Head of Integrative Computational Biology
The aim of my group is to develop state-of-the-art computational methods to break down barriers to aid the integration, visualisation, and analytics of biological datasets. We develop software tools and methodologies to interrogate a wide variety of modalities including spatial biology, imaging, genomics, transcriptomics, proteomics and epigenetics. This allows us to gain insight into the disease context and progression at a molecular and tissue level. Our work will enable opportunities for exploring cellular pathologies, discovering new biomarkers, and reclassifying disease taxonomies.
Multi-Dimensional Viewer (MDV)
Multi-Dimensional Viewer (MDV) allows user friendly analysis and visualisation of large multi-omic data sets https://github.com/Taylor-CCB-Group/MDV
SpOOx (Spatial Omics Oxford Pipeline)
This pipeline was developed in close collaboration with clinicians, computational biologists, laboratory scientists and mathematicians to comprehensively analyse spatial proteomics data. SpOOx automates the processing of data generated by the Hyperion Imaging System and we are developing it for other platforms. https://github.com/Taylor-CCB-Group/SpOOx/
LanceOtron : Deep learning for analysing epigenetic signals
LanceOtron, combines deep learning for recognizing peak shape with multifaceted enrichment calculations for assessing significance. In benchmarking ATAC-seq, ChIP-seq and DNase-seq, LanceOtron outperforms long-standing, gold-standard peak callers such as MACS2 through its improved selectivity and near-perfect sensitivity. https://github.com/LHentges/LanceOtron
Applications of Virtual, Mixed and Augmented Reality in Biomedicine
Previously seen as mainly for gaming, commercial and research institutions are investigating VR, MR and AR (XR) solutions to solve real world problems. In Biomedicine these include researching: training, simulation, mental health, data analysis, and studying disease progression. XR offers the promise of allowing new ways to interact with data and also accelerate patient therapy. https://medicalxr.molbiol.ox.ac.uk/
Systematic analysis of YFP traps reveals common mRNA/protein discordance in neural tissues.
Titlow JS. et al, (2023), J Cell Biol, 222
LanceOtron: a deep learning peak caller for genome sequencing experiments
Hentges LD. et al, (2022), Bioinformatics, 38, 4255 - 4263
Mental health needs of adolescents with HIV in Africa - Authors' reply.
Gooden TE. et al, (2022), The lancet. HIV, 9, e376 - e377
The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin.
Truch J. et al, (2022), Nature communications, 13
Bioinformatics and the Metaverse: Are We Ready?
Taylor S. and Soneji S., (2022), Frontiers in Bioinformatics, 2