- document
-
Huber, Katharina T. (author), van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Moulton, V.L. (author), Murakami, Yukihiro (author), Semple, Charles (author)This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network....journal article 2024
- document
-
Deen, Elise (author), van Iersel, L.J.J. (author), Janssen, Remie (author), Jones, M.E.L. (author), Murakami, Yukihiro (author), Zeh, Norbert (author)The maximum parsimony distance d<sub>MP</sub>(T<sub>1</sub>,T<sub>2</sub>) and the bounded-state maximum parsimony distance d<sub>MP</sub><sup>t</sup>(T<sub>1</sub>,T<sub>2</sub>) measure the difference between two phylogenetic trees T<sub>1</sub>,T<sub>2</sub> in terms of the maximum difference between their parsimony scores for any...journal article 2024
- document
-
Jones, M.E.L. (author), Schestag, J. (author)Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. We consider an extension of PD to phylogenetic networks. Given a phylogenetic network with weighted edges and a subset S of leaves, the all-paths phylogenetic diversity of S is the summed weight of all edges...conference paper 2023
- document
-
Giardina, Giorgia (author), Macchiarulo, V. (author), Foroughnia, Fatemeh (author), Jones, Joshua N. (author), Whitworth, Michael R.Z. (author), Voelker, Brandon (author), Milillo, Pietro (author), Penney, Camilla (author), Adams, Keith (author), Kijewski-Correa, Tracy (author)Remote reconnaissance missions are promising solutions for the assessment of earthquake-induced structural damage and cascading geological hazards. Space-borne remote sensing can complement in-field missions when safety and accessibility concerns limit post-earthquake operations on the ground. However, the implementation of remote sensing...journal article 2023
- document
-
van Iersel, L.J.J. (author), Jones, M.E.L. (author), Julien, E.A.T. (author), Murakami, Yukihiro (author)Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the network class ideal for capturing evolutionary histories that involve horizontal gene transfers. Here,...conference paper 2023
- document
- Richie, C.S. (author), Kesselheim, Aaron S. (author), Jones, David S. (author) journal article 2023
- document
-
Bravo, Úrsula (author), Cortés, Catalina (author), Lloyd, P.A. (author), Jones, Derek (author)Educational systems face increasingly complex demands, confronting teachers with multidimensional people-centred problems rarely solved by linear or standardised solutions. Nevertheless, teachers must juggle multiple variables simultaneously in their daily work. This can lead to routine and unreflective decisions that do not consider unique...journal article 2023
- document
- Richie, C.S. (author), Kesselheim, Aaron S. (author), Jones, David S. (author) journal article 2023
- document
-
Jones, Keith (author), Mulder, Femke (author), Morga, Mariantonietta (author), Wanigarathna, Nadeeshani (author)Background and aim - Improving the resilience of business organisations and critical infrastructure providers to disaster events is a major challenge facing many European organisations. Recent floods in Germany, Belgium and the Netherlands and earthquakes in Iceland, Italy, Romania and Greece have demonstrated the need for organisations to adopt...conference paper 2022
- document
-
Huber, Katharina T. (author), van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Moulton, Vincent (author), Murakami, Yukihiro (author)Recently it was shown that a certain class of phylogenetic networks, called level-2 networks, cannot be reconstructed from their associated distance matrices. In this paper, we show that they can be reconstructed from their induced shortest and longest distance matrices. That is, if two level-2 networks induce the same shortest and longest...journal article 2022
- document
-
Dwivedi, Yogesh K. (author), Hughes, Laurie (author), Cheung, Christy M.K. (author), Conboy, Kieran (author), Duan, Yanqing (author), Dubey, Rameshwar (author), Janssen, M.F.W.H.A. (author), Jones, Paul (author), Sigala, Marianna (author), Viglia, Giampaolo (author)The desk rejection of submitted articles can be a hugely frustrating and demotivating process from the perspective of the researcher, but equally, a time-consuming and vital step in the process for the Editor, tasked with selecting appropriate articles that meet the required criteria for further review and scrutiny. The feedback from journal...contribution to periodical 2022
- document
-
van Iersel, L.J.J. (author), Jones, M.E.L. (author), Weller, Mathias (author)Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called Tree Containment, arises when validating networks constructed by phylogenetic inference methods. We present the first algorithm for (rooted) Tree Containment using the treewidth t of the input...conference paper 2022
- document
-
van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Murakami, Yukihiro (author), Zeh, Norbert (author)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 of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in O((8 k) <sup>k</sup>poly (n,...journal article 2022
- document
-
Borst, Sander (author), van Iersel, L.J.J. (author), Jones, M.E.L. (author), Kelk, Steven (author)We study the problem of finding a temporal hybridization network containing at most k reticulations, for an input consisting of a set of phylogenetic trees. First, we introduce an FPT algorithm for the problem on an arbitrary set of m binary trees with n leaves each with a running time of O(5 <sup>k</sup>· n· m). We also present the concept...journal article 2022
- document
-
Eslami Mossallam, B. (author), Klein, M. (author), Smagt, Constantijn V.D. (author), Sanden, Koen V.D. (author), Jones, Stephen K. (author), Hawkins, John A. (author), Finkelstein, Ilya J. (author), Depken, S.M. (author)The S. pyogenes (Sp) Cas9 endonuclease is an important gene-editing tool. SpCas9 is directed to target sites based on complementarity to a complexed single-guide RNA (sgRNA). However, SpCas9-sgRNA also binds and cleaves genomic off-targets with only partial complementarity. To date, we lack the ability to predict cleavage and binding activity...journal article 2022
- document
-
Bulteau, Laurent (author), Jones, M.E.L. (author), Niedermeier, Rolf (author), Tantau, Till (author)In the NP-hard Longest Common Subsequence problem (LCS), given a set of strings, the task is to find a string that can be obtained from every input string using as few deletions as possible. LCS is one of the most fundamental string problems with numerous applications in various areas, having gained a lot of attention in the algorithms and...conference paper 2022
- document
-
van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Murakami, Yukihiro (author)Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional horizontal arcs. Therefore, they are closely...journal article 2022
- document
-
Mencarini, Eleonora (author), Rapp, Amon (author), Colley, Ashley (author), Daiber, Florian (author), Jones, Michael (author), Kosmalla, Felix (author), Lukosch, Stephan (author), Niforatos, E. (author), Zancanaro, Massimo (author)The contemporary digitalization of the sports experience brought new challenges for the HCI community. HCI researchers started exploring how mobile and wearable devices could support the physical, social, and environmental aspects of sports, while technological transformations like the metaverse, inbodied technologies, and AI have recently...journal article 2022
- document
-
Moody, Galan (author), Sorger, Volker J. (author), Blumenthal, Daniel J. (author), Juodawlkis, Paul W. (author), Loh, William (author), Jones, Alex E. (author), Pingault, B.J. (author), Elshaari, Ali W. (author), Zwiller, Val (author)Integrated photonics will play a key role in quantum systems as they grow from few-qubit prototypes to tens of thousands of qubits. The underlying optical quantum technologies can only be realized through the integration of these components onto quantum photonic integrated circuits (QPICs) with accompanying electronics. In the last decade,...journal article 2022
- document
-
Jones, S.A. (author), Bos, Robert (author), Lastovka, Vaclav (author), Farajzadeh, R. (author), Riyami, Mohammed (author)The efficiency of oil processes depends on the product of volumetric sweep and microscopic sweep. In oil recovery by steam injection the microscopic sweep is generally good; however, obtaining a good volumetric sweep can be challenging. This is caused by low density and viscosity of the injected steam combined with the reservoir heterogeneity...conference paper 2022