Amanda Clare BA (Oxon), MSc( Edinburgh), PhD

Senior Lecturer

Contact Details

Room Number..........:  E37
Building....................:  Llandinam
Phone.......................:   +44 (0)1970 622429
E-Mail........................:   afc
Home Page...............:   Personal

Research Groups

Teaching Areas

Modules Taught

  • CS12510: Functional Programming
  • CS24400: Scientific Python
  • CS24420: Scientific Python
  • CSM0120: Programming for Scientists
  • MA25200: Introduction to Numerical Analysis and its applications
  • MA25220: Introduction to Numerical Analysis and its applications
  • MT25200: Cyflwyniad i Ddadansoddiad Rhifiadol a'i gymhwysiadau
  • MT25220: Cyflwyniad i Ddadansoddiad Rhifiadol a'i gymhwysiadau

Publications

2017

Donkin, E., Dennis, P., Ustalakov, A., Warren, J., Clare, A. 2017. Replicating complex agent based models, a formidable task. Environmental Modelling and Software 92 pp. 142-151. Cadair

Ravenscroft, J.E., Liakata, M., Clare, A., Duma, D. 2017. Measuring scientific impact beyond academia: An assessment of existing impact metrics and proposed improvements. PLoS One e0173152 Cadair

2016

Donkin, E., Warren, J., Dennis, P., Clare, A. 2016. Meta-data analysis of plant trait databases: how are such databases used and how can they be improved? British Ecological Society. Cadair

Veneman, J.B., Saetnan, E., Clare, A., Newbold, C. 2016. MitiGate; an online meta-analysis database for quantification of mitigation strategies for enteric methane emissions. Science of the Total Environment 572 pp. 1166-1174. Cadair

Duma, D., Liakata, M., Clare, A., Ravenscroft, J., Klein, E. 2016. Rhetorical Classification of Anchor Text for Citation Recommendation. D-Lib Magazine 22 (9/10) Cadair

Nicholls, S.M., Clare, A., Randall, J. 2016. Goldilocks: A tool for identifying genomic regions that are ‘just right’. Bioinformatics 32 (13) pp. 2047-2049. Cadair

2015

Aubrey, W., Riley, M., Young, M., King, R.D., Oliver, S.G., Clare, A. 2015. A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation. PLoS One 10 (12) 0142494 Cadair

Sapstead, S., Daniel, I., Clare, A. 2015. Automatically Geotagging Articles in the Welsh Newspapers Online Collection. In M. Bramer., M. Petridis. (eds) Research and Development in Intelligent Systems XXXII: Incorporating Applications and Innovations in Intelligent Systems XXIII. Springer Nature pp. 367-373. Cadair

2014

Runciman, C., Clare, A., Harkness, R. 2014. Laboratory Automation in a Functional Programming Language. SLAS Technology 19 (6) pp. 569-576. Cadair

2013

Ravenscroft, J., Liakata, M., Clare, A.J. 2013. Partridge: An effective system for the automatic classification of the types of academic papers. In M. Bramer., M. Petridis. (eds) Research and Development in Intelligent Systems XXX: Incorporating Applications and Innovations in Intelligent Systems XXI Proceedings of AI-2013, The Thirty-third SGAI International Conference on Innovative Techniques and Applications of Artificial Intelligence. AI-2013: The Thirty-third SGAI International Conference. Springer Nature pp. 351-358. Cadair

Riley, M.C., Aubrey, W., Young, M., Clare, A. 2013. PD5: a general purpose library for primer design software. PLoS One 8 (11) e80156 Cadair

2012

Sparkes, A.C., Clare, A.J. 2012. AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory. Bioinformatics 28 (10) pp. 1390-1397.

2011

Clare, A., Croset, S., Grabmueller, C., Kafkas, S., Liakata, M., Oellrich, A., Rebholz-Schuhmann, D. 2011. Exploring the Generation and Integration of Publishable Scientic Facts Using the Concept of Nano-publications. Sepublica (workshop of Extended Semantic Web Conference). Cadair

2010

Pir, P., Dobson, P.D., Smallbone, K., Mendes, P., King, R.D., Lu, C., Oliver, S.G., Clare, A. 2010. Constraint-based optimisation tools for semi-automated refinement of genome-scale yeast metabolic models.

Alsberg, B., Clare, A.J. 2010. Wiki based management of chemometric research projects. Journal of Chemometrics 24 (7-8) 11th Scandinavian Symposium on Chemometrics. pp. 408-417.

Sparkes, A.C., King, R.D., Aubrey, W., Benway, M., Byrne, E.L., Clare, A.J., Liakata, M., Markham, M., Whelan, K.E., Young, M., Rowland, J. 2010. An Integrated Laboratory Robotic System for Autonomous Discovery of Gene Function. Journal of The Association for Laboratory Automation 15 (1) pp. 33-40.

Sparkes, A.C., Aubrey, W., Byrne, E.L., Clare, A.J., Khan, M., Liakata, M., Markham, M., Rowland, J., Soldatova, L.N., Whelan, K.E., Young, M., King, R.D. 2010. Towards Robot Scientists for autonomous scientific discovery. Automated Experimentation 2 (1) pp. 1759-4499.

2009

Byrne, E.L., Liakata, M., Whelan, K.E., Oliver, S.G., Rowland, J.J., Aubrey, W., Soldatova, L.N., Sparkes, A.C., Young, M., Markham, M., Clare, A.J., Pir, P., King, R.D. 2009. Letters - Make way for robot scientists. Science 325 (5943) pp. p945.

King, R.D., Rowland, J.J., Aubrey, W., Liakata, M., Markham, M., Soldatova, L.N., Whelan, K.E., Clare, A.J., Young, M., Sparkes, A.C., Oliver, S., Pir, P. 2009. The Robot Scientist Adam. Computer 42 (8) pp. 46-54.

King, R.D., Rowland, J.J., Oliver, S.G., Young, M., Aubrey, W., Byrne, E.L., Liakata, M., Markham, M., Pir, P., Soldatova, L.N., Sparkes, A.C., Whelan, K.E., Clare, A.J. 2009. The Automation of Science. Science 324 (5923) pp. 85-89.

2008

Soldatova, L.N., Aubrey, W., King, R.D., Clare, A.J. 2008. The EXACT description of biomedical protocols. Bioinformatics 24 (13) pp. i295-i303.

2007

Riley, M.C., Clare, A., King, R.D. 2007. Locational distribution of gene functional classes in Arabidopsis thaliana. BMC Bioinformatics 8 112

2006

Clare, A.J., Karwath, A., Ougham, H.J., King, R.D. 2006. Functional bioinformatics for Arabidopsis thaliana. Bioinformatics 22 (9) pp. 1130-1136.

Soldatova, L., Clare, A., Sparkes, A., King, R.D. 2006. An ontology for a Robot Scientist. Bioinformatics 22 (14) pp. 464-471.

Džeroski, S., Blockeel, H., Clare, A., Leander, S., Struyf, J. 2006. Decision Trees for Hierarchical Multilabel Classification: A Case Study in Functional Genomics. Knowledge Discovery in Databases: PKDD 2006. Springer Nature pp. 18-29.

2005

Clare, A. 2005. Integration of genomic and phenotypic data. Data Analysis and Visualization in Genomics and Proteomics. Wiley pp. 0-470.

Clare, A., Džeroski, S., Struyf, J., Blockeel, H. 2005. Hierarchical Multi-classification with Predictive Clustering Trees in Functional Genomics.

King, R.D., Whelan, K., Clare, A., Rowland, J.J. 2005. The Robot Scientist 'Adam'.

2004

Clare, A., Williams, H.E., Lester, N. 2004. Scalable Multi-Relational Association Mining.

King, R.D., Wise, P.H., Clare, A. 2004. Confirmation of Data Mining Based Predictions of Protein Function. Bioinformatics 20 (7) pp. 1110-1118.

2003

King, R.D., Clare, A. 2003. Predicting gene function in Saccharomyces cerevisiae. Bioinformatics 19 (S2) pp. 42-49.

Clare, A., King, R.D. 2003. Data mining the yeast genome in a lazy functional language.

2002

Clare, A., King, R.D. 2002. How well do we understand the clusters found in microarray data? In Silico Biology 2 (4) pp. 511-522.

Clare, A., King, R.D. 2002. Machine learning of functional class from phenotype data. Bioinformatics 18 (1) pp. 160-166.

2000

King, R., Karwath, A., Clare, A., Dehaspe, L. 2000. Accurate prediction of protein functional class from sequence in the <i>Mycobacterium tuberculosis</i> and <i>Escherichia coli</i> genomes using data mining. Yeast 17 (4) pp. 283-293. Cadair