Work history
Education
Zuzanna Kuczynska

Zuzanna Kuczynska

Work history

Data Science Intern

Novartis
Basel, Switzerland
05.2025 - Current
  • Developed and implemented an end-to-end computational pipeline for PhenoCycler multiplexed tissue imaging, covering raw image pre-processing, cell-level spatial analysis, and benchmarking of advanced algorithms to optimise segmentation accuracy and immune cell phenotype detection across multiple studies.
  • Co-authored a manuscript (in preparation) on multi-omics data analysis, including spatial approaches, highlighting integrative computational methods for immune-mediated disease research.
  • Invited speaker at the Second Spatial OMICS Symposium (Basel, September 2025) to present the pipeline and Novartis’s new approach to hilghly multiplexed image analysis, sharing analysis strategies with the research community.

Research Assistant

University of Glasgow
Glasgow, Glasgow City
11.2024 - 05.2025
  • Developed and optimized computational pipelines to improve cell segmentation, transcript recovery, and analysis outcomes.
  • Enhanced niche analysis by testing various methods (Tessera, BANKSY, Seurat, and a custom pipeline), improving the robustness of inferred niche information and enabling the identification of distinct niches.
  • Contributed to manuscript preparation utilizing spatial transcriptomics to analyze niche factors regulating healthy synovial macrophages.
  • Lead analysis of single-cell spatial transcriptomics, investigating fibroblasts, macrophages, and dendritic cells in autoimmune disease contexts.
  • Applied advanced computational techniques using R, Python, and HPC systems for studying cellular interactions and complex biological data.
  • Generate novel hypotheses and insights from spatial transcriptomics data for publication and presentations.
  • Collaborate effectively with a multidisciplinary team of wet-lab immunologists and clinical rheumatologists.
  • Prepare and present research findings at international conferences, such as the European Macrophage and Dendritic Cell Biology (EMDS) Meeting 2024 in Vienna.

Advanced Biomedical Support Worker

NHS Lothian
Edinburgh
01.2023 - 09.2024
  • Identify diagnostic approach based on sample type and patients medical history.
  • Experience with MALDI-TOF MS operation.
  • Systems and equipment initial troubleshooting (BD Kiestra InoqulA Sample Processor).

Senior scientist

SRG Synergy
05.2021 - 12.2022
  • Train new employees in (ISO015189 and ISO022870) UKAS accredited medical laboratory practices as well as being present as a leader during audits.
  • Identify and formulate incident reports comprising of CAPAs and possible updates to workplace protocols.
  • Work across multiple sites in United Kingdom.
  • Oversee daily lab process by ensuring the SOP standards and accuracy of results.
  • Prepare and present reports on lab's performance weekly.

Education

Master of Science - Bioinformatics

University of Glasgow
  • Explored spatial biology, focusing on single-cell spatial transcriptomics where I benchmarked five image- and transcript-based cell segmentation methods on tonsil, synovium, and skin tissues, leading to biologically meaningful segmentation.
  • Experience with bulk RNA-seq, single cell RNA-seq, spatial transcriptomics, metabolomics and genomics analysis.
  • Protein drug design and drug discovery workflow (prediction of protein structure, modelling of protein interactions, recognition and prediction of binding site, ligand-receptor site binding).
  • GUI development for chemical structure database created with SQL.
  • Performed computational analysis of mutation data to identify mutations distinguishing resistant and wild-type strains, including read trimming (TrimGalore), sequence alignment (Bowtie2), SNP calling (FreeBayes), variant filtering (vcffilter, bcftools), annotation (SnpEff), and extraction of non-synonymous variants, leading to pathway analysis and identification of resistance-associated mutations.

BSc (Hons) - Biological Sciences (Cell and Molecular Biology)

Heriot-Watt University, Edinburgh
05.2021

Similar Profiles

Create profile
Zuzanna Kuczynska