Topics
My research mostly focuses on mathematical phylogenetics, with the aim to accurately reconstruct evolutionary histories of (biological) species. My work involves graph theory, computational complexity, and algorithms for NP-hard problems.
Most code I wrote during my PhD has now been compiled in the python package PhyloX.
PhD Thesis
My PhD thesis is about rearrangement moves for phylogenetic networks can be downloaded here, with the accompanying propositions.
Articles
See also my google scholar page.
Journal Articles
1. Remie Janssen, Mark Jones, Peter L. Erdos, Leo van Iersel, and Celine Scornavacca. “Exploring the tiers of rooted phylogenetic network space using tail moves”. In: Bulletin of mathematical biology 80.8, pp. 2177–2208 (2018)
2. Yukihiro Murakami, Leo van Iersel, Remie Janssen, Mark Jones, and Vincent Moulton. “Reconstructing tree-child networks from reticulate-edge-deleted subnetworks”. In: Bulletin of mathematical biology 81.10, pp. 3823–3863 (2019)
3. Remie Janssen, Mark Jones, Steven Kelk, Georgios Stamoulis, and Taoyang Wu. “Treewidth of display graphs: Bounds, brambles and applications”. In: Journal of Graph Algorithms and Applications 23.4 (2019)
4. Remie Janssen and Jonathan Klawitter. “Rearrangement operations on unrooted phylogenetic networks”. In: Theory and Applications of Graphs 6.2 (2019)
5. Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, and Norbert Zeh. “Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation”. In: IEEE/ACM Transactions on Computational Biology and Bioinformatics 17.1, pp. 14–26 (2019)
6. Remie Janssen. “The Burning Number of Directed Graphs: Bounds and Computational Complexity”. In: Theory and Applications of Graphs 7.1, p. 8 (2020)
7. Remie Janssen and Yukihiro Murakami. “On cherry-picking and network containment”. In: Theoretical Computer Science (2020)
8. Remie Janssen. “Heading in the right direction? Using head moves to traverse phylogenetic network space”. In: Journal of Graph Algorithms and Applications, vol. 25, no. 1, pp. 263-310 (2021)
9. Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, and Norbert Zeh. “A Unifying Characterization of Tree-based Networks and Orchard Networks using Cherry Covers”. In: Advances in Applied Mathematics, vol. 129, no. 102222 (2021)
10. Elizabeth Gross, Leo van Iersel, Remie Janssen, Mark Jones, Colby Long, and Yukihiro Murakami. “Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes”. In: Journal of Mathematical Biology, vol. 83, no. 3, pp. 1-24 (2021)
11. Remie Janssen and Pengyu Liu. “Comparing the topology of phylogenetic network generators”. In: Journal of Bioinformatics and Computational Biology, vol. 19, no. 6 (2021)
12. Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, and Norbert Zeh. “A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees”. In: Algorithmica vol. 84, no. 4, pp. 917-960 (2022)
13. Remie Janssen and Leonie van Steijn. “Connectedness of Unit Distance Subgraphs Induced by Closed Convex Sets”. In: Theory and Applications of Graphs, vol. 9, issue. 1, article 2 (2022)
14. Katharina T. Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, and Yukihiro Murakami. “Level-2 networks from shortest and longest distances”. In: Discrete Applied Mathematics, vol. 9, pp. 138-165 (2022)
Conference Papers
1. Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, and Norbert Zeh. “Polynomial-Time Algorithms for Phylogenetic Inference Problems”. In: International Conference on Algorithms for Computational Biology. Springer. 2018, LNBI 10849: 37–49
2. Remie Janssen, Mark Jones, and Yukihiro Murakami. “Combining Networks Using Cherry Picking Sequences”. In: International Conference on Algorithms for Computational Biology. Springer. 2020, pp. 77–92
3. Remie Janssen and Yukihiro Murakami. “Linear Time Algorithm for Tree-Child Network Containment”. In: International Conference on Algorithms for Computational Biology. Springer. 2020, pp. 93–107
Preprints
1. Katharina T. Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami, and Charles Semple. “Orienting undirected phylogenetic networks”. In: arXiv preprint arXiv:1906.07430 (2019)
2. Mark Jones, Philippe Gambette, Leo van Iersel, Remie Janssen, Steven Kelk, Fabio Pardi, and Celine Scornavacca. “Cutting an alignment with Ockham’s razor”. In: arXiv preprint arXiv:1910.11041 (2019)
3. Leo van Iersel, Remie Janssen, Mark Jones, and Yukihiro Murakami. “Orchard Networks are Trees with Additional Horizontal Arcs”. In: arXiv preprint arXiv:2110.11065 (2021)