Cambridge Centre for Professor Paul Schofield
University Professor of Biomedical Informatics
Contact information
+441223333878
Dept of Physiology Development and Neuroscience
University of Cambridge
Cambridge
CB2 3EG
United Kingdom
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 Birmingham Prof Peter Robinson, Charite Berlin Prof John Sundberg, the Jackson Laboratory, Bar Harbor USA.
Publications
The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine (2022) Jacobsen, J.O.B., et. al. Nature Biotechnology. ( In Press) [Preprint on medRxiv 2021.11.27.21266944; doi: https://doi.org/10.1101/2021.11.27.21266944 ]
Slater LT, Williams JA, Karwath A, Fanning H, Ball S, Schofield PN, Hoehndorf R, Gkoutos GV. 2021. Multi-faceted semantic clustering with text-derived phenotypes. Comput Biol Med.138:104904. Epub 2021/10/03.
Kafkas S, Althubaiti S, Gkoutos GV, Hoehndorf R, Schofield PN. 2021. Linking common human diseases to their phenotypes; development of a resource for human phenomics. J Biomed Semantics.12:17. Epub 2021/08/25.
Abdelhakim M, McMurray E, Syed AR, Kafkas S, Kamau AA, Schofield PN, Hoehndorf R. 2020. DDIEM: drug database for inborn errors of metabolism. Orphanet J Rare Dis.15:146. Epub 2020/06/13.
Althubaiti S, Karwath A, Dallol A, Noor A, Alkhayyat SS, Alwassia R, Mineta K, Gojobori T, Beggs AD, Schofield PN, et al. 2019. Ontology-based prediction of cancer driver genes. Sci Rep.9:17405. Epub 2019/11/24.
Althubaiti S, Karwath A, Dallol A, Noor A, Alkhayyat SS, Alwassia R, Mineta K, Gojobori T, Beggs AD, Schofield PN et al: Ontology-based prediction of cancer driver genes. Sci Rep 2019, 9(1):17405.
Kafkas S, Abdelhakim M, Hashish Y, Kulmanov M, Abdellatif M, Schofield PN, Hoehndorf R: PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. Sci Data 2019, 6(1):79.
Boudellioua, I., Kulmanov, M., Schofield, P. N., Gkoutos, G. V. & Hoehndorf, R. DeepPVP:
phenotype-based prioritization of causative variants using deep learning. BMC Bioinformatics 20, 65, doi:10.1186/s12859-019-2633-8 (2019).
Alghamdi, S. M., Sundberg, B. A., Sundberg, J. P., Schofield, P. N. & Hoehndorf, R. Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. Sci Rep 9, 4025, doi:10.1038/s41598-019-40368-1 (2019).
Kafkas, S. et al. PathoPhenoDB, linking human pathogens to their phenotypes in support of
nfectious disease research. Sci Data 6, 79, doi:10.1038/s41597-019-0090-x (2019).
Kulmanov, M., Schofield, P. N., Gkoutos, G. V. & Hoehndorf, R. Ontology-based validation and identification of regulatory phenotypes. Bioinformatics 34, i857-i865, doi:10.1093/bioinformatics/bty605 (2018).
Gkoutos, G. V., Schofield, P. N. & Hoehndorf, R. The anatomy of phenotype ontologies: principles, properties and applications. Brief Bioinform 19, 1008-1021, doi:10.1093/bib/bbx035 (2018).
Boudellioua, I., Kulmanov, M., Schofield, P. N., Gkoutos, G. V. & Hoehndorf, R. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. Sci Rep 8, 14681, doi:10.1038/s41598-018-32876-3 (2018).
Rodriguez-Garcia, M. A., Gkoutos, G. V., Schofield, P. N. & Hoehndorf, R. Integrating phenotype ontologies with PhenomeNET. J Biomed Semantics 8, 58, doi:10.1186/s13326- 017-0167-4 (2017).
Boudellioua, I. et al. Semantic prioritization of novel causative genomic variants. PLoS Comput Biol 13, e1005500, doi:10.1371/journal.pcbi.1005500 (2017)