laydon, John A Lees, Tara Mangal, Thomas A Mellan, Gemma Nedjati-Gilani, Kris Varun Parag, Margarita Pons-Salort, Manon Ragonnet-Cronin, Steven Riley, H Juliette T Unwin, Robert J Verity, Michaela A C Vollmer, Erik M Volz, Patrick G T Walker, Caroline E Walters, Haowei Wang, Oliver John Watson, Charles Whittaker, Lilith K Whittles, Xiaoyue Xi, Neil M Ferguson, Christl Ann Donnelly
Reduction in mobility and COVID-19 transmission. Nature communications 12 (1) (2021)
Ruth McCabe, Mara D Kont, Nora Schmit, Charles Whittaker, Alessandra Lochen, Marc Baguelin, Edward S Knock, Lilith K Whittles, John A Lees, Nicholas F Brazeau, Patrick G T Walker, Azra C Ghani, Neil M Ferguson, Peter J White, Christl Ann Donnelly, Katharina D Hauck, Oliver John Watson
Modelling intensive care unit capacity under different epidemiological scenarios of the COVID-19 pandemic in three Western European countries. International journal of epidemiology 50 (3) (2021)
Oliver John Watson, Mervat Alhaffar, Zaki Mehchy, Charles Whittaker, Zack Akil, Nicholas F Brazeau, Gina Cuomo-Dannenburg, Arran Hamlet, Hayley A Thompson, Marc Baguelin, Richard G FitzJohn, Edward Knock, John A Lees, Lilith K Whittles, Thomas Mellan, Peter Winskill, null null, Natasha Howard, Hannah E Clapham, Francesco Checchi, Neil M Ferguson, Azra Ghani, Emma Beals, Patrick Walker
Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria. Nature communications 12 (1) (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)
John A Lees, T Tien Mai, Marco Galardini, Nicole E Wheeler, Samuel T Horsfield, Julian Parkhill, Jukka Corander
Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions. mBio 11 (4) (2020)
H Juliette T Unwin, Swapnil Mishra, Valerie C Bradley, Axel Gandy, Thomas A Mellan, Helen Coupland, Jonathan Ish-Horowicz, Michaela A C Vollmer, Charles Whittaker, Sarah L Filippi, Xiaoyue Xi, Mélodie Monod, Oliver Ratmann, Michael Hutchinson, Fabian Valka, Harrison Zhu, Iwona Hawryluk, Philip Milton, Kylie E C Ainslie, Marc Baguelin, Adhiratha Boonyasiri, Nick F Brazeau, Lorenzo Cattarino, Zulma Cucunuba, Gina Cuomo-Dannenburg, Ilaria Dorigatti, Oliver D Eales, Jeffrey W Eaton, Sabine L van Elsland, Richard G FitzJohn, Katy A M Gaythorpe, William Green, Wes Hinsley, Benjamin Jeffrey, Edward Knock, Daniel J Laydon, John A Lees, Gemma Nedjati-Gilani, Pierre Nouvellet, Lucy C Okell, Kris Varun Parag, Igor Siveroni, Hayley A Thompson, Patrick Walker, Caroline E Walters, Oliver John Watson, Lilith K Whittles, Azra C Ghani, Neil M Ferguson, Steven Riley, Christl Ann Donnelly, Samir Bhatt, Seth R Flaxman
State-level tracking of COVID-19 in the United States. Nature communications 11 (1) (2020)
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)
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study. Wellcome open research 3 (2018)
Gerry Q Tonkin-Hill, John A Lees, Stephen D Bentley, Simon D W Frost, Jukka Corander
RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome open research 3 (2018)
Pamela Shen, John A Lees, Gavyn Chern Wei Bee, Samuel P Brown, Jeffrey N Weiser
Pneumococcal quorum sensing drives an asymmetric owner-intruder competitive strategy during carriage via the competence regulon. Nature microbiology 4 (1) (2018)
John A Lees, Matthijs C Brouwer, Arie van der Ende, Julian Parkhill, Diederik van de Beek, Stephen D Bentley
Within-Host Sampling of a Natural Population Shows Signs of Selection on Pde1 during Bacterial Meningitis. Infection and immunity 85 (3) (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)
John A Lees, Minna Vehkala, Niko Välimäki, Simon R Harris, Claire Chewapreecha, Nicholas J Croucher, Pekka Marttinen, Mark R Davies, Andrew C Steer, Steven Y C Tong, Antti Honkela, Julian Parkhill, Stephen D Bentley, Jukka Corander
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nature communications 7 (2016)

John A Lees.css-eqlu8i{font-size:small;padding-left:4px;} (John Lees)

Publication Activity (10 Years)

Top Topics

Top Venues

John A Lees (John Lees)