Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

by Nicole E Wheeler, Paul P Gardner, Lars Barquist
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

Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae

by Kevin C. Ma, Tatum D. Mortimer, Marissa A. Duckett, Allison L. Hicks, Nicole E. Wheeler, Leonor Sánchez-Busó, Yonatan H. Grad
Published 2020-10-01

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.

by Matt Bawn, Nabil-Fareed Alikhan, Gaëtan Thilliez, Mark Kirkwood, Nicole E Wheeler, Liljana Petrovska, Timothy J Dallman, Evelien M Adriaenssens, Neil Hall, Robert A Kingsley
Published 2020-06-01

Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts

by Xiaoyun Ren, David A. Eccles, Gabrielle A. Greig, Jane Clapham, Nicole E. Wheeler, Stinus Lindgreen, Paul P. Gardner, Joanna K. MacKichan, Peter J. Turnbaugh
Published 2017-11-01

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

by Stinus Lindgreen, Sinan Uğur Umu, Alicia Sook-Wei Lai, Hisham Eldai, Wenting Liu, Stephanie McGimpsey, Nicole E Wheeler, Patrick J Biggs, Nick R Thomson, Lars Barquist, Anthony M Poole, Paul P Gardner
Published 2014-10-01

Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae

by Kevin C. Ma, Tatum D. Mortimer, Allison L. Hicks, Nicole E. Wheeler, Leonor Sánchez-Busó, Daniel Golparian, George Taiaroa, Daniel H. F. Rubin, Yi Wang, Deborah A. Williamson, Magnus Unemo, Simon R. Harris, Yonatan H. Grad
Published 2020-08-01

An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation

by Sandra Van Puyvelde, Derek Pickard, Koen Vandelannoote, Eva Heinz, Barbara Barbé, Tessa de Block, Simon Clare, Eve L. Coomber, Katherine Harcourt, Sushmita Sridhar, Emily A. Lees, Nicole E. Wheeler, Elizabeth J. Klemm, Laura Kuijpers, Lisette Mbuyi Kalonji, Marie-France Phoba, Dadi Falay, Dauly Ngbonda, Octavie Lunguya, Jan Jacobs, Gordon Dougan, Stijn Deborggraeve
Published 2019-09-01

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