@misc{brits2026full-identifiability,
  author = {Brits, Jari and Holtgrefe, Niels and van Iersel, Leo and Martin, Samuel},
  title = {{On Tree-Network Distinguishability and Full Identifiability of Phylogenetic Networks}},
  archivePrefix = {arXiv},
  eprint = {2607.12919},
  year = {2026}
}

@article{martin2026algebraic-invariants,
  author = {Martin, Samuel and Holtgrefe, Niels and Moulton, Vincent and Legget, Richard M},
  title = {{Algebraic Invariants for Inferring 4-leaf Semi-Directed Phylogenetic Networks}},
  journal = {Systematic Biology},
  volume = {75},
  number = {4},
  pages = {657-672},
  doi = {10.1093/sysbio/syaf071},
  year = {2026}
}

@misc{holtgrefe2026phylozoo,
  author = {Holtgrefe, Niels},
  title = {{PhyloZoo: a unified framework for phylogenetic network analysis in Python}},
  archivePrefix = {bioRxiv},
  eprint = {10.64898/2026.06.09.731120},
  year = {2026}
}

@misc{holtgrefe2026budgeted-pd,
  author = {Holtgrefe, Niels and Schestag, Jannik},
  title = {{Tractable Maximization of Budgeted Phylogenetic Diversity on Networks Utilizing Node Scanwidth}},
  archivePrefix = {arXiv},
  eprint = {2605.23319},
  year = {2026}
}

@article{frohn2026sequence-bounds,
  author = {Frohn, Martin and Holtgrefe, Niels and van Iersel, Leo and Jones, Mark and Kelk, Steven},
  title = {{Bounds on the Sequence Length Sufficient to Reconstruct Binary Level-1 Phylogenetic Networks Under the CFN Model}},
  journal = {Annals of Combinatorics},
  doi = {10.1007/s00026-026-00830-0},
  year = {2026}
}

@article{holtgrefe2026scanwidth-exact,
  author = {Holtgrefe, Niels and van Iersel, Leo and Jones, Mark},
  title = {{Exact and Heuristic Computation of the Scanwidth of Directed Acyclic Graphs}},
  journal = {Journal of Computer and System Sciences},
  volume = {160},
  pages = {103802},
  doi = {10.1016/j.jcss.2026.103802},
  year = {2026}
}

@misc{holtgrefe2026kernelization-pd,
  author = {Holtgrefe, Niels and Schestag, Jannik and Zeh, Norbert},
  title = {{Limits of Kernelization and Parametrization for Phylogenetic Diversity with Dependencies}},
  archivePrefix = {arXiv},
  eprint = {2602.12959},
  year = {2026}
}

@article{holtgrefe2026characterizing-sd,
  author = {Holtgrefe, Niels and Huber, Katharina T and van Iersel, Leo and Jones, Mark and Moulton, Vincent},
  title = {{Characterizing semi-directed phylogenetic networks and their multi-rootable variants}},
  journal = {Theory in Biosciences},
  volume = {145},
  number = {1},
  pages = {4},
  doi = {10.1007/s12064-025-00453-8},
  year = {2026}
}

@misc{holtgrefe2025panda,
  author = {Holtgrefe, Niels and van Iersel, Leo and Meuwese, Ruben and Murakami, Yukihiro and Schestag, Jannik},
  title = {{PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks}},
  archivePrefix = {bioRxiv},
  eprint = {10.1101/2025.11.14.688467},
  year = {2025}
}

@article{holtgrefe2025distinguishing-level2,
  author = {Holtgrefe, Niels and Allman, Elizabeth S and Baños, Hector and van Iersel, Leo and Moulton, Vincent and Rhodes, John A and Wicke, Kristina},
  title = {{Distinguishing Phylogenetic Level-2 Networks with Quartets and Inter-Taxon Quartet Distances}},
  journal = {Bulletin of Mathematical Biology},
  volume = {87},
  number = {12},
  pages = {168},
  doi = {10.1007/s11538-025-01549-4},
  year = {2025}
}

@misc{eckstein2025envision-sar,
  author = {Eckstein, Paul and McSweeney, Adam and Sikaneta, Ishuwa and Holtgrefe, Niels and Bannach, Max and Belgacem, Ines and Raynor, Holly and Geiger, Bernhard and Grieger, Björn and Mahieux, Arnaud and Gallardo i Peres, Gerard and Straume-Lindner, Anne Grete and Lefort, Jayne and Voirin, Thomas},
  title = {{Optimising the Synthetic Aperture Radar Repeat Imaging Strategy for the EnVision Mission}},
  howpublished = {Extended abstract, EPSC–DPS Joint Meeting 2025, Helsinki, Finland},
  doi = {10.5194/epsc-dps2025-1637},
  year = {2025}
}

@misc{englander2025identifiability-level2,
  author = {Englander, Aviva K and Frohn, Martin and Gross, Elizabeth and Holtgrefe, Niels and van Iersel, Leo and Jones, Mark and Sullivant, Seth},
  title = {{Identifiability of Phylogenetic Level-2 Networks under the Jukes-Cantor Model}},
  archivePrefix = {bioRxiv},
  eprint = {10.1101/2025.04.18.649493},
  year = {2025}
}

@article{frohn2025few-quarnets,
  author = {Frohn, Martin and Holtgrefe, Niels and van Iersel, Leo and Jones, Mark and Kelk, Steven},
  title = {{Reconstructing semi-directed level-1 networks using few quarnets}},
  journal = {Journal of Computer and System Sciences},
  volume = {152},
  pages = {103655},
  doi = {10.1016/j.jcss.2025.103655},
  year = {2025}
}

@article{holtgrefe2025squirrel,
  author = {Holtgrefe, Niels and Huber, Katharina T and van Iersel, Leo and Jones, Mark and Martin, Samuel and Moulton, Vincent},
  title = {{Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments}},
  journal = {Molecular Biology and Evolution},
  volume = {42},
  number = {4},
  pages = {msaf067},
  doi = {10.1093/molbev/msaf067},
  year = {2025}
}

@misc{frohn2024invariants-level1,
  author = {Frohn, Martin and Holtgrefe, Niels and van Iersel, Leo and Jones, Mark and Kelk, Steven},
  title = {{Invariants for level-1 phylogenetic networks under the random walk 4-state Markov model}},
  archivePrefix = {arXiv},
  eprint = {2407.11720},
  year = {2024}
}

@masterthesis{holtgrefe2023scanwidth-thesis,
  title={Computing the Scanwidth of Directed Acyclic Graphs},
  author={Niels Holtgrefe},
  year={2023},
  address={Delft, The Netherlands},
  note={Available at \url{http://resolver.tudelft.nl/uuid:9c82fd2a-5841-4aac-8e40-d4d22542cdf5}},
  school={Delft University of Technology},
  type= {MSc thesis}
}

@bachelorthesis{holtgrefe2021max-coverage-thesis,
  title={Maximum Coverage Problems: Theory and Application in Optimal Sensor Selection},
  author={Niels Holtgrefe},
  year={2021},
  address={Delft, The Netherlands},
  note={Available at \url{https://resolver.tudelft.nl/uuid:9d222076-f3e6-4a36-9325-40de3dde0e9d}},
  school={Delft University of Technology},
  type= {BSc thesis}
}