Y. Murakami

Research

I am interested in applications of combinatorics and algorithms in mathematical phylogenetics.

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Preprints

  1. How Many Cherry-Picking Sequences Are Needed to Reduce All Subtrees of a Phylogenetic Tree?

    B. Kollmann, Y. Murakami, T. Suzuki. arXiv:2608.19916 (2026).

  2. Metropolis-Hastings Sampling of Phylogenetic Networks: Correcting for Symmetries

    L. van Iersel, R. Janssen, M. Jones, Y. Murakami, C. Reichling. arXiv:2608.12430 (2026).

  3. Proximity Measures for Classes of Phylogenetic Networks

    L. van Iersel, M. Jones, E. Julien, Y. Long, Y. Murakami. arXiv:2607.11325 (2026).

  4. List 3-Coloring C4-Free Graphs of Diameter-2 in Polynomial Time

    Y. Murakami. arXiv:2606.30282 (2026).

  5. Note on the Maximum Number of Trees Displayed by a Tree-Child Network

    Y. Murakami, C. Semple. arXiv:2606.14464 (2026).

  6. PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks

    N. Holtgrefe, L. van Iersel, R. Meuwese, Y. Murakami, J. Schestag. bioRxiv (2025). (Accepted at RECOMB 2026)

  7. A Wild Sheep Chase Through an Orchard

    J. Dempsey, L. van Iersel, M. Jones, Y. Murakami, N. Zeh. arXiv:2408.10769 (2024).

  8. Orienting Undirected Phylogenetic Networks to Tree-Child Network

    S. Maeda, Y. Kaneko, H. Muramatsu, Y. Murakami, M. Hayamizu. arXiv:2305.10162 (2023). (Poster presentation at WABI 2023)

Journal & Conference Publications

  1. Burning Graph Powers and Branching Trees

    J. Jansson, S. Kulamarva, Y. Murakami, N. Verhulst. MFCS 2026, LIPIcs 386, 18:1–18:13. (arXiv version)

  2. Metrics for Classes of Semi-Binary Phylogenetic Networks Using μ-Representations

    C. Reichling, L. van Iersel, Y. Murakami. Advances in Applied Mathematics 172, 102953 (2026).

  3. Fence Decompositions and Cherry Covers in Non-Binary Phylogenetic Networks

    J. C. Pons, P. Vives López, Y. Murakami, L. van Iersel. IEEE Transactions on Computational Biology and Bioinformatics 22(5):2173–2183 (2025).

  4. The Burning Number Conjecture is True for Trees without Degree-2 Vertices

    Y. Murakami. Graphs and Combinatorics 40(4):82 (2024).

  5. Resolving Unresolved Resolved and Unresolved Triplets Consistency Problems

    D. J. Harvey, J. Jansson, M. Marciniak, Y. Murakami. IWOCA 2024, LNCS 14764, 193–205.

  6. Orienting Undirected Phylogenetic Networks

    K. T. Huber, L. van Iersel, R. Janssen, M. Jones, V. Moulton, Y. Murakami, C. Semple. Journal of Computer and System Sciences 140:103480 (2024).

  7. A Near-Linear Kernel for Bounded-State Parsimony Distance

    E. Deen, L. van Iersel, R. Janssen, M. Jones, Y. Murakami, N. Zeh. Journal of Computer and System Sciences 140:103477 (2024).

  8. Making a Network Orchard by Adding Leaves

    L. van Iersel, M. Jones, E. Julien, Y. Murakami. WABI 2023, LIPIcs 273, 7:1–7:20. (arXiv version)

  9. Polynomial Invariants for Cactuses

    L. van Iersel, V. Moulton, Y. Murakami. Information Processing Letters 182:106394 (2023).

  10. Orchard Networks are Trees with Additional Horizontal Arcs

    L. van Iersel, R. Janssen, M. Jones, Y. Murakami. Bulletin of Mathematical Biology 84(8):76 (2022).

  11. A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees

    L. van Iersel, R. Janssen, M. Jones, Y. Murakami, N. Zeh. Algorithmica 84(4):917–960 (2022).

  12. Level-2 Networks from Shortest and Longest Distances

    K. T. Huber, L. van Iersel, R. Janssen, M. Jones, V. Moulton, Y. Murakami. Discrete Applied Mathematics 306:138–165 (2022).

  13. Distinguishing Level-1 Phylogenetic Networks on the Basis of Data Generated by Markov Processes

    E. Gross, L. van Iersel, R. Janssen, M. Jones, C. Long, Y. Murakami. Journal of Mathematical Biology 83(3):32 (2021).

  14. A Unifying Characterization of Tree-Based Networks and Orchard Networks Using Cherry Covers

    L. van Iersel, R. Janssen, M. Jones, Y. Murakami, N. Zeh. Advances in Applied Mathematics 129:102222 (2021).

  15. On Cherry-Picking and Network Containment

    R. Janssen, Y. Murakami. Theoretical Computer Science 856:121–150 (2021).

  16. Reconstructibility of Unrooted Level-k Phylogenetic Networks from Distances

    L. van Iersel, V. Moulton, Y. Murakami. Advances in Applied Mathematics 120:102075 (2020).

  17. Recognizing and Realizing Cactus Metrics

    M. Hayamizu, K. T. Huber, V. Moulton, Y. Murakami. Information Processing Letters 157:105916 (2020).

  18. Linear Time Algorithm for Tree-Child Network Containment

    R. Janssen, Y. Murakami. AlCoB 2020, LNCS 12099, 93–107.

  19. Combining Networks Using Cherry Picking Sequences

    R. Janssen, M. Jones, Y. Murakami. AlCoB 2020, LNCS 12099, 77–92.

  20. Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation

    L. van Iersel, R. Janssen, M. Jones, Y. Murakami, N. Zeh. IEEE/ACM TCBB 17(1):14–26 (2020).

  21. Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks

    Y. Murakami, L. van Iersel, R. Janssen, M. Jones, V. Moulton. Bulletin of Mathematical Biology 81:3823–3863 (2019).

Doctoral thesis

On Phylogenetic Encodings and Orchard Networks

Y. Murakami. Delft University of Technology (2021).

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