Postdoctoral Research Scientist
I specialise in using next-generation sequencing and long-read sequencing to study the expression of specific cell types in the brain during healthy ageing and disease.
By using Spatial Transcriptomics and Translating Ribosome Affinity Purification (TRAP) to isolate the transcriptome of individual cells, I have identified novel distinguishing features of dopaminergic neurons that may confer vulnerability to degeneration.
I am driven to using modern computational approaches to explore 'big data'. I am always looking for opportunities to collaborate and/or share expertise in such methods.
I am also a Veterinary Surgeon and teach anaesthesia and surgery as part of the Home Office course for Personal Licence applicants.
Computational Methods in use:
- Differential gene & transcript expression in bulk, single-cell and high-resolution (200 nm) spatial transcriptomic data
- Weighted gene co-expression network analysis (WGCNA)
- De novo transcript assembly from short and long-read data
- Enrichment heritability from GWAS data
- Cell type specificity analysis from ribosome affinity profiling and single-cell data
- Nucleus-imputed single-cell segmentation of spatial transcriptomic data
- Somatic & germline mutation calling from transcriptomic and genomic data
- Proteogenomic analysis including using MaxQuant to detect putative novel peptides
- Genome-wide CRISPR screen enrichment analysis
- Pythonic image analysis methods and neural network-guided segmentation and object recognition (including the use of Mask-RCNN and U-Net)
- Preparation of self-hosted R Shiny-based websites to provide a resource for result querying
Molecular Methods in use:
- Translating ribosome affinity purification of RNA from specific cell types in Cre-transgenic mouse lines
- Short- and long-read library preparation for sequencing
- Genomic, transcriptomic, and amplicon-targeted long-read sequencing on the Oxford Nanopore MinION
- Oligonucleotide-based fragment pulldown
- Single-molecule fluorescence in situ hybridization for visualizing and quantifying RNA expression in individual cells
- ELISA, immunohistochemical methods & quantitative PCR
- Generation, breeding and maintenance of genetically-modified rodents
- Surgery and minor procedures in rodents
Inhibition of the SUV4-20 H1 histone methyltransferase increases frataxin expression in Friedreich's ataxia patient cells.
Vilema-Enríquez G. et al, (2020), J Biol Chem, 295, 17973 - 17985