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agnjuh/README.md

Hej, I'm Ágnes

I am a biomedical scientist and molecular biotechnologist working across molecular biology, regenerative and developmental biology, spatial biology, and computational genomics. I integrate experimental systems such as stem cells, organoids, imaging, and genome engineering with data-driven approaches for large-scale omics analysis.


Focus areas

  • Experimental molecular biology: CRISPR editing, stem cells, organoids, advanced microscopy
  • Spatial and imaging-based biology: spatial transcriptomics, high-resolution imaging, quantitative image analysis
  • Computational genomics: NGS library preparation and sequencing QC; RNA-seq, ATAC-seq, ChIP-seq; variant analysis and integrative multi-omics; pathway and signalling network analysis; GWAS and gene–environment modelling
  • Machine learning in biology: classification, feature-level interpretation, predictive modelling
  • Workflow automation: reproducible pipelines with Snakemake and Conda

Repositories & projects

Some of my current projects involve experimental and computational workflows that are not publicly available while work is ongoing.

This profile includes selected public examples and smaller code snippets that illustrate my analytical and methodological approaches. 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.

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  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. mRNA-seq_K562_heatshock mRNA-seq_K562_heatshock Public

    Bulk mRNA-seq analysis of heat shock response in the K562 human leukemia cell line, aligned to the T2T-CHM13 v2.0 genome.

    Python

  3. ATAC-seq_ChIP-seq_T-cell-regulatory-programs ATAC-seq_ChIP-seq_T-cell-regulatory-programs Public

    Integrative analysis of ATAC-seq and ChIP-seq in primary human CD4 T cells during activation (naive vs anti-CD3/CD28 + IL-2), profiling chromatin accessibility and transcription factor binding to c…

    Python

  4. ECGml ECGml Public

    A modular ECG signal analysis framework designed for reproducible research and machine learning applications. The pipeline integrates classical signal-processing workflows with delineation tools an…

    Python 1

  5. gene-IPI_GWAS_GxE gene-IPI_GWAS_GxE Public

    Forked from PerinatalLab/gene-IPI

    The repository implements genome-wide gene–environment interaction analyses to assess how interpregnancy interval (IPI) and prior miscarriage modify maternal genetic effects on gestational duration.

    R

  6. rtpcr_detox_genes_vitD_LCA rtpcr_detox_genes_vitD_LCA Public

    RT-qPCR analysis of detoxification gene expression in colon cancer cells treated with vitamin D and lithocholic acid (LCA).

    R