I am a senior research fellow in the Artificial Intelligence Applications Institute, part of the School of Informatics of the University of Edinburgh. In addition to the research outlined here, I am involved in the transfer of AI technologies, including knowledge-based and data mining methods, to commerce and industry. I also teach on the Knowledge Management fourth year/MSc course.

Systems Biology

Single-cell data on mRNA expression from the Bertrand Lab, Montpellier, shows transcription in yeast to be a noisy process. I have developed stochastic models to explain the cell-to-cell variability observed.
In collaboration with the Beggs Lab, the kinetics of transcription and splicing in the same yeast reporter have been investigated by modelling transcription and the two steps of the splicing reaction.

NEW! Bayesian evidence analysis tools for systems biology

New methods for model comparison and parameter inference will be developed in a new BBSRC tools and resources project. Nested sampling will be used to compute both the Bayesian evidence and the bounds on optimal parameter values for systems models. More details can be found on the project pages.

Bio-Ontologies

I have worked on, and led, several bio-ontology projects. Beginning with XSPAN, a stand-alone ontology editor, COBrA, was developed that allowed two ontologies to be loaded at once and ontology mappings created between them. A GUI for editing OBO ontologies in Protege was implemented in a later project, and currently the BioSphere ontology portal supports collaborative editing in a community. All of this work is in collaboration with Jonathan Bard now a visitor at Oxford CBRG.

Categories, networks and sequences

I have supervised many projects on biological data mining, including the learning of categories for microarray data; learning housekeeping genes; inferring networks from expression data; and, most recently, the identification of regulatory sequences in DNA. Probabilistic and instance-based learning are common themes in this work.