Browsing Computational Biology and Bioinformatics by Author "Clare, Amanda"

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Browsing Computational Biology and Bioinformatics by Author "Clare, Amanda"

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  • AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory 
    Clare, Amanda; Sparkes, Andrew (2012-06-13)
    Motivation: Modern automated laboratories need substantial data management solutions to both store and make accessible the details of the experiments they perform. To be useful, a modern Laboratory Information Management ...
  • Confirmation of Data Mining Based Predictions of Protein Function 
    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 ...
  • Constraint-based optimisation tools for semi-automated refinement of genome-scale yeast metabolic models 
    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 ...
  • Data mining the yeast genome in a lazy functional language 
    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 ...
  • Decision Trees for Hierarchical Multilabel Classification: A Case Study in Functional Genomics 
    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 ...
  • The EXACT description of biomedical protocols 
    King, Ross Donald; Aubrey, Wayne; Soldatova, Larisa; Clare, Amanda (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 ...
  • Hierarchical Multi-classification with Predictive Clustering Trees in Functional Genomics 
    Clare, Amanda; Džeroski, Sašo; Struyf, Jan; Blockeel, Hendrik (2005)
    This paper investigates how predictive clustering trees can be used to predict gene function in the genome of the yeast Saccharomyces cerevisiae. We consider the MIPS FunCat classification scheme, in which each gene is ...
  • How well do we understand the clusters found in microarray data? 
    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 ...
  • Integration of genomic and phenotypic data 
    Clare, Amanda (Wiley, London, 2005)
  • Locational distribution of gene functional classes in Arabidopsis thaliana 
    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 ...
  • Machine learning of functional class from phenotype data 
    Clare, Amanda; King, Ross Donald (2002)
    Motivation: Mutant phenotype growth experiments are an important novel source of functional genomics data which have received little attention in bioinformatics. We applied supervised machine learning to the problem of ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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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