Browsing Bioinformatics and Computational Biology Group by Issue Date

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  • Pritchard, Leighton; Corne, D.; Kell, Douglas B.; Winson, Mike K.; Rowland, Jeremy John (2005-06-21)
    In this paper, we generalise a previously-described model of the error-prone polymerase chain reaction (PCR) reaction to conditions of arbitrarily variable amplification efficiency and initial population size. Generalisation ...
  • Džeroski, Sašo; Blockeel, Hendrik; Clare, Amanda; Leander, Schietgat; Struyf, Jan (2006)
    Hierarchical multilabel classification (HMC) is a variant of classification where instances may belong to multiple classes organized in a hierarchy. The task is relevant for several application domains. This paper presents ...
  • Soldatova, Larisa; Clare, Amanda; Sparkes, Andrew; King, Ross Donald (2006)
    Motivation: A Robot Scientist is a physically implemented robotic system that can automatically carry out cycles of scientific experimentation. We are commissioning a new Robot Scientist designed to investigate gene function ...
  • Fiehn, Oliver; Kristal, Bruce; Ommen, Ben van; Sumner, Lloyd W.; Sansone, Susanna-Assunta; Taylor, Chris F.; Hardy, Nigel; Kaddurah-Daouk, Rima (2006-06)
    Metabolite concentrations in cellular systems are very much dependent on the physiological, environmental, and genetic status of an organism and are regarded as the ultimate result of cellular regulation, resulting in the ...
  • Spasić, Irena; Dunn, Warwick B.; Velarde, Giles; Tseng, Andy; Jenkins, Helen; Hardy, Nigel; Oliver, Stephen G.; Kell, Douglas B. (2006-06-05)
    Background The genome sequencing projects have shown our limited knowledge regarding gene function, e.g. S. cerevisiae has 5–6,000 genes of which nearly 1,000 have an uncertain function. Their gross influence on the behaviour ...
  • King, Ross Donald; Soldatova, Larisa (2006-12-22)
    The formal description of experiments for efficient analysis, annotation and sharing of results is a fundamental part of the practice of science. Ontologies are required to achieve this objective. A few subject-specific ...
  • Jenkins, Helen Ann; Beckmann, Manfred; Draper, John; Hardy, Nigel William (Springer, 2007)
  • 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 ...
  • Riley, Michael Charles; Clare, Amanda; King, Ross Donald (2007-03-30)
    Background: We are interested in understanding the locational distribution of genes and their functions in genomes, as this distribution has both functional and evolutionary significance. Gene locational distribution is ...
  • Soldatova, Larisa; Schierz, Amanda; King, Ross Donald (2007-04)
    The Brookhaven Protein Data Bank was once a pioneering database, but its organization of structural data is now outdated and in need of an upgrade.
  • Devos, Andy; Van Huffel, Sabine; Lu, Chuan; Suykens, Johan A. K.; Arus, Carles (2007-05)
    This work investigates variable selection and classification for biomedical datasets with a small sample size and a very high input dimension. The sequential sparse Bayesian learning methods with linear bases are used as ...
  • Van Calster, Ben; Timmerman, Dirk; Lu, Chuan; Suykens, Johan A. K.; Valentin, Lil; Van Holsbeke, Caroline; Amant, Frédéric; Vergote, Ignace; Van Huffel, Sabine (2007-05)
    Objectives To develop flexible classifiers that predict malignancy in adnexal masses using a large database from nine centers. Methods The database consisted of 1066 patients with at least one persistent adnexal mass for ...
  • Schierz, Amanda; Soldatova, Larisa; King, Ross Donald (2007-08)
  • Sumner, Lloyd W.; Amberg, Alexander; Barrett, Dave; Beale, Michael H.; Beger, Richard; Daykin, Clare; Fan, Teresa; Fiehn, Oliver; Goodacre, Royston; Griffin, Julian L.; Hankemeier, Thomas; Hardy, Nigel; Harnly, James; Higashi, Richard; Kopka, Joachim; Lane, Andrew N.; Lindon, John C.; Marriott, Philip; Nicholls, Andrew W.; Reily, Michael D.; Thaden, John J.; Viant, Mark R. (2007-09-01)
    There is a general consensus that supports the need for standardized reporting of metadata or information describing large-scale metabolomics and other functional genomics data sets. Reporting of standard metadata provides ...
  • Fiehn, Oliver; Robertson, Donald; Griffin, Julian L.; van der Werf, Mariet; Nikolau, Basil; Morrison, Norman; Sumner, Lloyd W.; Goodacre, Royston; Hardy, Nigel; Taylor, Chris F.; Fostel, Jennifer; Kristal, Bruce; Kaddurah-Daouk, Rima; Mendes, Pedro; van Ommen, B.; Lindon, John C.; Sansone, Susanna-Assunta (2007-09-01)
    In 2005, the Metabolomics Standards Initiative has been formed. An outline and general introduction is provided to inform about the history, structure, working plan and intentions of this initiative. Comments on any of the ...
  • Hardy, Nigel; Taylor, Chris F. (2007-09-01)
    This briefing lays out the initial objectives and intent of the Data Exchange Working Group of the Metabolomics Standards Initiative (MSI), which operates under the aegis of the Metabolomics Society. The MSI has now reached ...
  • Rubtsov, Denis V.; Jenkins, Helen; Ludwig, Christian; Easton, John; Viant, Mark R.; Günther, Ulrich; Griffin, Julian L.; Hardy, Nigel (2007-09-01)
    The amount of data generated by NMR-based metabolomic experiments is increasing rapidly. Furthermore, diverse techniques increase the need for informative and comprehensive meta-data. These factors present a challenge in ...
  • Jones, Andrew R.; Miller, Michael; Aebersold, Ruedi; Apweiler, Rolf; Ball, Catherine A.; Brazma, Alvis; DeGreef, James; Hardy, Nigel; Hermjakob, Henning; Hubbard, Simon J.; Hussey, Peter; Igra, Mark; Jenkins, Helen; Julian Jr, Randall K.; Laursen, Kent; Oliver, Stephen G.; Paton, Norman W.; Sansone, Susanna-Assunta; Sarkans, Ugis; Stoeckert Jr, Christian J.; Taylor, Chris F.; Whetzel, Patricia L.; White, Joseph A.; Spellman, Paul; Pizarro, Angel (2007-10-05)
    The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components of an experimental ...
  • Hardy, Nigel; Jenkins, Helen (Springer, 2007-10-26)
    Metabolomic studies generate large quantities of data. Metabolomics data sets have complex structure and will typically be subjected to a variety of processing and analysis techniques. The data sets are expensive to collect ...
  • Schierz, Amanda (2007-11-01)
    The diffusion and transfer of knowledge is central to the process of innovation and is of importance to both academics and industrialists. In this paper, we propose that academic articles and patent documents referring to ...

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