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Dr Paul Schofield

Departments and Institutes

Department of Physiology, Development and Neuroscience:
Reader in Biomedical Informatics

Research Interests

My research interests centre around the use of formal semantics for the understanding of disease. We work extensively with bioontologies and use automated reasoning and machine learning on large datasets from model organisms, particularly the mouse, and human patients to understand underlying disease mechanisms and to develop novel therapeutic approaches.

I collaborate extensively with:

Dr Robert Hoehndorf, King Abdullah University of Science and Technology (KAUST), Saudi Arabia.

Dr George Gkoutos, University of Aberystwyth

Prof Peter Robinson, Charite Berlin

Prof John Sundberg, the Jackson Laboratory, Bar Harbor USA.

Keywords

Automated reasoning ; Disease ; Phenotypes ; Biological ontologies

Key Publications

Hoehndorf R, Hancock JM, Hardy NW, et al. Analyzing gene expression data in mice with the Neuro Behavior Ontology. Mammalian genome 2014;25(1-2):32-40 doi: 10.1007/s00335-013-9481-z

Hoehndorf R, Hiebert T, Hardy NW, et al. Mouse model phenotypes provide information about human drug targets. Bioinformatics 2014;30(5):719-25 doi: 10.1093/bioinformatics/btt613.

Kohler S, Doelken SC, Mungall CJ, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic acids research 2014;42(Database issue):D966-74 doi: 10.1093/nar/gkt1026

Ibn-Salem J, Kohler S, Love MI, et al. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome biology 2014;15(9):423 doi: 10.1186/s13059-014-0423-1

Hoehndorf R, Hardy NW, Osumi-Sutherland D, et al. Systematic analysis of experimental phenotype data reveals gene functions. PloS one 2013;8(4):e60847 doi: 10.1371/journal.pone.0060847

Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV: The mouse pathology ontology, MPATH; structure and applications. Journal of biomedical semantics 2013, 4(1):18.

Doelken SC, Kohler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN et al: Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Disease models & mechanisms 2012, 6(2):358-372.

Hoehndorf R, Dumontier M, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV: Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PloS one 2011, 6(7):e22006.

Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV: A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics (Oxford, England) 2011, 27(7):1001-1008.

Hoehndorf R, Schofield PN, Gkoutos GV: PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic acids research 2011:1-12.

Kohler S, Bauer S, Mungall CJ, Carletti G, Smith CL, Schofield P, Gkoutos GV, Robinson PN: Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC bioinformatics 2011, 12:418.