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

Positions

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
2023
Software Developer Valley Optics BV, Delft graphical user-interface development within a software team; Valley Optics is a TNO spin-off building software for optical systems
2022
Research Intern Valley Optics BV, Delft neural networks for image recognition

Publications

Summary
16 works 7 journal articles · 7 preprints · 2 theses. Full list with abstracts and BibTeX on the Publications page.
Selected

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

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 contributed talk
2025
Squirrel: Reconstructing semi-directed phylogenetic level-1 networks Mathematical and Computational Evolutionary Biology (MCEB), Granada contributed talk
See the Conferences page for the full list of talks and posters.

Teaching & service

Teaching
  • Discrete Mathematics (TW1-31) — Instructor
    2025–2026
    2024–2025
  • Transport, Routing & Scheduling (WI4062TU) — Course grader
    2025–2026
    2023–2024
  • Mathematics 1 (WBMT1050) — Guest lecturer, 2023–2024
  • Mathematics 2 — Calculus (KT1002) — Course grader, 2023–2024
  • Optimization (AM2020) — Teaching assistant
    2022–2023
    2021–2022
    2020–2021
  • Caleidoscope — Introduction to Mathematics (AM1020) — Teaching assistant
    2021–2022
    2020–2021
    2019–2020
  • Mathematical Structures (AM1010) — Course grader, 2019–2020
Student supervision
  • Distinguishing phylogenetic trees from networks — BSc thesis supervision (Jari Brits), 2026
  • Identifiability of Phylogenetic Trinets — BSc thesis supervision (Guuske Kouwenhoven), 2025
Service & leadership
  • Discrete Optimization; Operations Research Letters; Involve: a Journal of Mathematics — Reviewer, 2024–present
  • RECOMB-CG (Comparative Genomics); WADS (Algorithms & Data Structures Symposium) — Sub-reviewer, 2025–present
  • DIAM PhD Forum — Member, 2025–present
  • Delft Student Handball Association Torius — Chair, 2025–present
More detail 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)