Browsing Computational Biology and Bioinformatics by Title

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Browsing Computational Biology and Bioinformatics by Title

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  • 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    The Brookhaven Protein Data Bank was once a pioneering database, but its organization of structural data is now outdated and in need of an upgrade.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)
  • Towards Robot Scientists for autonomous scientific discovery 
    King, Ross Donald; Rowland, Jem; Liakata, Maria; Magdalena, Markham; Sparkes, Andrew; Clare, Amanda; Young, Michael; Whelan, Ken; Soldatova, Larisa; Khan, Muhammed; Aubrey, Wayne; Byrne, Emma (2010-01-04)
    We review the main components of autonomous scientific discovery, and how they lead to the concept of a Robot Scientist. This is a system which uses techniques from artificial intelligence to automate all aspects of the ...
  • Uberon, an integrative multi-species anatomy ontology 
    Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V.; Lewis, Suzanna E.; Haendel, Melissa A. (2012)
    We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology ...
  • The use of Inductive Logic Programming in drug design 
    King, Ross Donald; Enot, David (2002)
  • Using a logical model to predict the growth of yeast 
    King, Ross Donald; Whelan, Ken (2008-02-12)
    Background: A logical model of the known metabolic processes in S. cerevisiae was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG online pathway database. ...
  • Wiki based management of chemometric research projects 
    Alsberg, Bjorn; Clare, Amanda (2010-07)
    As research projects grow in size, there is a tendency for the number of management tasks to increase even faster. There are many different data objects and relations which need to be managed as part of the whole project: ...

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