Genetic Variation in Neisseria meningitidis Does Not Influence Disease Severity in Meningococcal Meningitis

by Philip H. C. Kremer, John A. Lees, John A. Lees, Bart Ferwerda, Bart Ferwerda, Arie van de Ende, Arie van de Ende, Matthijs C. Brouwer, Stephen D. Bentley, Diederik van de Beek
Published 2020-11-01

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS [version 1; referees: 2 approved]

by Gerry Tonkin-Hill, John A. Lees, Stephen D. Bentley, Simon D.W. Frost, Jukka Corander
Published 2018-07-01

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study [version 1; referees: 1 approved, 2 approved with reservations]

by John A. Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D. Bentley, Simon R. Harris
Published 2018-03-01

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study [version 2; referees: 2 approved, 1 approved with reservations]

by John A. Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D. Bentley, Simon R. Harris
Published 2018-05-01

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

by John A. Lees, T. Tien Mai, Marco Galardini, Nicole E. Wheeler, Samuel T. Horsfield, Julian Parkhill, Jukka Corander
Published 2020-07-01

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

by John A Lees, Nicholas J Croucher, David Goldblatt, François Nosten, Julian Parkhill, Claudia Turner, Paul Turner, Stephen D Bentley
Published 2017-07-01

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

by 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
Published 2016-09-01

Producing polished prokaryotic pangenomes with the Panaroo pipeline

by Gerry Tonkin-Hill, Neil MacAlasdair, Christopher Ruis, Aaron Weimann, Gal Horesh, John A. Lees, Rebecca A. Gladstone, Stephanie Lo, Christopher Beaudoin, R. Andres Floto, Simon D.W. Frost, Jukka Corander, Stephen D. Bentley, Julian Parkhill
Published 2020-07-01

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

by Anna K. Pöntinen, Janetta Top, Sergio Arredondo-Alonso, Gerry Tonkin-Hill, Ana R. Freitas, Carla Novais, Rebecca A. Gladstone, Maiju 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
Published 2021-03-01

Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria

by Oliver J. 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, Imperial College COVID-19 Response Team, Natasha Howard, Hannah Clapham, Francesco Checchi, Neil Ferguson, Azra Ghani, Emma Beals, Patrick Walker
Published 2021-04-01

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impactResearch in context

by Rebecca A. Gladstone, Stephanie W. Lo, John A. Lees, Nicholas J. Croucher, 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, Susan A. Nzenze, Shabir A. Madhi, Paulina A. Hawkins, Dean B. Everett, Martin Antonio, Ron Dagan, Keith P. Klugman, Anne von Gottberg, Lesley McGee, Robert F. Breiman, Stephen D. Bentley
Published 2019-05-01

Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population ge...

by Rebecca A Gladstone, PhD, Alan McNally, ProfPhD, Anna K Pöntinen, PhD, Gerry Tonkin-Hill, MSc, John A Lees, PhD, Kusti Skytén, MSc, François Cléon, PhD, Martin O K Christensen, MSc, Bjørg C Haldorsen, MSc, Kristina K Bye, BSc, Karianne W Gammelsrud, PhD, Reidar Hjetland, PhD, Angela Kümmel, MD, Hege E Larsen, BSc, Paul Christoffer Lindemann, MD, Iren H Löhr, MD, Åshild Marvik, PhD, Einar Nilsen, MD, Marie T Noer, MSc, Gunnar S Simonsen, ProfPhD, Martin Steinbakk, MD, Ståle Tofteland, PhD, Marit Vattøy, BSc, Stephen D Bentley, ProfPhD, Nicholas J Croucher, PhD, Julian Parkhill, ProfPhD, Pål J Johnsen, ProfPhD, Ørjan Samuelsen, ProfPhD, Jukka Corander, ProfPhD
Published 2021-07-01

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

by 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
Published 2019-05-01

Reduction in mobility and COVID-19 transmission

by Pierre Nouvellet, Sangeeta 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. Cucunuba, 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 Hauck, Wes Hinsley, Natsuko Imai, Benjamin Jeffrey, Edward Knock, Daniel J. Laydon, John A. Lees, Tara Mangal, Thomas A. Mellan, Gemma Nedjati-Gilani, Kris V. Parag, Margarita Pons-Salort, Manon Ragonnet-Cronin, Steven Riley, H. Juliette T. Unwin, Robert Verity, Michaela A. C. Vollmer, Erik Volz, Patrick G. T. Walker, Caroline E. Walters, Haowei Wang, Oliver J. Watson, Charles Whittaker, Lilith K. Whittles, Xiaoyue Xi, Neil M. Ferguson, Christl A. Donnelly
Published 2021-02-01

Database of epidemic trends and control measures during the first wave of COVID-19 in mainland China

by Han Fu, Haowei Wang, Xiaoyue Xi, Adhiratha Boonyasiri, Yuanrong Wang, Wes Hinsley, Keith J. Fraser, Ruth McCabe, Daniela Olivera Mesa, Janetta Skarp, Alice Ledda, Tamsin Dewé, Amy Dighe, Peter Winskill, Sabine L. van Elsland, Kylie E.C. Ainslie, Marc Baguelin, Samir Bhatt, Olivia Boyd, Nicholas F. Brazeau, Lorenzo Cattarino, Giovanni Charles, Helen Coupland, Zulma M. Cucunuba, Gina Cuomo-Dannenburg, Christl A. Donnelly, Ilaria Dorigatti, Oliver D. Eales, Richard G. FitzJohn, Seth Flaxman, Katy A.M. Gaythorpe, Azra C. Ghani, William D. Green, Arran Hamlet, Katharina Hauck, David J. Haw, Benjamin Jeffrey, Daniel J. Laydon, John A. Lees, Thomas Mellan, Swapnil Mishra, Gemma Nedjati-Gilani, Pierre Nouvellet, Lucy Okell, Kris V. Parag, Manon Ragonnet-Cronin, Steven Riley, Nora Schmit, Hayley A. Thompson, H.Juliette T. Unwin, Robert Verity, Michaela A.C. Vollmer, Erik Volz, Patrick G.T. Walker, Caroline E. Walters, Oliver J. Watson, Charles Whittaker, Lilith K. Whittles, Natsuko Imai, Sangeeta Bhatia, Neil M. Ferguson
Published 2021-01-01

Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study

by Alexandra B Hogan, PhD, Britta L Jewell, PhD, Ellie Sherrard-Smith, PhD, Juan F Vesga, PhD, Oliver J Watson, PhD, Charles Whittaker, MSc, Arran Hamlet, PhD, Jennifer A Smith, DPhil, Peter Winskill, PhD, Robert Verity, PhD, Marc Baguelin, PhD, John A Lees, PhD, Lilith K Whittles, PhD, Kylie E C Ainslie, PhD, Samir Bhatt, DPhil, Adhiratha Boonyasiri, MD, Nicholas F Brazeau, PhD, Lorenzo Cattarino, PhD, Laura V Cooper, MPhil, Helen Coupland, MRes, Gina Cuomo-Dannenburg, MMath, Amy Dighe, MRes, Bimandra A Djaafara, MRes, Christl A Donnelly, ProfScD, Jeff W Eaton, PhD, Sabine L van Elsland, PhD, Richard G FitzJohn, PhD, Han Fu, PhD, Katy A M Gaythorpe, PhD, William Green, MRes, David J Haw, PhD, Sarah Hayes, MSc, Wes Hinsley, PhD, Natsuko Imai, PhD, Daniel J Laydon, PhD, Tara D Mangal, PhD, Thomas A Mellan, PhD, Swapnil Mishra, PhD, Gemma Nedjati-Gilani, PhD, Kris V Parag, PhD, Hayley A Thompson, MPH, H Juliette T Unwin, PhD, Michaela A C Vollmer, PhD, Caroline E Walters, PhD, Haowei Wang, MSc, Yuanrong Wang, Xiaoyue Xi, MSc, Neil M Ferguson, ProfDPhil, Lucy C Okell, PhD, Thomas S Churcher, PhD, Nimalan Arinaminpathy, DPhil, Azra C Ghani, ProfPhD, Patrick G T Walker, PhD, Timothy B Hallett, ProfPhD
Published 2020-09-01