Postdoctoral Researcher
MRC Weatherall Institute of Molecular Medicine (WIMM)
University of Oxford
🔬 Milne Group – Epigenetics & Gene Regulation in Leukaemia
📍 Oxford, UK | 🧪 Computational & Experimental Epigenomics | 💡 Enhancer Biology in Cancer
I'm a postdoctoral researcher investigating enhancer dynamics in cancer, with a particular focus on MLL-AF4 Acute Lymphoblastic Leukaemia (ALL). My work sits at the interface of experimental epigenomics and computational biology, aiming to unravel how chromatin architecture drives transcriptional dysregulation in leukaemia.
To address these questions, I generate and integrate diverse high-throughput datasets using:
- Epigenomic profiling: ChIP-seq, low-input ChIPmentation, ATAC-seq, CUT&Tag, CUT&RUN
- Transcriptomics: Bulk RNA-seq, TT-seq, POINT-seq
- Chromatin conformation: NG Capture-C, Tiled-C, Micro-Capture-C
- Epigenetic modifications: DNA methylation profiling - TAPS/Bisulphite based methods
- Single cell Transcriptomics and Epigenomics: 10x scMultiome, scCUT&TAG
These data are analysed using custom workflows, statistical modelling, and machine learning to identify regulatory mechanisms underpinning transcriptional dysregulation in leukemia.
I build open-source tools designed for performance, reproducibility, and ease of use in large-scale genomics.
- 🔄 SeqNado: Modular Snakemake pipelines for processing ChIP-seq, ATAC-seq, RNA-seq, CUT&Tag, WGS, CRISPR screens, and Micro-Capture-C (MCC) data
- 🧬 CapCruncher: Toolkit for analysing NG Capture-C, Tri-C, and Tiled-C chromatin interaction data
- ⚡ BamNado: A fast, Rust-based utility for efficient BAM file manipulation
- 📊 PlotNado: Command-line genomic visualisation in a genome browser-like style
- Languages: Python, Rust, R, Bash
- Frameworks & Tools: Snakemake, Conda, Docker, Git, Apptainer, AWS
- Domains: Epigenomics, transcriptomics, chromatin architecture, multi-omics integration
- Focus Areas: Reproducible workflows, NGS tool development, cancer epigenetics
- 🔬 Milne Group @ Oxford
- 🧪 ORCID