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Articles by van Iersel
Quantitative Biology > Populations and Evolution
Phylogenetic networks generalize phylogenetic trees as models of evolutionary history, allowing lineages to merge as well as to diverge. For many types of genetic data the root position of such a network cannot be recovered, so that only a semi-directed network can be inferred: a mixed graph in which only the edges entering a reticulation vertex are directed.
Computer Science > Data Structures and Algorithms
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Computer Science > Data Structures and Algorithms
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
[2507.18772] Characterizing (multi-)semi-directed phylogenetic networks
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
Characterizing gut microbial dysbiosis and exploring the effect of prebiotic fiber supplementation in patients with COPD - European Journal of Nutrition
Abstract Chronic Obstructive Pulmonary Disease (COPD) is associated with poor dietary quality that may lead to gut microbiota imbalances. A healthy gut microbiome contributes to metabolic health and immune function through production of metabolites like short-chain fatty acids. Prebiotic fibers positively influence microbiota by promoting the production of beneficial metabolites.
[2409.08440] A Simple 4-Approximation Algorithm for Maximum Agreement Forests on Multiple Unrooted Binary Trees
arXiv:2409.08440 (cs) View PDF HTML (experimental) Comments: Subjects: Data Structures and Algorithms (cs.DS) Cite as: arXiv:2409.08440 [cs.DS] (or arXiv:2409.08440v1 [cs.DS] for this version) https://doi.org/10.48550/arXiv.2409.08440 Submission history From: Jordan Dempsey [ view email] [v1] Fri, 13 Sep 2024 00:13:25 UTC (14 KB) Bibliographic Tools Bibliographic Explorer Toggle Bibliographic Explorer () Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are...
[2409.06034] Reconstructing semi-directed level-1 networks using few quarnets
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
Varying Light Intensities Affect Lettuce Growth and Physiology in Controlled Indoor Environments
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[2408.12997] When are quarnets sufficient to reconstruct semi-directed phylogenetic networks?
[Submitted on 23 Aug 2024 ( v1 ), last revised 10 Jan 2025 (this version, v2)] Title:When are quarnets sufficient to reconstruct semi-directed phylogenetic networks? View a PDF of the paper titled When are quarnets sufficient to reconstruct semi-directed phylogenetic networks?, by Katharina T. Huber and 3 other authors View PDF HTML (experimental) Abstract:Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa.
[2408.10769] A Wild Sheep Chase Through an Orchard
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
[2407.11720] Invariants for level-1 phylogenetic networks under the random walk 4-state Markov model
[2405.01091] Phylogenetic Network Diversity Parameterized by Reticulation Number and Beyond
arXiv:2405.01091 (cs) [Submitted on 2 May 2024 (v1), last revised 19 Nov 2025 (this version, v2)] View PDF HTML (experimental) Subjects: Computational Complexity (cs.CC) Cite as: arXiv:2405.01091 [cs.CC] (or arXiv:2405.01091v2 [cs.CC] for this version) https://doi.org/10.48550/arXiv.2405.01091 Submission history From: Jannik Theodor Schestag [ view email] [v1] Thu, 2 May 2024 08:43:47 UTC (236 KB) [v2] Wed, 19 Nov 2025 12:08:51 UTC (243 KB) Bibliographic Tools Bibliographic Explorer Toggle...
[2403.12734] Exact and Heuristic Computation of the Scanwidth of Directed Acyclic Graphs
[Submitted on 19 Mar 2024 (v1), last revised 17 Feb 2026 (this version, v2)] View PDF Comments: Subjects: Data Structures and Algorithms (cs.DS); Discrete Mathematics (cs.DM); Combinatorics (math.CO) Cite as: arXiv:2403.12734 [cs.DS] (or arXiv:2403.12734v2 [cs.DS] for this version) https://doi.org/10.48550/arXiv.2403.12734
The Energy Requirement for Supplemental Greenhouse Lighting Can Be Reduced by Considering ‘Excess’ Light from the Previous Day
1. Introduction Daily light integral (DLI), the amount of photosynthetically active radiation delivered over a 24-h period, varies daily depending on the weather [1,2]. This inconsistency of sunlight in greenhouses can result in insufficient DLI for crop growth on certain days and excessive DLI on others. Multiple studies strongly recommend maintaining a consistent DLI throughout the growing season to promote optimal crop growth [3,4].
Federalising Tendencies of the Principle of Sincere Cooperation in the Area of Common Foreign and Security Policy
Mota, C. and van Iersel, D. (2021) Federalising Tendencies of the Principle of Sincere Cooperation in the Area of Common Foreign and Security Policy. Warwick Undergraduate Law Journal, 1, pp. 19-64. Full text not currently available from Enlighten. Publisher's URL: https://warwick.ac.uk/fac/soc/law/aboutus/wulj/article_2.pdf Item Type: Articles Status: Published Refereed: Yes Glasgow Author(s) Enlighten ID: Ramaglia Mota, Carlos Gabriel Authors: Mota, C., and van Iersel, D.
BridgeDb
Published November 5, 2023 | Version release_3.1.0 Software Open Creators Awasthi, Manas Basaric, Helena Conklin, Bruce R. Evelo, Chris T. Gao, Jianjiong Gray, Alasdair Hanspers, Kristina Isaac, Ho Kelder, Thomas Kerber, Randy Kutmon, Martina Mélius, Jonathan Nunes, Nuno Pico, Alexander R. Riutta, Anders Slenter, Denise Soiland-Reyes, Stian Van Iersel, Martijn P. Willighagen, Egon L. Minor change, big impact: this is the UniProtKB release, where the full name of the S data sources is changed.
Constructing phylogenetic networks via cherry picking and machine learning
Algorithms for Molecular Biology, Sep 2023 Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers of phylogenetic trees or are limited to severely restricted classes of networks.
The validity of ultrasound and shear wave elastography to assess the quality of the rotator cuff
European Radiology, Aug 2023 US with shear wave elastography (SWE) could reduce the burden and costs of the diagnostic process for patients with rotator cuff disorders. The aim of this study is to investigate the validity of US and SWE in preoperative assessment of fatty infiltration (FI) and muscle atrophy of the supraspinatus (SSP) and infraspinatus (ISP) muscles. Patients with a rotator cuff disorder and a recent shoulder CT or MRI scan were eligible to participate.
Forecasting Infections with Spatio-Temporal Graph Neural Networks: the Dutch SARS-CoV-2 spreading case of study
Cosimo Della Santina1, 2* Maxime Croft1, 3 Senna van Iersel3 1Delft University of Technology, Netherlands 2Robotics Institute, Delft University of Technology, Netherlands 3National Institute for Public Health and the Environment (Netherlands), Netherlands The final, formatted version of the article will be published soon.
[2207.00574] Embedding phylogenetic trees in networks of low treewidth
arXiv:2207.00574 (q-bio) [Submitted on 1 Jul 2022 (v1), last revised 19 Sep 2023 (this version, v5)] Download PDF Subjects: Populations and Evolution (q-bio.PE); Discrete Mathematics (cs.DM) Cite as: arXiv:2207.00574 [q-bio.PE] (or arXiv:2207.00574v5 [q-bio.PE] for this version) https://doi.org/10.48550/arXiv.2207.00574 Submission history From: Mark Jones Dr [ view email] [v1] Fri, 1 Jul 2022 17:51:57 UTC (315 KB) [v2] Thu, 7 Jul 2022 09:22:30 UTC (314 KB) [v3] Mon, 26 Sep 2022 14:51:29 UTC...
[2305.03106] Making Orchard by Adding Leaves
[Submitted on 4 May 2023] Title:Making Orchard by Adding Leaves Download a PDF of the paper titled Making Orchard by Adding Leaves, by Leo van Iersel and 3 other authors Download PDF Abstract: 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.
Frontiers | Cadmium Exposure is Associated With Increased Transcript Abundance of Multiple Heavy Metal Associated Transporter Genes in Roots of Hemp (Cannabis sativa L.)
Amanda O. Marabesi1*, Timothy W. Coolong1*, Savithri U. Nambeesan1, Marc W. Van Iersel1 and Jason T. Lessl1 1University of Georgia, United States The final, formatted version of the article will be published soon. Receive an email when it is updated Industrial hemp (Cannabis sativa L.) has demonstrated promise for phytoremediation due to an extensive root system, large biomass, and ability to survive under relatively high levels of heavy metals.
Image-based phenotyping to estimate anthocyanin concentrations in lettuce
Changhyeon Kim1* and Marc W. Van Iersel2 1Department of Horticulture and Crop Science, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, United States 2Department of Horticulture, College of Agricultural and Environmental Sciences, University of Georgia, United States The final, formatted version of the article will be published soon. Receive an email when it is updated Anthocyanins provide blue, red, and purple color to fruits, vegetables, and flowers.
On the Nature of Explanations Offered by Network Science: A Perspective From and for Practicing Neuroscientists
Abstract Network neuroscience represents the brain as a collection of regions and inter‐regional connections. Given its ability to formalize systems‐level models, network neuroscience has generated unique explanations of neural function and behavior. The mechanistic status of these explanations and how they can contribute to and fit within the field of neuroscience as a whole has received careful treatment from philosophers.
Expert consensus document: Advances in the evaluation of anorectal function
Abstract Faecal incontinence and evacuation disorders are common, impair quality of life and incur substantial economic costs worldwide. As symptoms alone are poor predictors of underlying pathophysiology and aetiology, diagnostic tests of anorectal function could facilitate patient management in those cases that are refractory to conservative therapies.
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