Welcome to my GitHub page! I am a PhD researcher in bioinformatics researcher with a focus on data processing, data analysis and machine learning models for clinical, genomic and transcriptomic data. Ultimately aiming to improve individual patient care. Here, you will find projects related to my research interests and contributions to open-source tools in bioinformatics.
Projects that I am currently working on include:
- PISCES: Pathology Spatial & Single CELL Omics. Development of analysis workflows for spatial and single-cell transcriptomics to support the pathology department within EMC.
- PATH2XNAT: Reproducible spatial transcriptomics and digital pathology workflows in Galaxy for COVID-19 data analysis.
- Mongoose: Multi-task learning for perturbation modelling in single-cell and spatial transcriptomics data.
- A systematic benchmark of copy number variation detection tools for high density SNP genotyping arrays, Genomics, In Press, 2024.
- Borderline (suspicious) for T-cell-mediated rejection, the Banff classification's Achilles’ heel, Nephrology Dialysis Transplantation, 2024.
- A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel, Frontiers in Immunology, 2022.
- aCNVbench: A Nextflow workflow for detecting and benchmarking CNVs from SNP-array data.
- KidneyRejectionClassifier: Decentralized kidney transplant biopsy classifier developed using genes of the Banff-Human Organ Transplant Panel.
Feel free to reach out or connect on LinkedIn or check out my Google Scholar profile for a full list of publications!