We devise and implement novel data analysis solutions for biomedical research, particularly when proteomics data is involved. The lab is based in the School of Biological and Chemical Sciences at Queen Mary, University of London and led by Prof Conrad Bessant.
The lab is responsible for the Galaxy Integrated Omics (GIO) web-based platform for integrated analysis of transcriptomic and proteomic data, and PITDB - a database of translated genomic elements identified from proteomics informed by transcriptomics (PIT) experiments. We also produced Classyfire, an R package for performing robustly validated machine learning experiments.
Hijazi, M., Smith, R., Rajeeve, V., Bessant, C. & Cutillas, P.R. (2020). Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring. Nature Biotechnology.
Saha, S., Matthews, D.A., Bessant, C. (2018). High throughput discovery of protein variants using proteomics informed by transcriptomics. Nucleic Acids Research, 46(10), 4893–4902.
Pearce, O.M., Delaine-Smith, R.M., Maniati, E., Nichols, S., Wang, J., Böhm, S., … & Balkwill, F.R. (2018). Deconstruction of a metastatic tumor microenvironment reveals a common matrix response in human cancers. Cancer Discovery, 8(3), 304-319.
Saha, S., Chatzimichali, E.A., Matthews, D.A., Bessant, C. (2018). PITDB: a database of translated genomic elements. Nucleic Acids Research 46.D1, D1223-D1228.
Chatzimichali, E.A., & Bessant, C. (2016). Novel application of heuristic optimisation enables the creation and thorough evaluation of robust support vector machine ensembles for machine learning applications. Metabolomics, 12(1), 16.
Fan, J., Saha, S., Barker, G., Heesom, K.J., Ghali, F., Jones, A.R., … & Bessant, C. (2015). Galaxy integrated omics: web-based standards-compliant workflows for proteomics informed by transcriptomics. Molecular & Cellular Proteomics, 14(11), 3087-3093.
Evans, V. C., Barker, G., Heesom, K. J., Fan, J., Bessant, C., & Matthews, D. A. (2012). De novo derivation of proteomes from transcriptomes for transcript and protein identification. Nature Methods, 9(12), 1207.
Proteome Informatics (Royal Society of Chemistry, 2016)
Building Bioinformatics Solutions (Oxford University Press, 2014)
As a postdoc: We welcome enquiries from postdocs seeking to apply for Marie Skłodowska-Curie Action Individual Fellowships. Please email Conrad Bessant (firstname.lastname@example.org) with your CV, inluding MSCA in the subject line.
As a PhD student: Funded PhD studentship opportunities are available occasionally, typically for candidates from the UK and EU member states. These will be advertised widely, e.g. on findaphd.com. We are also willing to consider applications from PhD students funded by scholarships, or other means of self-funding, from any country.
An an MSc student: Our MSc Bioinformatics programme is one of the most popular in Europe. Apply now for late September start.
Phone etc: See Conrad’s official QMUL profile page