Dr Alina Kurjan

Entelo Bio

• Develop and maintain reproducible, end-to-end analysis pipelines for short- and long-read RNA-seq across bulk, single-cell, single-nucleus, and spatial modalities.
• Lead the evaluation and integration of machine learning and foundation model approaches within single-cell workflows, with a focus on QC, robust annotation, and biologically grounded interpretation.
• Partner with cross-functional teams to translate biological questions into computational strategy, delivering analyses that inform experimental design, prioritisation, and decision-making.
• Contribute beyond analysis through business development, operational planning, and scientific storytelling, connecting platform capability to product direction and partnership narratives.

The Botnar Institute, NDORMS, University of Oxford (Prof Sarah Snelling)

• Lead and support analysis of human tendon single-nucleus RNA-seq as part of the Tendon Seed Network initiative, delivering reproducible results and clear biological interpretation.
• Mentor junior researchers and trainees in computational best practices, including single-cell QC, integration, differential expression, and reproducible analysis in Python and R.

Oxford Biomedical Data Science (OBDS) Training Programme, MRC WIMM Centre for Computational Biology, University of Oxford

• Designed and delivered a 5-day in-person module on Python for single-cell analysis, combining lectures on core theory with advanced hands-on tutorials for end-to-end, multi-sample workflows.
• Taught key concepts and best practices including alignment, QC, batch correction and integration, normalisation, feature selection, dimensionality reduction, and cell type annotation.
• Consistently received strong feedback for the thoroughness of the material and an accessible, supportive teaching style.

The Botnar Institute, NDORMS, University of Oxford (Prof Sarah Snelling, Dr Mathew Baldwin, AsProf Adam Cribbs, Prof Christopher Buckley)

• Led end-to-end multi-modal research in human connective tissue biology, including foetal and adult tissue dissection, tissue processing, and bulk, single-nucleus, and spatial RNA-seq.
• Performed integrated histology and imaging workflows, including sectioning, staining, multiplex immunofluorescence, and immunohistochemistry, to connect molecular programs to tissue structure.
• Analysed a large multi-year dataset (>200,000 cells/nuclei) from raw BCL/FASTQ through downstream single-cell analytics, including QC, batch integration, trajectory inference, RNA velocity, pseudobulk differential expression, and gene regulatory network analysis.
• Built and maintained reproducible analysis workflows in Python, R, and Bash, using HPC, Git/GitHub, Conda environments, and Jupyter/RStudio/VS Code.
• Authored multi-language pipelines for bulk and snRNA-seq analysis adopted within and beyond the lab (cribbslab package).
• Mentored junior researchers in computational methods

University of Glasgow (Prof Matthew Dalby, Dr Hannah Donnelly)

• Investigated a plasma polymerised PEA–FN–TGF-β scaffold platform to drive chondrogenic differentiation of human pericytes isolated from microtia patient ear biopsies, contributing to the Donnelly et al. publication.
• Performed primary cell culture and molecular assays including RT-qPCR, Western blot, and in-cell Western, alongside flow cytometry and immunostaining.
• Conducted fluorescence microscopy and atomic force microscopy; accelerated image quantification by writing ImageJ/FIJI macros to streamline high-throughput analysis.
• Analysed and presented experimental results using FIJI and GraphPad Prism.

AstraZeneca, Cambridge (Dr Larissa Carnevalli, Dr Jon Travers, Dr Anisha Solanki)

• Developed and optimised ex vivo assays to characterise drug effects on tumour antigen–specific T cells across three syngeneic mouse models (CT26, 4T1, MC38).
• Established robust workflows for immune cell isolation from spleens and tumours, including MDSC and T cell enrichment using FACS, magnetic bead selection, and Percoll gradients.
• Executed tissue processing, cell culture, and multi-parameter immunostaining with multicolour flow cytometry; analysed datasets in FlowJo, BD FACSDiva, and GraphPad Prism.

Wolfson Wohl Cancer Research Centre, University of Glasgow (Prof Julia Cordero, Dr Philippe Parvy)

• Built a Drosophila cancer cachexia model by generating tumour-bearing larvae with sustained Ras oncogene overexpression.
• Quantified the impact of JAK/STAT pathway perturbations (Stat and/or Domeless knockdown) on tumour burden, tumour cell death, and muscle wasting.
• Performed larval synchronisation and dissection, immunostaining, and RT-qPCR; acquired images with confocal microscopy and analysed/quantified results using Fiji, Volocity, and GraphPad Prism.

Cancer Research UK Beatson Institute, Glasgow (Prof Julia Cordero, Dr Philippe Parvy)

• Investigated anti-tumour properties of defensin peptides by engineering Drosophila genetic crosses targeting Toll and Imd signalling in tumour backgrounds; work contributed to Parvy et al. (2019).
• Quantified defensin gene expression, tumour volume, and cell death using confocal microscopy and image-based analysis pipelines (ZEN, Fiji, Volocity).
• Developed constructs to visualise microvesicle-mediated exchange between immune cells and tumours, supporting mechanistic studies of tumour–immune interactions.