Below you can find my publications sorted by journals, with links and toggleable abstracts.
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Discrete Applied Mathematics
[4]
A multivariate complexity analysis of the Generalized Noah's Ark Problem
Christian Komusiewicz and Jannik Schestag
Journal article
In terms of laymen Suppose each endangered species can receive different conservation measures, each with its own cost and effect on the species' chance of survival. This paper studies how to choose among those measures under a limited budget so that as much evolutionary history as possible is expected to survive, and determines which aspects of the problem make this choice easier or harder to compute. In Laiensprache (German translation) Angenommen, für jede bedrohte Art stehen verschiedene Schutzmaßnahmen zur Verfügung, die jeweils unterschiedliche Kosten verursachen und ihre Überlebenswahrscheinlichkeit unterschiedlich stark erhöhen. Diese Arbeit untersucht, wie solche Maßnahmen bei begrenztem Budget ausgewählt werden sollten, damit voraussichtlich möglichst viel Evolutionsgeschichte erhalten bleibt. Außerdem wird bestimmt, welche Eigenschaften des Problems diese Entscheidung rechnerisch leichter oder schwieriger machen.
Abstract In the Generalized Noah's Ark Problem, one is given a phylogenetic tree on a set of species \(X\) and a set of conservation projects for each species. Each project comes with a cost and raises the survival probability of the corresponding species. The aim is to select a conservation project for each species such that the total cost of the selected projects does not exceed some given threshold and the expected phylogenetic diversity is as large as possible. We study the complexity of Generalized Noah's Ark Problem and some of its special cases with respect to several parameters related to the input structure, such as the number of different costs, the number of different survival probabilities, or the number of species, \(|X|\).
@article{komusiewicz2026multivariate,
  title = {{A multivariate complexity analysis of the Generalized Noah's Ark Problem}},
  author = {Komusiewicz, Christian and Schestag, Jannik},
  journal = {Discrete Applied Mathematics},
  volume = {382},
  pages = {137--154},
  year = {2026},
  publisher = {Elsevier},
  doi = {10.1016/j.dam.2025.11.037}
}
Discrete Mathematics & Theoretical Computer Science
[3]
Destroying Bicolored \(P_3\)s by Deleting Few Edges
Niels Grüttemeier, Christian Komusiewicz, Jannik Schestag, and Frank Sommer
Journal article
In terms of laymen Consider a network whose connections are colored red or blue, and suppose we want to remove only a few connections so that no path through three vertices uses both colors. This paper shows that finding such a small set of deletions is difficult in general, but gives faster algorithms, useful preprocessing techniques, and special graph classes on which the problem can be solved efficiently. In Laiensprache (German translation) Betrachten wir ein Netzwerk, dessen Verbindungen rot oder blau gefärbt sind. Gesucht sind möglichst wenige Verbindungen, die entfernt werden müssen, sodass kein Pfad über drei Knoten mehr beide Farben verwendet. Diese Arbeit zeigt, dass das Finden einer solchen kleinen Menge im Allgemeinen schwierig ist, entwickelt aber schnellere Algorithmen und nützliche Vorverarbeitungstechniken und identifiziert spezielle Netzwerkklassen, für die sich das Problem effizient lösen lässt.
Abstract We introduce and study the Bicolored \(P_3\) Deletion problem defined as follows. The input is a graph \(G = (V, E)\) where the edge set \(E\) is partitioned into a set \(E_r\) of red edges and a set \(E_b\) of blue edges. The question is whether we can delete at most \(k\) edges such that \(G\) does not contain a bicolored \(P_3\) as an induced subgraph. Here, a bicolored \(P_3\) is a path on three vertices with one blue and one red edge. We show that Bicolored \(P_3\) Deletion is NP-hard and cannot be solved in \(2^{o(|V|+|E|)}\) time on bounded-degree graphs if the ETH is true. Then, we show that Bicolored \(P_3\) Deletion is polynomial-time solvable when \(G\) does not contain a bicolored \(K_3\), that is, a triangle with edges of both colors. We also provide a polynomial-time algorithm for the case that \(G\) contains no blue \(P_3\), red \(P_3\), blue \(K_3\), and red \(K_3\). Finally, we show that Bicolored \(P_3\) Deletion can be solved in \(\mathcal{O}(1.84^k \cdot |V | \cdot |E|)\) time and that it admits a kernel with \(\mathcal{O}(k \Delta \min(k, \Delta))\) vertices, where \(\Delta\) is the maximum degree of \(G\).
@article{gruttemeier2021destroying,
  title = {{Destroying Bicolored P3s by Deleting Few Edges}},
  author = {Gr{\"u}ttemeier, Niels and Komusiewicz, Christian and Schestag, Jannik and Sommer, Frank},
  journal = {Discrete Mathematics \& Theoretical Computer Science},
  volume = {23},
  number = {1},
  year = {2021},
  publisher = {Episciences.org},
  doi = {10.46298/dmtcs.6108}
}
Journal of Computational Biology
[2]
PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks
Niels Holtgrefe, Leo van Iersel, Ruben Meuwese, Yukihiro Murakami, and Jannik Schestag
Journal article
In terms of laymen When only some species can be protected, conservationists would like to choose those that preserve as much evolutionary history as possible. PaNDA provides algorithms and an interactive software tool for solving and visualizing this problem on complex evolutionary networks, with experiments showing that realistically large networks can be handled efficiently. In Laiensprache (German translation) Wenn nur ein Teil der Arten geschützt werden kann, möchte man diejenigen auswählen, durch deren Schutz möglichst viel Evolutionsgeschichte erhalten bleibt. PaNDA stellt Algorithmen und ein interaktives Softwarewerkzeug bereit, mit denen dieses Problem auf komplexen evolutionären Netzwerken gelöst und visualisiert werden kann. Experimente zeigen, dass sich damit auch realistisch große Netzwerke effizient bearbeiten lassen.
Abstract Phylogenetic diversity plays an important role in biodiversity, conservation, and evolutionary studies by measuring the diversity of a set of taxa based on their phylogenetic relationships. In phylogenetic trees, a subset of \(k\) taxa with maximum phylogenetic diversity can be found by a simple and efficient greedy algorithm. However, this algorithmic tractability is lost when considering phylogenetic networks, which incorporate reticulate evolutionary events such as hybridization and horizontal gene transfer. To address this challenge, we introduce PaNDA (Phylogenetic Network Diversity Algorithms), the first software package and interactive graphical user-interface for exploring, visualizing and maximizing diversity in phylogenetic networks. PaNDA includes a novel algorithm to find a subset of \(k\) taxa with maximum diversity, running in polynomial time for networks of bounded canwidth, a measure of tree-likeness of a network that grows slower than the well-known level measure. This algorithm considers the variant of phylogenetic diversity on networks in which the branch lengths of all paths from the root to the selected taxa contribute towards their diversity. We demonstrate the scalability of this algorithm on simulated networks, successfully analyzing level-15 networks with up to 200 taxa in seconds. We also provide a proof-of-concept analysis using a phylogenetic network on Xiphophorus species, illustrating how the tool can support diversity studies based on real genomic data. The software is easily installable and freely available at https://github.com/nholtgrefe/panda. Additionally, we extend the definition of phylogene- tic diversity to semi-directed phylogenetic networks, which are mixed graphs increasingly used in phylogenetic analysis to model uncertainty of the root location. We prove that finding a subset of \(k\) taxa with maximum diversity remains NP-hard on semi-directed networks, but do present a polynomial-time algorithm for networks with bounded level.
@article{holtgrefe2026panda,
  title = {{PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks}},
  author = {Holtgrefe, Niels and van Iersel, Leo and Meuwese, Ruben and Murakami, Yukihiro and Schestag, Jannik},
  year = {2026},
  journal = {Journal of Computational Biology},
  publisher={Springer},
  doi = {10.1101/2025.11.14.688467}
}
Journal of Graph Algorithms and Applications
[1]
On Critical Node Problems with Vulnerable Vertices
Jannik Schestag, Niels Grüttemeier, Christian Komusiewicz, and Frank Sommer
Journal article
In terms of laymen In some networks, particular vertices are especially important or vulnerable, and one may want to isolate them from as much of the remaining network as possible by removing only a few vertices. This paper studies two versions of that problem and determines a range of conditions under which it can be solved efficiently, as well as cases that remain computationally difficult. In Laiensprache (German translation) In manchen Netzwerken sind bestimmte Knoten besonders wichtig oder gefährdet. Dann kann das Ziel darin bestehen, diese durch das Entfernen möglichst weniger anderer Knoten von einem möglichst großen Teil des restlichen Netzwerks abzutrennen. Diese Arbeit untersucht zwei Varianten dieses Problems und bestimmt sowohl Bedingungen, unter denen es effizient gelöst werden kann, als auch Fälle, die rechnerisch schwierig bleiben.
Abstract A vertex pair in an undirected graph is called connected if the two vertices are connected by a path. In the NP-hard Critical Node Problem (CNP), the input is an undirected graph \(G\) with integers \(k\) and \(x\), and the question is whether one can transform \(G\) by deleting at most \(k\) vertices into a graph whose total number of connected vertex pairs is at most \(x\). In this work, we introduce and study two NP- hard variants of CNP where a subset of the vertices is marked as vulnerable, and we aim to obtain a graph with at most \(x\) connected vertex pairs containing at least one vulnerable vertex. In the first variant, which generalizes CNP, we may delete vulnerable and non-vulnerable vertices. In the second variant, we may only delete non-vulnerable vertices.
We perform a parameterized complexity study of both problems. For example, we show that both problems are FPT with respect to \(k + x\). Furthermore, in the case of deletable vulnerable nodes, we provide a polynomial kernel for the parameter \(vc +k\), where \(vc\) is the vertex cover number. In the case of non-deletable vulnerable nodes, we prove NP-hardness even when there is only one vulnerable node.
@article{schestag2024critical,
  title = {{On Critical Node Problems with Vulnerable Vertices}},
  author = {Schestag, Jannik and Gruettemeier, Niels and Komusiewicz, Christian and Sommer, Frank},
  journal = {Journal of Graph Algorithms and Applications},
  volume = {28},
  number = {1},
  pages = {1--26},
  year = {2024},
  doi = {10.7155/jgaa.v28i1.2922}
}