Search Results - "Lees, John"

pyseer: a comprehensive tool for microbial pangenome-wide association studies by Lees, John A, Galardini, Marco, Bentley, Stephen D, Weiser, Jeffrey N, Corander, Jukka

“…Abstract Summary Genome-wide association studies (GWAS) in microbes have different challenges to GWAS in eukaryotes. These have been addressed by a number of…”
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Producing polished prokaryotic pangenomes with the Panaroo pipeline by Tonkin-Hill, Gerry, MacAlasdair, Neil, Ruis, Christopher, Weimann, Aaron, Horesh, Gal, Lees, John A., Gladstone, Rebecca A., Lo, Stephanie, Beaudoin, Christopher, Floto, R. Andres, Frost, Simon D.W., Corander, Jukka, Bentley, Stephen D., Parkhill, Julian

“…Abstract Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene…”
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Fast hierarchical Bayesian analysis of population structure by Tonkin-Hill, Gerry, Lees, John A, Bentley, Stephen D, Frost, Simon D W, Corander, Jukka

“…We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly identifies an approximate fit to a Dirichlet process mixture model…”
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Fast and flexible bacterial genomic epidemiology with PopPUNK by Lees, John A, Harris, Simon R, Tonkin-Hill, Gerry, Gladstone, Rebecca A, Lo, Stephanie W, Weiser, Jeffrey N, Corander, Jukka, Bentley, Stephen D, Croucher, Nicholas J

“…The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and…”
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Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation by Lees, John A., Tonkin-Hill, Gerry, Yang, Zhirong, Corander, Jukka

“…In less than a decade, population genomics of microbes has progressed from the effort of sequencing dozens of strains to thousands, or even tens of thousands…”
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Genealogical inference and more flexible sequence clustering using iterative-PopPUNK by Zhao, Bin, Lees, John A, Wu, Hongjin, Yang, Chao, Falush, Daniel

“…Bacterial genome data are accumulating at an unprecedented speed due to the routine use of sequencing in clinical diagnoses, public health surveillance, and…”
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Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study by Sonabend, Raphael, Whittles, Lilith K, Imai, Natsuko, Perez-Guzman, Pablo N, Knock, Edward S, Rawson, Thomas, Gaythorpe, Katy A M, Djaafara, Bimandra A, Hinsley, Wes, FitzJohn, Richard G, Lees, John A, Kanapram, Divya Thekke, Volz, Erik M, Ghani, Azra C, Ferguson, Neil M, Baguelin, Marc, Cori, Anne

“…England's COVID-19 roadmap out of lockdown policy set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as…”
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Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes by Lees, John A., Vehkala, Minna, Välimäki, Niko, Harris, Simon R., Chewapreecha, Claire, Croucher, Nicholas J., Marttinen, Pekka, Davies, Mark R., Steer, Andrew C., Tong, Steven Y. C., Honkela, Antti, Parkhill, Julian, Bentley, Stephen D., Corander, Jukka

“…Bacterial genomes vary extensively in terms of both gene content and gene sequence. This plasticity hampers the use of traditional SNP-based methods for…”
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Intermittent fasting induces chronic changes in the hepatic gene expression of Red Jungle Fowl (Gallus gallus) by Lindholm, Caroline, Batakis, Petros, Altimiras, Jordi, Lees, John

“…Intermittent fasting (IF), the implementation of fasting periods of at least 12 consecutive hours on a daily to weekly basis, has received a lot of attention…”
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Immune exclusion by naturally acquired secretory IgA against pneumococcal pilus-1 by Binsker, Ulrike, Lees, John A, Hammond, Alexandria J, Weiser, Jeffrey N

“…Successful infection by mucosal pathogens requires overcoming the mucus barrier. To better understand this key step, we performed a survey of the interactions…”
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Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions by Lees, John A, Mai, T Tien, Galardini, Marco, Wheeler, Nicole E, Horsfield, Samuel T, Parkhill, Julian, Corander, Jukka

“…Discovery of genetic variants underlying bacterial phenotypes and the prediction of phenotypes such as antibiotic resistance are fundamental tasks in bacterial…”
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Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era by Pöntinen, Anna K., Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R., Novais, Carla, Gladstone, Rebecca A., Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A., Jamrozy, Dorota, Bentley, Stephen D., Lanza, Val F., Torres, Carmen, Peixe, Luisa, Coque, Teresa M., Parkhill, Julian, Schürch, Anita C., Willems, Rob J. L., Corander, Jukka

“…Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist…”
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Adults with suspected central nervous system infection: A prospective study of diagnostic accuracy by Khatib, Ula, van de Beek, Diederik, Lees, John A, Brouwer, Matthijs C

“…Summary Objectives To study the diagnostic accuracy of clinical and laboratory features in the diagnosis of central nervous system (CNS) infection and…”
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Accurate and fast graph-based pangenome annotation and clustering with ggCaller by Horsfield, Samuel T, Tonkin-Hill, Gerry, Croucher, Nicholas J, Lees, John A

“…Bacterial genomes differ in both gene content and sequence mutations, which underlie extensive phenotypic diversity, including variation in susceptibility to…”
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Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England by Knock, Edward S, Whittles, Lilith K, Lees, John A, Perez-Guzman, Pablo N, Verity, Robert, FitzJohn, Richard G, Gaythorpe, Katy A M, Imai, Natsuko, Hinsley, Wes, Okell, Lucy C, Rosello, Alicia, Kantas, Nikolas, Walters, Caroline E, Bhatia, Sangeeta, Watson, Oliver J, Whittaker, Charlie, Cattarino, Lorenzo, Boonyasiri, Adhiratha, Djaafara, Bimandra A, Fraser, Keith, Fu, Han, Wang, Haowei, Xi, Xiaoyue, Donnelly, Christl A, Jauneikaite, Elita, Laydon, Daniel J, White, Peter J, Ghani, Azra C, Ferguson, Neil M, Cori, Anne, Baguelin, Marc

“…We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional surveillance data for England. Compared with other approaches, our…”
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Stem cells and heterotopic ossification: Lessons from animal models by Lees-Shepard, John B., Goldhamer, David J.

“…Put most simply, heterotopic ossification (HO) is the abnormal formation of bone at extraskeletal sites. HO can be classified into two main subtypes, genetic…”
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RhierBAPS: An R implementation of the population clustering algorithm hierBAPS by Tonkin-Hill, Gerry, Lees, John A, Bentley, Stephen D, Frost, Simon D W, Corander, Jukka

“…Identifying structure in collections of sequence data sets remains a common problem in genomics. hierBAPS, a popular algorithm for identifying population…”
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The potential public health consequences of COVID-19 on malaria in Africa by Sherrard-Smith, Ellie, Hogan, Alexandra B., Hamlet, Arran, Watson, Oliver J., Whittaker, Charlie, Winskill, Peter, Ali, Fatima, Mohammad, Audu B., Uhomoibhi, Perpetua, Maikore, Ibrahim, Ogbulafor, Nnenna, Nikau, Jamilu, Kont, Mara D., Challenger, Joseph D., Verity, Robert, Lambert, Ben, Cairns, Matthew, Rao, Bhargavi, Baguelin, Marc, Whittles, Lilith K., Lees, John A., Bhatia, Sangeeta, Knock, Edward S., Okell, Lucy, Slater, Hannah C., Ghani, Azra C., Walker, Patrick G. T., Okoko, Okefu Oyale, Churcher, Thomas S.

“…The burden of malaria is heavily concentrated in sub-Saharan Africa (SSA) where cases and deaths associated with COVID-19 are rising 1 . In response, countries…”
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Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration by Lees, John A, Croucher, Nicholas J, Goldblatt, David, Nosten, François, Parkhill, Julian, Turner, Claudia, Turner, Paul, Bentley, Stephen D

“…is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease,…”
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Within-country age-based prioritisation, global allocation, and public health impact of a vaccine against SARS-CoV-2: A mathematical modelling analysis by Hogan, Alexandra B., Winskill, Peter, Watson, Oliver J., Walker, Patrick G.T., Whittaker, Charles, Baguelin, Marc, Brazeau, Nicholas F., Charles, Giovanni D., Gaythorpe, Katy A.M., Hamlet, Arran, Knock, Edward, Laydon, Daniel J., Lees, John A., Løchen, Alessandra, Verity, Robert, Whittles, Lilith K., Muhib, Farzana, Hauck, Katharina, Ferguson, Neil M., Ghani, Azra C.

“…•The global dose supply of COVID-19 vaccines will be constrained in 2021.•Within a country, prioritising doses to protect those at highest mortality risk is…”
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