Now showing items 1-20 of 99

  • 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 ...
  • 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
  • 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 ...
  • 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 ...
  • 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) - Conference item
    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 ...
  • Circular designs balanced for neighbours at distances one and two 

    Aldred, R. E. L.; Bailey, R. A.; Mckay, Brendan D.; Wanless, Ian M. (2014-12) - Journal article
    We define three types of neighbour-balanced designs for experiments where the units are arranged in a circle or single line in space or time. The designs are balanced with respect to neighbours at distance one and at ...
  • Circular designs balanced for neighbours at distances one and two 

    Aldred, R. E. L.; Bailey, R. A.; Mckay, Brendan D.; Wanless, Ian M. (2014-12) - Journal article
    We define three types of neighbour-balanced designs for experiments where the units are arranged in a circle or single line in space or time. The designs are balanced with respect to neighbours at distance one and at ...
  • The classification of partition homogeneous groups with applications to semigroup theory 

    André, Jorge; Araúo, Joāo; Cameron, Peter Jephson (2016-04-15) - Journal article
    Let λ=(λ1,λ2,...) be a partition of n, a sequence of positive integers in non-increasing order with sum n. Let Ω:={1,...,n}. An ordered partition P=(A1,A2,...) of Ω has type λ if |Ai|=λi.Following Martin and Sagan, we say ...
  • A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy 

    Noorani, Ayesha; Bornschein, Jan; Lynch, Andy G; Secrier, Maria; Achilleos, Achilleas; Eldridge, Matthew; Bower, Lawrence; Weaver, Jamie M.J.; Crawte, Jason; Ong, Chin-Ann; Shannon, Nicholas; MacRae, Shona; Grehan, Nicola; Nutzinger, Barbara; O'Donovan, Maria; Hardwick, Richard; Tavaré, Simon; Fitzgerald, Rebecca C.; on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium (2017-06-01) - Journal article
    The scientific community has avoided using tissue samples from patients that have been exposed to systemic chemotherapy to infer the genomic landscape of a given cancer. Esophageal adenocarcinoma is a heterogeneous, ...
  • Complex Region Spatial Smoother (CReSS) 

    Scott Hayward, Lindesay Alexandra Sarah; MacKenzie, Monique Lea; Donovan, Carl Robert; Walker, Cameron; Ashe, Erin (University of St Andrews, 2011) - Report
    Conventional smoothing over complicated coastal and island regions may result in errors across boundaries, due to the use of Euclidean distances to represent inter-point similarity. The new Complex Region Spatial Smoother ...
  • A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing 

    Alioto, Tyler S.; Buchhalter, Ivo; Derdak, Sophia; Hutter, Barbara; Eldridge, Matthew D.; Hovig, Eivind; Heisler, Lawrence E.; Beck, Timothy A.; Simpson, Jared T.; Tonon, Laurie; Sertier, Anne-Sophie; Patch, Ann-Marie; Jaeger, Natalie; Ginsbach, Philip; Drews, Ruben; Paramasivam, Nagarajan; Kabbe, Rolf; Chotewutmontri, Sasithorn; Diessl, Nicolle; Previti, Christopher; Schmidt, Sabine; Brors, Benedikt; Feuerbach, Lars; Heinold, Michael; Groebner, Susanne; Korshunov, Andrey; Tarpey, Patrick S.; Butler, Adam P.; Hinton, Jonathan; Jones, David; Menzies, Andrew; Raine, Keiran; Shepherd, Rebecca; Stebbings, Lucy; Teague, Jon W.; Ribeca, Paolo; Giner, Francesc Castro; Beltran, Sergi; Raineri, Emanuele; Dabad, Marc; Heath, Simon C.; Gut, Marta; Denroche, Robert E.; Harding, Nicholas J.; Yamaguchi, Takafumi N.; Fujimoto, Akihiro; Nakagawa, Hidewaki; Quesada, Ctor; Valdes-Mas, Rafael; Nakken, Sigve; Vodak, Daniel; Bower, Lawrence; Lynch, Andrew G.; Anderson, Charlotte L.; Waddell, Nicola; Pearson, John V.; Grimmond, Sean M.; Peto, Myron; Spellman, Paul; He, Minghui; Kandoth, Cyriac; Lee, Semin; Zhang, John; Letourneau, Louis; Ma, Singer; Seth, Sahil; Torrents, David; Xi, Liu; Wheeler, David A.; Lopez-Otin, Carlos; Campo, Elias; Campbell, Peter J.; Boutros, Paul C.; Puente, Xose S.; Gerhard, Daniela S.; Pfister, Stefan M.; McPherson, John D.; Hudson, Thomas J.; Schlesner, Matthias; Lichter, Peter; Eils, Roland; Jones, David T. W.; Gut, Ivo G. (2015-12-09) - Journal article
    As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different ...
  • Computing in matrix groups without memory 

    Cameron, Peter Jephson; Fairbairn, Ben; Gadouleau, Maximilien (2014-11-02) - Journal article
    Memoryless computation is a novel means of computing any function of a set of registers by updating one register at a time while using no memory. We aim to emulate how computations are performed on modern cores, since they ...
  • Computing in permutation groups without memory 

    Cameron, Peter Jephson; Fairbairn, Ben; Gadouleau, Maximilien (2014-11-02) - Journal article
    Memoryless computation is a new technique to compute any function of a set of registers by updating one register at a time while using no memory. Its aim is to emulate how computations are performed in modern cores, since ...