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

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

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

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

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

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