Now showing items 1-20 of 148

  • 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer 

    Uribe-Lewis, Santiago; Stark, Rory; Carroll, Thomas; Dunning, Mark J.; Bachman, Martin; Ito, Yoko; Stojic, Lovorka; Halim, Silvia; Vowler, Sarah L.; Lynch, Andy G.; Delatte, Benjamin; de Bony, Eric J.; Colin, Laurence; Defrance, Matthieu; Krueger, Felix; Silva, Ana Luisa; ten Hoopen, Rogier; Ibrahim, Ashraf E.K.; Fuks, François; Murrell, Adele (2015-04-01) - Journal article
    Background : The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is ...
  • Acoustic and foraging behavior of a Baird’s beaked whale, Berardius bairdii, exposed to simulated sonar 

    Stimpert, Alison; De Ruiter, Stacy Lynn; Southall, Brandon; Moretti, David; Falcone, Erin; Goldbogen, Jeremy; Friedlaender, Ari; Schorr, Greg; Calambokidis, John (2014-11-13) - Journal article
    Beaked whales are hypothesized to be particularly sensitive to anthropogenic noise, based on previous strandings and limited experimental and observational data. However, few species have been studied in detail. We describe ...
  • An analysis of pilot whale vocalization activity using hidden Markov models 

    Popov, Valentin Mina; Langrock, Roland; De Ruiter, Stacy Lynn; Visser, Fleur (2017-01) - Journal article
    Vocalizations of cetaceans form a key component of their social interactions. Such vocalization activity is driven by the behavioral states of the whales, which are not directly observable, so that latent-state models are ...
  • Animal population estimation using mark-recapture and plant-capture 

    Gormley, Richard (University of St Andrews, 2012) - Thesis
    Mark-recapture is a method of population estimation that involves capturing a number of animals from a population of unknown size on several occasions, and marking those animals that are caught each time. By observing ...
  • Annual report on the implementation of Council Regulation (EC) No 812/2004 during 2014 

    Northridge, Simon; Kingston, Al; Thomas, Len (European Commission, 2015-06-01) - Report
  • Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data 

    Camacho, Niedzica; Van Loo, Peter; Edwards, Sandra; Kay, Jonathan D.; Matthews, Lucy; Haase, Kerstin; Clark, Jeremy; Dennis, Nening; Thomas, Sarah; Kremeyer, Barbara; Zamora, Jorge; Butler, Adam P.; Gundem, Gunes; Merson, Sue; Luxton, Hayley; Hawkins, Steve; Ghori, Mohammed; Marsden, Luke; Lambert, Adam; Karaszi, Katalin; Pelvender, Gill; Massie, Charlie E.; Kote-Jarai, ZSofia; Raine, Keiran; Jones, David; Howat, William J.; Hazell, Steven; Livni, Naomi; Fisher, Cyril; Ogden, Christopher; Kumar, Pardeep; Thompson, Alan; Nicol, David; Mayer, Erik; Dudderidge, Tim; Yu, Yongwei; Zhang, Hongwei; Shah, Nimish C.; Gnanapragasam, Vincent J.; Group, The CRUK-ICGC Prostate; Isaacs, William; Visakorpi, Tapio; Hamdy, Freddie; Berney, Dan; Verrill, Clare; Warren, Anne Y.; Wedge, David C.; Lynch, Andrew G.; Foster, Christopher S.; Lu, Yong Jie; Bova, G. Steven; Whitaker, Hayley C.; McDermott, Ultan; Neal, David E.; Eeles, Rosalind; Cooper, Colin S.; Brewer, Daniel S. (2017-09-25) - Journal article
    A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively ...
  • An approximate Bayesian method applied to estimating the trajectories of four British grey seal (Halichoerus grypus) populations from pup counts. 

    Lonergan, Michael Edward; Thompson, David; Thomas, Leonard Joseph; Duck, Callan David (2011) - Journal article
    1. For British grey seals, as with many pinniped species, population monitoring is implemented by aerial surveys of pups at breeding colonies. Scaling pup counts up to population estimates requires assumptions about ...
  • An assessment of the population of cotton-top tamarins (Saguinus oedipus) and their habitat in Colombia 

    Savage, Anne; Thomas, Len; Feilen, Katie L.; Kidney, Darren; Soto, Luis H.; Pearson, Mackenzie; Medina, Felix S.; Emeris, German; Guillen, Rosamira R. (2016-12-28) - Journal article
    Numerous animals have declining populations due to habitat loss, illegal wildlife trade, and climate change. The cotton-top tamarin (Saguinus oedipus) is a Critically Endangered primate species, endemic to northwest Colombia, ...
  • Assigning stranded bottlenose dolphins to source stocks using stable isotope ratios following the Deepwater Horizon oil spill 

    Hohn, A. A.; Thomas, L.; Carmichael, R. H.; Litz, J.; Clemons-Chevis, C.; Shippee, S. F.; Sinclair, C.; Smith, S.; Speakman, T. R.; Tumlin, M. C.; Zolman, E. S. (2017-01-31) - Journal article
    The potential for stranded dolphins to serve as a tool for monitoring free-ranging populations would be enhanced if their stocks of origin were known. We used stable isotopes of carbon, nitrogen, and sulfur from skin to ...
  • Authentication and characterisation of a new oesophageal adenocarcinoma cell line : MFD-1 

    Garcia, Edwin; Hayden, Annette; Birts, Charles; Britton, Edward; Cowie, Andrew; Pickard, Karen; Mellone, Massimiliano; Choh, Clarisa; Derouet, Mathieu; Duriez, Patrick; Noble, Fergus; White, Michael J.; Primrose, John N.; Strefford, Jonathan C.; Rose-Zerilli, Matthew; Thomas, Gareth J.; Ang, Yeng; Sharrocks, Andrew D.; Fitzgerald, Rebecca C.; Underwood, Timothy J.; Lynch, Andy G. (2016-09-07) - Journal article
    New biological tools are required to understand the functional significance of genetic events revealed by whole genome sequencing (WGS) studies in oesophageal adenocarcinoma (OAC). The MFD-1 cell line was isolated from a ...
  • Automatic generation of generalised regular factorial designs 

    Kobilinsky, André; Monod, Hervé; Bailey, R. A. (2017-09) - Journal article
    The R package planor enables the user to search for, and construct, factorial designs satisfying given conditions. The user specifies the factors and their numbers of levels, the factorial terms which are assumed to be ...
  • Avoidance of wind farms by harbour seals is limited to pile driving activities 

    Russell, Deborah J. F.; Hastie, Gordon D.; Thompson, David; Janik, Vincent M.; Hammond, Philip S.; Scott-Hayward, Lindesay A. S.; Matthiopoulos, Jason; Jones, Esther L.; McConnell, Bernie J. (2016-12) - Journal article
    1. As part of global efforts to reduce dependence on carbon-based energy sources there has been a rapid increase in the installation of renewable energy devices. The installation and operation of these devices can result ...
  • A Bayesian approach to modelling field data on multi-species predator prey-interactions 

    Asseburg, Christian (University of St Andrews, 2006) - Thesis
    Multi-species functional response models are required to model the predation of generalist preda- tors, which consume more than one prey species. In chapter 2, a new model for the multi-species functional response is ...
  • Bayesian modelling of integrated data and its application to seabird populations 

    Reynolds, Toby J. (University of St Andrews, 2010-11-30) - Thesis
    Integrated data analyses are becoming increasingly popular in studies of wild animal populations where two or more separate sources of data contain information about common parameters. Here we develop an integrated population ...
  • Bayesian multi-species modelling of non-negative continuous ecological data with a discrete mass at zero 

    Swallow, Ben (University of St Andrews, 2015) - Thesis
    Severe declines in the number of some songbirds over the last 40 years have caused heated debate amongst interested parties. Many factors have been suggested as possible causes for these declines, including an increase ...
  • Bayesian point process modelling of ecological communities 

    Nightingale, Glenna Faith (University of St Andrews, 2013-06-28) - Thesis
    The modelling of biological communities is important to further the understanding of species coexistence and the mechanisms involved in maintaining biodiversity. This involves considering not only interactions between ...
  • Bayesian sequential tests of the initial size of a linear pure death process 

    Goudie, I.B.J. (2015-05) - Journal article
    We provide a recursive algorithm for determining the sampling plans of invariant Bayesian sequential tests of the initial size of a linear pure death process of unknown rate. These tests compare favourably with the ...
  • Behavioural changes of a long-ranging diver in response to oceanographic conditions 

    Photopoulos, Theoni (2007) - Thesis
    The development of an animal-borne instrument that can record oceanographic measurements (CTD-SRDL) has enabled the collection of oceanographic data at a scale relevant to the counterpart behavioural data, both in time and ...
  • Chains of subsemigroups 

    Cameron, Peter J.; Gadouleau, Maximilien; Mitchell, James D.; Peresse, Yann (2017-06) - Journal article
    We investigate the maximum length of a chain of subsemigroups in various classes of semigroups, such as the full transformation semigroups, the general linear semigroups, and the semigroups of order-preserving transformations ...
  • The challenges of analyzing behavioral response study data : an overview of the MOCHA (Multi-study OCean acoustics Human effects Analysis) project 

    Harris, Catriona M; Thomas, Len; Sadykova, Dinara; De Ruiter, Stacy Lynn; Tyack, Peter Lloyd; Southall, Brandon L.; Read, Andrew J.; Miller, Patrick (Springer Science and Business Media, 2016)
    This paper describes the MOCHA project which aims to develop novel approaches for the analysis of data collected during Behavioral Response Studies (BRSs). BRSs are experiments aimed at directly quantifying the effects of ...