4 Works

Data from: Two-phase importance sampling for inference about transmission trees

Elina Numminen, Claire Chewapreecha, Jukka Sirén, Claudia Turner, Paul Turner, Stephen D. Bentley, Jukka Corander & J. Siren
There has been growing interest in the statistics community to develop methods for inferring transmission pathways of infectious pathogens from molecular sequence data. For many datasets, the computational challenge lies in the huge dimension of the missing data. Here, we introduce an importance sampling scheme in which the transmission trees and phylogenies of pathogens are both sampled from reasonable importance distributions, alleviating the inference. Using this approach, arbitrary models of transmission could be considered, contrary...

Data from: Repeated land mass reformation limits diversification in the widespread littoral zone mosquito Anopheles sundaicus sensu lato in the Indo-Oriental Region

Magdalena Zarowiecki, Yvonne-Marie Linton, Rory J. Post, Michael J. Bangs, Pe Than Htun, Thaung Hlaing, Chang Moh Seng, Visut Baimai, Trung Ho Ding, Tho Sochantha & Catherine Walton
Southeast Asia harbours abundant biodiversity, hypothesized to have been generated by Pliocene and Pleistocene climatic and environmental change. Vicariance between the island of Borneo, the remaining Indonesian archipelago and mainland Southeast Asia caused by elevated sea levels during interglacial periods has been proposed to lead to diversification in the littoral zone mosquito Anopheles (Cellia) sundaicus (Rodenwaldt) sensu lato. To test this biogeographical hypothesis, we inferred the population history and assessed gene flow of A. sundaicus...

Data from: Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse

Tia DiTommaso, Lynelle K. Jones, Denny L. Cottle, The WTSI Mouse Genetics Program, Anna-Karin Gerdin, Valerie E. Vancollie, Fiona M. Watt, Ramiro Ramirez-Solis, Allan Bradley, Karen P. Steel, John P. Sundberg, Jacqueline K. White, Ian Smyth & Ian M. Smyth
The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP). A total of 562 different mouse lines were...

Data from: Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

Samuel K. Sheppard, Lu Cheng, Guillaume Méric, Caroline P. A. De Haan, Ann-Katrin Llarena, Pekka Marttinen, Ana Vidal, Anne Ridley, Felicity Clifton-Hadley, Thomas R. Connor, Norval J. C. Strachan, Ken Forbes, Frances M. Colles, Keith A. Jolley, Stephen D. Bentley, Martin C. J. Maiden, Marja-Liisa Hänninen, Julian Parkhill, William P. Hanage & Jukka Corander
Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major...

Registration Year

  • 2014
    4

Resource Types

  • Dataset
    4

Affiliations

  • Wellcome Trust
    4
  • Mahidol University
    2
  • University of Helsinki
    2
  • University of Aberdeen
    1
  • Smithsonian Institution
    1
  • Aalto University
    1
  • Jackson Laboratory
    1
  • King's College London
    1
  • Department of Health
    1
  • University of Manchester
    1