20 citations · 40 across the 19 of their papers we have counts for
20 papers
Metropolis-Hastings Sampling of Phylogenetic Networks: Correcting for Symmetries
Leo van Iersel, Remie Janssen, Mark Jones +2
In phylogenetics, Metropolis-Hastings methods are commonly used to sample phylogenetic trees or networks, for example from Bayesian posteriors. These methods generally use transiti…
A Near-Linear Kernel for Two-Parsimony Distance
Elise Deen, Leo van Iersel, Remie Janssen +3
The maximum parsimony distance and the bounded-state maximum parsimony distance measure the difference between two phylogene…
Orchard Networks are Trees with Additional Horizontal Arcs
Leo van Iersel, Remie Janssen, Mark Jones +1
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits,…
Comparing the topology of phylogenetic network generators
Remie Janssen, Pengyu Liu
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. Th…
Connectedness of Unit Distance Subgraphs Induced by Closed Convex Sets
Remie Janssen, Leonie van Steijn
The unit distance graph is the infinite graph whose nodes are points in , with an edge between two points if the Euclidean distance between these…
Level- networks from shortest and longest distances
Katharina T. Huber, Leo van Iersel, Remie Janssen +3
Recently it was shown that a certain class of phylogenetic networks, called level- networks, cannot be reconstructed from their associated distance matrices. In this paper, we s…
Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
Elizabeth Gross, Leo van Iersel, Remie Janssen +3
Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such a…
A Unifying Characterization of Tree-based Networks and Orchard Networks using Cherry Covers
Leo van Iersel, Remie Janssen, Mark Jones +2
Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which…
The Burning Number of Directed Graphs: Bounds and Computational Complexity
Remie Janssen
The burning number of a graph was recently introduced by Bonato et al. Although they mention that the burning number generalises naturally to directed graphs, no further research o…
Combining Networks using Cherry Picking Sequences
Remie Janssen, Mark Jones, Yukihiro Murakami
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks…
Cutting an alignment with Ockham's razor
Mark Jones, Philippe Gambette, Leo van Iersel +4
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task i…
A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees
Leo van Iersel, Remie Janssen, Mark Jones +2
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number…
Orienting undirected phylogenetic networks
Katharina T. Huber, Leo van Iersel, Remie Janssen +4
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undir…
Rearrangement operations on unrooted phylogenetic networks
Remie Janssen, Jonathan Klawitter
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic t…
On Cherry-picking and Network Containment
Remie Janssen, Yukihiro Murakami
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks…
Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks
Yukihiro Murakami, Leo van Iersel, Remie Janssen +2
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level- networks. In a tree-c…
Heading in the right direction? Using head moves to traverse phylogenetic network space
Remie Janssen
Head moves are a type of rearrangement moves for phylogenetic networks. They have mostly been studied as part of more encompassing types of moves, such as rSPR moves. Here, we stud…
Treewidth of display graphs: bounds, brambles and applications
Remie Janssen, Mark Jones, Steven Kelk +2
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or…
Polynomial-Time Algorithms for Phylogenetic Inference Problems involving duplication and reticulation
Leo van Iersel, Remie Janssen, Mark Jones +2
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Min…
Exploring the tiers of rooted phylogenetic network space using tail moves
Remie Janssen, Mark Jones, Péter L. Erdős +2
Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rNNI (rooted Nearest Neighbour Interchange) and rSPR (rooted Subtree Prune and…