Browsing by Author "King, Ross Donald"

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Browsing by Author "King, Ross Donald"

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  • Enot, David Pierre Louis; King, Ross Donald (Springer, 2003)
    Developments in physical and biological technology have resulted in a rapid rise in the amount of data available on the 3D structure of protein-ligand complexes. The extraction of knowledge from this data is central to the ...
  • Taylor, Janet; King, Ross Donald; Altmann, Thomas; Fiehn, Oliver (2002)
    MOTIVATION: Metabolomics is a post genomic technology which seeks to provide a comprehensive profile of all the metabolites present in a biological sample. This complements the mRNA profiles provided by microarrays, and ...
  • King, Ross Donald; Soldatova, Larisa (2005)
  • Liakata, Maria; Soldatova, Larisa; Batchelor, Colin; Lewis, Stuart; Fielding, Helen; King, Ross Donald (2007)
    The paper describes initial work on an ontology based tool, ART, for the semantic annotation of papers stored in digital repositories. ART is intended for the annotation not only of data and metadata about a paper, but ...
  • Lu, Chuan; King, Ross Donald (2010-03)
    We present an automated procedure of identifying and filling of reaction gaps in genome-scale metabolic networks within the framework of flux balance analysis. This computational approach exploits the constraint-based ...
  • King, Ross Donald; Rowland, Jeremy John; Oliver, Stephen G.; Young, Michael; Aubrey, Wayne; Byrne, Emma Louise; Liakata, Maria; Markham, Magdalena; Pir, Pinar; Soldatova, Larisa Nikolaevna; Sparkes, Andrew Charles; Whelan, Kenneth Edward; Clare, Amanda Janet (2009-04-03)
    The basis of science is the hypothetico-deductive method and the recording of experiments in sufficient detail to enable reproducibility. We report the development of Robot Scientist 'Adam,' which advances the automation ...
  • Ferre, Sebastien; King, Ross Donald (2004)
    BLID (Bio-Logical Intelligent Database) is a bioinformatic system designed to help biologists extract new knowledge from raw genome data by providing high-level facilities for both data browsing and analysis. We describe ...
  • King, Ross Donald; Wise, P. H.; Clare, Amanda (2004)
    Motivation: A central problem in bioinformatics is the assignment of function to sequenced open reading frames (ORFs). The most common approach is based on inferred homology using a statistically based sequence similarity ...
  • Pir, Pinar; Dobson, Paul D.; Smallbone, Kieran; Mendes, Pedro; King, Ross Donald; Lu, Chuan; Oliver, Stephen G.; Clare, Amanda (2010-10)
    Background: Genome-scale metabolic network models have been widely used for analysing the cellular behaviour of organisms both qualitatively and quantitatively. An iterative semi-automated procedure for model validation ...
  • Clare, Amanda; King, Ross Donald (2003)
    Critics of lazy functional languages contend that the languages are only suitable for toy problems and are not used for real systems. We present an application (PolyFARM) for distributed data mining in relational bioinformatics ...
  • Ferre, Sebastien; King, Ross Donald (2004-11)
    Abstract. Many application domains make use of specific data structures such as sequences and graphs to represent knowledge. These data structures are ill-fitted to the standard representations used in machine learning and ...
  • King, Ross Donald; Srinivasan, A.; Bain, M. E. (2003-07)
    Inductive Logic Programming (ILP) systems constructmodels for data using domain-specific background information. When using these systems, it is typically assumed that sufficient human expertise is at hand to rule out ...
  • Scott, Ian Morris; Vermeer, Cornelia P.; Liakata, Maria; Corol, Delia I.; Ward, Jane L.; Lin, Wanchang; Johnson, Helen E.; Whitehead, Lynne; Kular, Baldeep; Baker, John M.; Walsh, Sean; Dave, Anuja; Larson, Tony R.; Graham, Ian A.; Wang, Trevor L.; King, Ross Donald; Draper, John; Beale, Michael H. (2010-08)
    Metabolite fingerprinting of Arabidopsis (Arabidopsis thaliana) mutants with known or predicted metabolic lesions was performed by 1H-nuclear magnetic resonance, Fourier transform infrared, and flow injection electrospray-mass ...
  • Soldatova, Larisa Nikolaevna; Aubrey, Wayne; King, Ross Donald; Clare, Amanda Janet (2008-07-01)
    Motivation: Many published manuscripts contain experiment protocols which are poorly described or deficient in information. This means that the published results are very hard or impossible to repeat. This problem is being ...
  • Clare, Amanda Janet; Karwath, Andreas; Ougham, Helen Joan; King, Ross Donald (2006-02-15)
    Motivation: The genome of Arabidopsis thaliana, which has the best understood plant genome, still has approximately one-third of its genes with no functional annotation at all from either MIPS or TAIR. We have applied our ...
  • King, Ross Donald; Whelan, Kenneth Edward; Jones, Ffion M.; Reiser, Philip G. K.; Bryant, Christopher H.; Muggleton, Stephen H.; Kell, Douglas B.; Oliver, Stephen G. (2004-01-15)
    The question of whether it is possible to automate the scientific process is of both great theoretical interest and increasing practical importance because, in many scientific areas, data are being generated much faster ...
  • Dobson, Paul D.; Smallbone, Kieran; Jameson, Daniel; Simeonidis, Evangelos; Lanthaler, Karin; Pir, Pınar; Lu, Chuan; Swainston, Neil; Dunn, Warwick B.; Fisher, Paul; Hull, Duncan; Brown, Marie; Oshota, Olusegun; Stanford, Natalie J.; Kell, Douglas B.; King, Ross Donald; Oliver, Stephen G.; Stevens, Robert D.; Mendes, Pedro (2010-10-28)
    Background. To date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, ...
  • Catchpole, Gareth; Beckmann, Manfred; Enot, David Pierre Louis; Mondhe, Madhav; Zywicki, Britta; Taylor, Janet; Hardy, Nigel William; Smith, Aileen Roberta; King, Ross Donald; Kell, Douglas B.; Fiehn, Oliver; Draper, John (2005-10-04)
    There is current debate whether genetically modified (GM) plants might contain unexpected, potentially undesirable changes in overall metabolite composition. However, appropriate analytical technology and acceptable metrics ...
  • Karwath, Andreas; King, Ross Donald (2002-04-23)
    Background: The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify ~50% of homologies (with a false positive rate set at 1/ 1000). Results: We present ...
  • Clare, Amanda; King, Ross Donald (2002)
    We wished to quantify the state-of-the-art of our understanding of clusters in microarray data. To do this we systematically compared the clusters produced on sets of microarray data using a representative set of clustering ...

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