Maria Shirley

PhD

MSc Student

16S rRNA Sequencing 2D and 3D cell culture systems Cancer Bioinformatics Cellular and Molecular Immunology ChIP-Seq Data Analysis Metagenomics NGS data analysis (WGS Translational oncology

UPF1 and RNA Polymerase II Dynamics in Drosophila • Developed a computational workflow to analyse RNA Polymerase II ChIP-seq datasets in Drosophila melanogaster. • Performed quality control, sequence alignment, BAM processing, and signal normalisation using industry-standard genomics tools. • Conducted metagene profiling and statistical analysis using Python and R. • Identified increased accumulation of elongating Ser2 Pol II following UPF1 depletion.

PDAC Microbiome Multi-Omics Analysis • Developing a computational pipeline to identify microbiome biomarkers associated with pancreatic ductal adenocarcinoma (PDAC). • Integrating longitudinal biological datasets german and Spanish cohorts from EBI and identifying the microbiomes involved in cancer progression using unsupervised machine learning approaches.

Differential Gene Expression and Pathway Analysis • Analysed cancer datasets using Limma and empirical Bayes statistical methods. • Generated visualisations and performed pathway enrichment analysis using KEGG and REACTOME databases. Machine Learning for Disease Classification • Built predictive classification models using Random Forest, SVM, and Logistic Regression algorithms. • Applied dimensionality reduction and clustering methods achieving 88% classification accuracy and F1 score of 0.85