I am a bioinformatician and medical doctor with seven years experience utilising bioinformatics methods to analyse biological data. I have extensive knowledge and expertise in analysing numerous genetic data sets, and engineering best practice bioinformatics pipelines, with a substantial foundation in cancer genetics and medicine.
Read our brilliant study which reveals glioblastoma multiforme (GBM) evades immune attack through epigenetic changes in GBM stem cells, leading to an immunosuppressive tumor environment and increased recruitment of tumor-associated macrophages. Check out the original article here and a great explainer here.
Check out a great blog post on hands on mutational signature analysis here. The article covers de novo signature discovery using non-negative matrix factorization (NMF) and signature refitting using the Catalogue of Somatic Mutations in Cancer (COSMIC). It includes a hands-on example using the MutationalPatterns package in R, discussing necessary inputs, analyzing test data, and visualizing the genetic information.
Read my experiences learning and developing a best practice Nextflow pipeline here
Find our recent nf-core/rnasplice pipeline here.
Synthetic super-enhancers enable selective expression of anti-cancer payloads for viral gene therapy.
Koeber, U., Matjusaitis, M., White, R., Alfazema, N., Morisse, G., Navarette, M., Blin, C., Dewari, P., Hamdan, A., Southgate, B. et al. (Manuscript in preparation)
Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion.
Southgate, B., Gangoso, E., Bradley, L. et al. (2021) Cell. Cell Press. doi: 10.1016/j.cell.2021.03.023.
Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants.
Bressan, R. B., Southgate, B. et al. (2021) Cell Stem Cell. Cell Press. doi: 10.1016/j.stem.2021.01.016.
LRIG1 is a gatekeeper to exit from quiescence in adult neural stem cells.
Marqués-Torrejón, M. Á., Williams, C., Southgate, B. et al. (2021) Nature Communications. Nature Research. doi: 10.1038/s41467-021-22813-w.
Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications.
Southgate, J. A., Bull, M.,Brown, C., Watkins, J., Corden, S., Southgate, B. et al. (2020) Bioinformatics. Oxford University Press, 36(6), pp. 1681-1688. doi: 10.1093/bioinformatics/btz814.
An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein.
Dewari, P. S., Southgate, B. et al. (2018) eLife, 7. doi: 10.7554/eLife.35069.