Niels Holtgrefe

PhD candidate in applied math

I am a PhD candidate at TU Delft with a background in discrete mathematics, working at the intersection of applied mathematics, theoretical computer science, and phylogenetics. My research focuses on the mathematical and algorithmic foundations of phylogenetic networks, with particular emphasis on identifiability, network combinatorics, and algorithmic principles. In parallel, I develop open-source software and user interfaces that translate theoretical results into accessible tools for biological applications.

Education

2023–present
PhD in Applied Mathematics Delft University of Technology Discrete Mathematics & Optimization group. Advisors: Leo van Iersel, Mark Jones, and Steven Kelk. Topic: inference, identifiability, and combinatorics of phylogenetic networks, and parameterized complexity.
2021–2023
MSc in Applied Mathematics Delft University of Technology Specialisation: Optimisation. Thesis: Computing the Scanwidth of Directed Acyclic Graphs.
2018–2021
BSc in Applied Mathematics Delft University of Technology Minor: Quantum Science & Quantum Information. Thesis: Maximum Coverage Problems: Theory and Application in Optimal Sensor Selection.
2012–2018
Grammar school ('gymnasium') Chr. Gymnasium Sorghvliet, The Hague

Experience

2023–present
PhD Candidate Delft Institute of Applied Mathematics, TU Delft
2024
Extended research visit ICERM, Brown University (Providence, RI, USA) semester program on Theory, Methods, and Applications of Quantitative Phylogenomics

Honours & distinctions

2023
MSc Applied Mathematics — cum laude grade 9.2/10; thesis 9.5/10
2021
BSc Applied Mathematics — cum laude grade 8.4/10; thesis 9.5/10
2018
Grammar school ('gymnasium') — summa cum laude grade 9.0/10

Publications

Summary
16 works 8 journal articles · 1 conference proceeding · 5 preprints · 2 theses. Full list with abstracts on the Publications page.
Selected

Organization

January 2026
The A in DIAM — 4th Annual PhD Forum Event Delft, the NetherlandsA day on the applications of mathematical research, for the PhD candidates and postdocs of the Delft Institute of Applied Mathematics

Selected talks

2026
PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks RECOMB, Thessaloniki, Greece contributed talk
2026
PhyloZoo: A Python Package for Analyzing and Exploring Phylogenetic Networks International Workshop on Probabilistic, Combinatorial, and Algorithmic Phylogenetics, Taipei, Taiwan contributed talk
2025
Squirrel: Reconstructing semi-directed phylogenetic level-1 networks Mathematical and Computational Evolutionary Biology (MCEB), Granada, Spain contributed talk
See the Conferences page for every event attended, spoken at, or organized.

Teaching & service

Teaching
8 courses · instructor, course grader, exercise tester, guest lecturer, teaching assistant.
Student supervision
2 MSc theses · 2 BSc theses.
Review service
5 journal reviews · 2 conference sub-reviews.
Other service
  • Confidential contact person, 2026–present · Delft Student Handball Association Torius
  • DIAM PhD Forum member, 2025–present
  • Chairman, 2025–2026 · Delft Student Handball Association Torius
Courses, supervised students, and review venues on the Teaching & Service page.

Skills & software

Programming
Python, R, Macaulay2, Matlab, Maple, LaTeX, Excel, Qt, HTML, Git, TensorFlow, Keras
Open-source software
author/maintainer of PhyloZoo, Squirrel, PaNDA, and scanwidth (see the Software page)
Languages
Dutch (native), German (native), English (fluent), French (basic), Italian (learning)