Browsing Computational Biology and Bioinformatics by Title

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Browsing Computational Biology and Bioinformatics by Title

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  • On the formalization and reuse of scientific research 
    Liakata, Maria (2011-10-07)
    The reuse of scientific knowledge obtained from one investigation in another investigation is basic to the advance of science. Scientific investigations should therefore be recorded in ways that promote the reuse of the ...
  • On the use of qualitative reasoning to simulate and identify metabolic pathways 
    Coghill, George; King, Ross Donald; Garrett, Simon (2005-01-12)
    Motivation: Perhaps the greatest challenge of modern biology is to develop accurate in silico models of cells. To do this we require computational formalisms for both simulation (how according to the model the state of the ...
  • An ontology for a Robot Scientist 
    Clare, Amanda; Sparkes, Andrew; King, Ross Donald; Soldatova, Larisa (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 ...
  • An Ontology for Description of Drug Discovery Investigations 
    Qi, Da; King, Ross D.; Hopkins, Andrew L.; Bickerton, G.; Richard, J.; Soldatova, Larisa N. (2010)
    The paper presents an ontology for the description of Drug Discovery Investigation (DDI). This has been developed through the use of a Robot Scientist “Eve”, and in consultation with industry. DDI aims to define the principle ...
  • An Ontology of Scientific Experiments 
    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 ...
  • Overhauling the PDB 
    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    The Brookhaven Protein Data Bank was once a pioneering database, but its organization of structural data is now outdated and in need of an upgrade.
  • PhenomeNET: a whole-phenome approach to disease gene discovery 
    Hoehndorf, Robert; Schofield, Paul N.; Gkoutos, Georgios V. (2011-10)
    Phenotypes are investigated in model organisms to understand and reveal the molecular mechanisms underlying disease. Phenotype ontologies were developed to capture and compare phenotypes within the context of a single ...
  • Poly-transformation 
    King, Ross Donald; Ouali, M. (2004)
    Poly-transformation is the extension of the idea of ensemble learning to the transformation step of Knowledge Discovery in Databases (KDD). In poly-transformation multiple transformations of the data are made before learning ...
  • Predicting gene function in Saccharomyces cerevisiae 
    King, Ross Donald; Clare, Amanda (2003)
    Motivation S. cerevisiae is one of the most important model organisms, and has has been the focus of over a century of study. In spite of these efforts, 40% of its open reading frames (ORFs) remain classified as having ...
  • Preoperative diagnosis of ovarian tumors using Bayesian kernel-based methods 
    Amant, Frédéric; Vergote, Ignace; Lu, Chuan; Van Calster, Ben; Suykens, Johan A. K.; Van Huffel, Sabine; Van Holsbeke, Caroline; Valentin, Lil; Timmerman, Dirk (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 ...
  • Primary and secondary metabolism, and post-translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolor 
    Hesketh, A. R.; Chandra, G.; Shaw, Adrian; Rowland, Jem; Kell, Douglas B.; Bibb, M. J.; Chater, K. F. (2002)
    The newly sequenced genome of Streptomyces coelicolor is estimated to encode 7825 theoretical proteins. We have mapped approximately 10% of the theoretical proteome experimentally using two-dimensional gel electrophoresis ...
  • Prospective internal validation of mathematical models to predict malignancy in adnexal masses: results from the International Ovarian Tumor Analysis (IOTA) Study 
    Timmerman, Dirk; Valentin, Lil; Domali, Ekaterini; Lu, Chuan; Van Huffel, Sabine; Testa, Antonia C.; Van Holsbeke, Caroline; Van Calster, Ben (2009-01)
    PURPOSE: To prospectively test the mathematical models for calculation of the risk of malignancy in adnexal masses that were developed on the International Ovarian Tumor Analysis (IOTA) phase 1 data set on a new data set ...
  • Rapid detection method for microbial spoilage using FT-IR and machine learning 
    Rowland, Jem; Broadhurst, David I.; Ellis, David I.; Goodacre, Royston (Wageningen Academic Publishers, 2005)
  • Report on structural comparison and validation of the genome scale metabolic models for Saccharomyces cerevisiae 
    Lu, Chuan; King, Ross Donald; Whelan, Ken (Unknown Publisher, 2010-05-04)
  • Response to: Realism about PDB 
    Soldatova, Larisa; Schierz, Amanda; King, Ross Donald (2007-08)
  • The Robot Scientist Adam 
    Rowland, Jem; Oliver, Stephen; Sparkes, Andrew; Markham, Magdalena; Pir, Pnar; Clare, Amanda; King, Ross Donald; Liakata, Maria; Whelan, Ken; Aubrey, Wayne; Soldatova, Larisa; Young, Michael (2009-08-01)
    Despite science's great intellectual prestige, developing robot scientists will probably be simpler than developing general AI systems because there is no essential need to take into account the social milieu. Computer ...
  • The Robot Scientist 'Adam' 
    King, Ross Donald; Whelan, K.; Clare, Amanda; Rowland, Jem (Aberystwyth University, 2005)
    The Robot Scientist Project is a multidisciplinary research project involving expertise from Computer Science and Microbiology, and is one of the projects of the Computational Biology research group at the University of ...
  • Scalable Multi-Relational Association Mining 
    Clare, Amanda; Williams, Hugh E.; Lester, Nicholas (2004)
    We propose the new RADAR technique for multi-relational data mining. This permits the mining of very large collections and provides a new technique for discovering multi-relational associations. Results show that RADAR is ...
  • Statistical Evaluation of the Predictive Toxicology Challenge 2000-2001 
    King, Ross Donald; Toivonen, H.; Srinivasan, A.; Kramer, S.; Helma, C. (2003)
    Motivation: The development of in silico models to predict chemical carcinogenesis from molecular structure would help greatly to prevent environmentally caused cancers. The Predictive Toxicology Challenge (PTC) competition ...
  • Structure based drug design with inductive logic programming 
    King, Ross Donald; Enot, David (2003)

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