My name is Niels Holtgrefe and I am a PhD candidate at the Delft Institute of Applied Mathematics at the TU Delft in the Netherlands. I work in the Discrete Mathematics & Optimization group, advised by Dr. Leo van Iersel.
My research is focused on algorithms and the mathematical theory of phylogenetics: the study of the evolutionary history of organisms. I also work on parameterized complexity, specifically structural parameters of phylogenetic networks that govern algorithmic tractability. I develop open-source software tools and apply these methods to real biological datasets.
In the fall semester of 2024 I was a visiting researcher at ICERM, Brown University (Providence, RI, USA) as part of the research semester program on Theory, Methods, and Applications of Quantitative Phylogenomics. Previously, I obtained my MSc and BSc degrees in Applied Mathematics at TU Delft, both with cum laude distinction.
On this website, you can read about my research, view my publications and software, and see the conferences you might have seen me present or attend. There is also an overview of my teaching & service and a full CV.
Selected publications
all publications →- PhyloZoo: a unified framework for phylogenetic network analysis in Python bioRxiv:10.64898/2026.06.09.731120, 2026
- Bounds on the Sequence Length Sufficient to Reconstruct Binary Level-1 Phylogenetic Networks Under the CFN Model Annals of Combinatorics, 2026
- PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks bioRxiv:10.1101/2025.11.14.688467, 2025
- Identifiability of Phylogenetic Level-2 Networks under the Jukes-Cantor Model bioRxiv:10.1101/2025.04.18.649493, 2025
- Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments Molecular Biology and Evolution, 2025