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agnjuh/README.md

Hej, I'm Ágnes

Biomedical consultant scientist and molecular biotechnologist with experience spanning immunology, haematology, cancer biology, regenerative and developmental biology. I work at the interface of experimental and computational research, integrating stem cells, organoids, genome engineering, perturbation-based studies, and multi-omics analysis to understand cellular plasticity, immune regulation, and disease-associated state transitions. I also serve on the Bio-protocol Peer Reviewer Board, reviewing experimental protocols in molecular biology, cell biology, immunology, haematology, cancer biology, and related biomedical sciences.


Focus areas

  • Immunology, haematology, and cancer biology
  • Cellular plasticity, immune-cell states, and disease mechanisms
  • Stem cells, organoids, CRISPR, and experimental molecular biology
  • Single-cell transcriptomics and systems biology
  • Perturbation analysis, transcriptional regulation, and multi-omics integration
  • Machine learning for biological data analysis
  • Reproducible computing with Python, R, and Snakemake

Repositories & projects

Some of my current projects involve experimental and computational workflows that are not publicly available while work is ongoing. In collaborative or professional contexts, additional technical details can be shared, and access to specific materials may be possible under appropriate confidentiality agreements.


Contact

Professional enquiries can be sent through the contact form.


Picture: Huang B, Medina P, He J, et al. Spatially patterned kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling. Cell Stem Cell. 2025;32(10):1614-1633.e13. doi:10.1016/j.stem.2025.08.013

Pinned Loading

  1. dengue_bcell-clonal-architecture-scRNA dengue_bcell-clonal-architecture-scRNA Public

    Single-cell RNA and BCR repertoire analysis of B cells in secondary dengue infection. This project integrates 10x Genomics gene expression and VDJ data to characterise clonal expansion, V gene usag…

    Python

  2. bioactivity_prediction_pharmbio bioactivity_prediction_pharmbio Public

    Machine learning analysis of molecular bioactivity using RDKit descriptors, fingerprint representations, dimensionality reduction, and ensemble modelling

    Python

  3. melanoma_spatial_immune_landscapes melanoma_spatial_immune_landscapes Public

    Morphology-aware spatial transcriptomic analysis of melanoma tumour microenvironments v1.0.0

    Python

  4. alzheimers_neuroinflammatory_niches alzheimers_neuroinflammatory_niches Public

    Spatial transcriptomic analysis of neuroinflammatory niches and cell-type associations in the human entorhinal cortex.

    Python