Katarína Grešová
CV
Curriculum vitae
Positions, education, teaching and talks. Longer write-ups of the software live on the building page and the courses on the teaching page; the full publication list is on the publications page.
Research positions
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2025 – present
Postdoctoral researcher
Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center, Berlin
Interpretable machine learning for RNA regulation: what in an mRNA's own sequence sets how much protein a cell makes from it, and what that explains about health and disease.
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2023 – 2025
Researcher
Intelligent Systems for Complex Data group, Masaryk University, Brno
Protein-structure similarity search at proteome scale — adapting pretrained networks to produce structure embeddings, and the pipelines to run them on HPC.
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2024 – 2025
Pre-doctoral fellow
Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore
Senescent-cell classification from single-cell long-read sequencing in the ageing mouse brain, and shared senescence markers across cell types from transcriptomic and proteomic data.
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2023 – 2024
Visiting researcher
Alexiou Lab, University of Malta, Msida
Led the miRBench project. Taught deep learning and interpretability, and supervised four junior researchers.
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2020 – 2023
Research specialist
Alexiou group, CEITEC, Masaryk University, Brno
Genomic Benchmarks, attribution-based interpretation of sequence models, and deep learning for RNA. Ran the group's workshops and hackathons.
Education
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2020 – 2025
Ph.D. in Genomics and Proteomics
Masaryk University, Brno
Dissertation: Modeling small RNA binding rules using machine learning, supervised by Panagiotis Alexiou. Awarded summa cum laude.
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2018 – 2020
M.Sc. in Bioinformatics and Biocomputing
Brno University of Technology
Thesis: Bacteria classification into taxonomic categories based on properties of 16S rRNA. Graduated with honours.
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2015 – 2018
B.Sc. in Information Technology
Brno University of Technology
Thesis: Searching semantically annotated texts. Graduated with honours.
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2022
Oxford Machine Learning Summer School
Health and finance tracks, online
Recognition
- Ph.D. awarded summa cum laude, Masaryk University, 2025
- Pre-doctoral fellowship, National Institute on Aging, NIH, 2024 – 2025
- Oxford Machine Learning Summer School, health and finance tracks, 2022
- Top-five poster, ENBIK 2022
- M.Sc. and B.Sc. both graduated with honours, Brno University of Technology
Software engineering
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2023
Machine learning engineer
Melown Technologies, Brno
Reading street signs out of many low-quality images at once, inside a large-scale 3D city-model pipeline — research prototype through to production.
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2021 – 2022
Machine learning specialist
Proficio / Databy, Brno
NLP for product matching across e-commerce catalogues, and the cleaning pipelines that made the text usable.
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2020 – 2021
Software developer
Oracle NetSuite, Brno
SuiteAnalytics Connect — third-party analytics access to NetSuite data. Java, SQL, ODBC.
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2018 – 2020
Software developer
Tieto, Brno
Test infrastructure and continuous integration for a large Java system.
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2016 – 2018
Research scholar
Knowledge Technology group, Brno University of Technology
Corpora Processing Software — tooling for large annotated text corpora.
Software and data
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2025 – present
Genomic Benchmarks QC
Automated quality control for genomic machine-learning datasets. It scores the biases, duplicate sequences and train/test leakage...
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2024 – 2025
miRBench
Benchmark datasets and a Python package for miRNA target-site prediction, built to remove the frequency-class bias...
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2021 – 2023
Genomic Benchmarks
Eight curated datasets for genomic sequence classification across human, mouse and roundworm, each with a sensible...
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2022 – 2026
miRBind and miRBind2
Deep learning models that decide whether a microRNA binds a given site, trained on chimeric read...
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2022 – 2023
Attribution sequence alignment
A way to make a model say what it noticed. Attribution gives you one importance score...
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2023 – 2026
AlphaFind and AlphaFind2
Structure-similarity search across the whole of AlphaFold DB. Pretrained networks compress each structure into an embedding,...
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2023 – 2024
RBP-Tar
A searchable database of experimentally determined RNA-binding protein sites, pulled out of published CLIP experiments and...
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2024 – 2026
Senescence marker discovery and scoring
The machine learning behind the SenCat paper, written as a Snakemake workflow: transcriptomic and proteomic profiles...
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2024 – 2025
Isoform remodeling in the ageing mouse brain
The single-cell long-read pipeline behind the ageing mouse brain paper — nanopore reads through to which...
Teaching and supervision
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2024
Deep Learning for Genomics
Three-day course, University of Malta
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2023
Explainability for Deep Neural Networks
MALTAomics Summer School, University of Malta
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2021
Inside the black box: explainable deep learning for biological data
Tutorial, ECCB 2021
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2020 – 2021
Introduction to Bioinformatics
Teaching assistant, Faculty of Medicine, Masaryk University
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ongoing
The Missing Skills
Project-based tutorials on the computational skills a science degree leaves out — version control, the shell,...
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2021 – 2022
Biology Crash Course
Molecular biology from the ground up, written for computer scientists who need enough of it to...
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2025 – present
Master's thesis supervision
Max Delbrück Center, Berlin
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2023 – 2025
Master's thesis co-supervision
University of Malta
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2023 – 2024
Bachelor internships
University of Malta
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2022 – 2023
Hackathons on miRNA binding and Genomic Benchmarks
CEITEC and University of Malta
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2023
International workshop on similarity search
Masaryk University
Talks and outreach
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2026
GenBenchQC: automated quality control of genomic sequence benchmarks reveals widespread biases in deep learning datasets
EMBO | EMBL Symposium: AI and biology, EMBL Heidelberg
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2026
GenBenchQC: automated quality control of genomic sequence benchmarks reveals widespread biases in deep learning datasets
Short talk, RECOMB-Seq 2026, Thessaloniki
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2024
Digital revolution of proteins
Researchers' Night, Brno
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2024
miRBench: benchmark datasets for microRNA binding site prediction
Poster, ECCB 2024, Turku
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2024
miRBench: benchmark datasets for microRNA binding site prediction
Poster, Microsymposium on RNA Biology, Vienna
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2023
Understanding miRNA binding site prediction through deep learning models
Data Science Platform Seminars, University of Malta
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2023
Attribution-based interpretation of deep learning models
Molecular Medicine Seminars, CEITEC, Masaryk University
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2022
Computational modelling of miRNA targets
XXI. Meeting of Biochemists and Molecular Biologists, Brno
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2022
Genomic Benchmarks: a collection of datasets for genomic sequence classification
Poster, ENBIK 2022 — selected in the top five
Skills
- Python — PyTorch, TensorFlow, scikit-learn, Hugging Face, pandas, NumPy, Jupyter
- Also Java, C++, R, SQL and rather a lot of Bash
- Snakemake pipelines, Git, CI/CD, HPC
- Deep learning, explainable AI, model benchmarking, NLP, computer vision
- Genomics: sequence models, RNA-seq (bulk and single-cell), long-read sequencing, CLIP and chimeric-read protocols, protein structure