Items where Author is "Moulton, Vincent"

Lafond, Manuel and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2025) Path partitions of phylogenetic networks. Theoretical Computer Science, 1024. ISSN 0304-3975

Huber, Katharina T., van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Scholz, Guillaume E. (2025) Is this network proper forest-based? Information Processing Letters, 187. ISSN 0020-0190

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Scholz, Guillaume E. (2024) Shared ancestry graphs and symbolic arboreal maps. SIAM Journal on Discrete Mathematics, 38 (4). pp. 2553-2577. ISSN 0895-4801

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Scholz, Guillaume (2024) Compatible split systems on a multiset. Electronic Journal of Combinatorics. ISSN 1077-8926 (In Press)

Huber, Katharina, Linz, Simone, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Semple, Charles (2024) Phylogenetic trees defined by at most three characters. Electronic Journal of Combinatorics. ISSN 1077-8926 (In Press)

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wicke, Kristina (2024) Phylogenetic diversity indices from an affine and projective viewpoint. Bulletin of Mathematical Biology, 86 (8). ISSN 0092-8240

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Owen, Megan, Spillner, Andreas and St. John, Katherine (2024) The space of equidistant phylogenetic cactuses. Annals of Combinatorics, 28. pp. 1-32. ISSN 0218-0006

Huber, Katharina T., van Iersel, Leo, Janssen, Remie, Jones, Mark, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Murakami, Yuki and Semple, Charles (2024) Orienting undirected phylogenetic networks. Journal of Computer and System Sciences, 140. ISSN 0022-0000

Holland, Barbara, Huber, Katharina T. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2024) A distance-based model for convergent evolution. Journal of Mathematical Biology, 88. ISSN 0303-6812

Bryant, David, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Tupper, Paul F. (2023) Diversities and the generalized circumradius. Discrete and Computational Geometry, 70 (4). 1862–1883. ISSN 0179-5376

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2023) Computing consensus networks for collections of 1-nested phylogenetic networks. Journal of Graph Algorithms and Applications, 27 (7). pp. 541-563. ISSN 1526-1719

van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Murakami, Yukihiro (2023) Polynomial invariants for cactuses. Information Processing Letters, 182. ISSN 0020-0190

Hellmuth, Marc, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Scholz, Guillaume E. and Stadler, Peter F. (2023) Injective split systems. Graphs and Combinatorics, 39 (4). ISSN 0911-0119

Seemann, Carsten R., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Stadler, Peter F. and Hellmuth, Marc (2023) Planar median graphs and cubesquare-graphs. Discrete Applied Mathematics, 331. pp. 38-58. ISSN 0166-218X

Duncan, Anthony, Barry, Kerrie, Daum, Chris, Eloe-Fadrosh, Emiley, Roux, Simon, Schmidt, Katrin, Tringe, Susannah G., Valentin, Klaus U., Varghese, Neha, Salamov, Asaf, Grigoriev, Igor V., Leggett, Richard M., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 (2023) Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms. Data in Brief, 47. ISSN 2352-3409

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2023) Planar rooted phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20 (2). pp. 1289-1297. ISSN 1545-5963

Winder, Johanna C. ORCID: https://orcid.org/0000-0002-7509-772X, Boulton, William, Salamov, Asaf, Eggers, Sarah Lena, Metfies, Katja, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 (2023) Genetic and structural diversity of prokaryotic ice-binding proteins from the central Arctic Ocean. Genes, 14 (2). ISSN 2073-4425

Francis, Andrew, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2023) Encoding and ordering X-cactuses. Advances in Applied Mathematics, 142. ISSN 0196-8858

Alzahrani, Salma, Applegate, Christopher, Swarbreck, David, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Folkes, Leighton and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2022) Degradome assisted plant MicroRNA prediction under alternative annotation criteria. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19 (6). pp. 3374-3383. ISSN 1545-5963

van Iersel, Leo, Kole, Sjors, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Nipius, Leonie (2022) An algorithm for reconstructing level-2 phylogenetic networks from trinets. Information Processing Letters, 178. ISSN 0020-0190

Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, Boulton, William, Balmonte, John Paul, Barry, Kevin, Bertilsson, Stefan, Bowman, Jeff, Buck, Moritz, Bratbak, Gunnar, Chamberlain, Emelia J., Cunliffe, Michael, Creamean, Jessie, Ebenhöh, Oliver, Eggers, Sarah Lena, Fong, Allison A., Gardner, Jessie, Gradinger, Rolf, Granskog, Mats A., Havermans, Charlotte, Hill, Thomas, Hoppe, Clara J. M., Korte, Kerstin, Larsen, Aud, Müller, Oliver, Nicolaus, Anja, Oldenburg, Ellen, Popa, Ovidiu, Rogge, Swantje, Schäfer, Hendrik, Shoemaker, Katyanne, Snoeijs-Leijonmalm, Pauline, Torstensson, Anders, Valentin, Klaus, Vader, Anna, Barry, Kerrie, Chen, I.-M. A., Clum, Alicia, Copeland, Alex, Daum, Chris, Eloe-Fadrosh, Emiley, Foster, Brian, Foster, Bryce, Grigoriev, Igor V., Huntemann, Marcel, Ivanova, Natalia, Kuo, Alan, Kyrpides, Nikos C., Mukherjee, Supratim, Palaniappan, Krishnaveni, Reddy, T. B. K., Salamov, Asaf, Roux, Simon, Varghese, Neha, Woyke, Tanja, Wu, Dongying, Leggett, Richard M., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Metfies, Katja (2022) Multiomics in the central Arctic Ocean for benchmarking biodiversity change. PLoS Biology, 20 (10). ISSN 1544-9173

Huber, K. T., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 and Scholz, G. E. (2022) Forest-based networks. Bulletin of Mathematical Biology, 84. ISSN 0092-8240

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2022) Posets and spaces of k-noncrossing RNA structures. SIAM Journal on Discrete Mathematics, 36 (3). pp. 1586-1611. ISSN 0895-4801

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2022) Order distances and split systems. Order, 39 (2). 291–308. ISSN 0167-8094

Duncan, Anthony, Barry, Kerrie, Daum, Chris, Eloe-Fadrosh, Emiley, Roux, Simon, Schmidt, Katrin, Tringe, Susannah G., Valentin, Klaus U., Varghese, Neha, Salamov, Asaf, Grigoriev, Igor V., Leggett, Richard M., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 (2022) Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. Microbiome, 10. ISSN 2049-2618

Huber, Katharina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Scholz, Guillaume (2022) Overlaid species forests. Discrete Applied Mathematics, 309. pp. 110-122. ISSN 0166-218X

Huber, Katharina, van Iersel, Leo, Janssen, Remie, Jones, Mark, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Murakami, Yuki (2022) Level-2 networks from shortest and longest distances. Discrete Applied Mathematics, 306. pp. 138-165. ISSN 0166-218X

Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, Hodgkinson, Kat, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Duncan, Anthony, Oosterhout, Cock van ORCID: https://orcid.org/0000-0002-5653-738X and Pichler, Monica (2022) Structure and Evolution of Diatom Nuclear Genes and Genomes. In: The Molecular Life of Diatoms. Springer, pp. 111-145. ISBN 9783030924980

Huber, Katharina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2021) Optimal realizations and the block decomposition of a finite metric space. Discrete Applied Mathematics, 302. pp. 103-113. ISSN 0166-218X

Martin, Kara, Schmidt, Katrin, Toseland, Andrew, Boulton, Chris A., Barry, Kerrie, Beszteri, Bánk, Brussaard, Corina P. D., Clum, Alicia, Daum, Chris G., Eloe-Fadrosh, Emiley, Fong, Allison, Foster, Brian, Foster, Bryce, Ginzburg, Michael, Huntemann, Marcel, Ivanova, Natalia N., Kyrpides, Nikos C., Lindquist, Erika, Mukherjee, Supratim, Palaniappan, Krishnaveni, Reddy, T. B. K., Rizkallah, Mariam R., Roux, Simon, Timmermans, Klaas, Tringe, Susannah G., Van De Poll, Willem H., Varghese, Neha, Valentin, Klaus U., Lenton, Timothy M., Grigoriev, Igor V., Leggett, Richard M., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 (2021) The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. Nature Communications, 12 (1). ISSN 2041-1723

Huber, Katharina T., Linz, Simone and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2021) The rigid hybrid number for two phylogenetic trees. Journal of Mathematical Biology, 82 (5). ISSN 0303-6812

van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Murakami, Yuki (2020) Reconstructibility of unrooted level-k phylogenetic networks from distances. Advances in Applied Mathematics, 120. ISSN 0196-8858

Luca, Bogdan, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Ellis, Christopher, Connell, Shea P., Brewer, Daniel ORCID: https://orcid.org/0000-0003-4753-9794 and Cooper, Colin ORCID: https://orcid.org/0000-0003-2013-8042 (2020) Convergence of prognostic gene signatures suggests underlying mechanisms of human prostate cancer progression. Genes, 11 (7). ISSN 2073-4425

Thody, Joshua, Folkes, Leighton and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2020) NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs. Nucleic Acids Research, 48 (12). 6481–6490. ISSN 0305-1048

Delabre, Matteo, El-Mabrouk, Nadia, Huber, Katharina, Lafond, Manuel, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Noutahi, Emmanuel and Sautie Castellanos, Miguel (2020) Evolution through segmental duplications and losses: A super-reconciliation approach. Algorithms for Molecular Biology, 15 (1). ISSN 1748-7188

Luca, Bogdan, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Ellis, Christopher, Edwards, Dylan R. ORCID: https://orcid.org/0000-0002-3292-2064, Campbell, Colin, Cooper, Rosalin A., Clark, Jeremy, Brewer, Daniel S. ORCID: https://orcid.org/0000-0003-4753-9794 and Cooper, Colin S. ORCID: https://orcid.org/0000-0003-2013-8042 (2020) A novel stratification framework for predicting outcome in patients with prostate cancer. British Journal of Cancer, 122 (10). 1467–1476. ISSN 0007-0920

Hayamizu, Momoko, Huber, Katharina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Murakami, Yukihiro (2020) Recognizing and realizing cactus metrics. Information Processing Letters, 157. ISSN 0020-0190

Thody, Joshua, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Mohorianu, Irina (2020) PAREameters: a tool for computational inference of plant miRNA–mRNA targeting rules using small RNA and degradome sequencing data. Nucleic Acids Research, 48 (5). 2258–2270. ISSN 0305-1048

Araujo-Granda, Pablo, Gras, Anna, Ginovart, Marta and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2020) INDISIM-Denitrification, an individual-based model for study the denitrification process. Journal of Industrial Microbiology and Biotechnology, 47. pp. 1-20. ISSN 1367-5435

Hellmuth, Marc, Huber, Katharina and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2019) Reconciling event-labeled gene trees with MUL-trees and species networks. Journal of Mathematical Biology, 79 (5). pp. 1885-1925. ISSN 0303-6812

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Scholz, Guillaume E. (2019) Three-way symbolic tree-maps and ultrametrics. Journal of Classification, 36 (3). pp. 513-540. ISSN 0176-4268

Murakami, Yukihiro, van Iersel, Leo, Janssen, Remie, Jones, Mark and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2019) Reconstructing tree-child networks from reticulate-edge-deleted subnetworks. Bulletin of Mathematical Biology, 81 (10). 3823–3863. ISSN 0092-8240

Scholz, Guillaume E., Popescu, Andrei-Alin, Taylor, Martin I. ORCID: https://orcid.org/0000-0002-3858-0712, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Huber, Katharina T. (2019) OSF-Builder: A new tool for constructing and representing evolutionary histories involving introgression. Systematic Biology, 68 (5). 717–729. ISSN 1063-5157

Huber, Katharina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2019) Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks. Journal of Classification, 36 (2). pp. 200-231. ISSN 0176-4268

Huber, Katharina T, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Sagot, Marie-France and Sinaimeri, Blerina (2019) Exploring and visualising spaces of tree reconciliations. Systematic Biology, 68 (4). pp. 607-618. ISSN 1063-5157

Huber, Katharina, Koolen, Jack H. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2019) The polytopal structure of the tight-span of a totally split-decomposable metric. Discrete Mathematics, 342 (3). pp. 868-878. ISSN 0012-365X

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2019) Phylogenetic flexibility via Hall-type inequalities and submodularity. Journal of Mathematical Biology, 81 (2). 598–617. ISSN 0303-6812

Lafond, Manuel, El-Mabrouk, Nadia, Huber, Katharina T. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2019) The complexity of comparing multiply-labelled trees by extending phylogenetic-tree metrics. Theoretical Computer Science, 760. pp. 15-34. ISSN 0304-3975

Luca, Bogdan-Alexandru, Brewer, Daniel S. ORCID: https://orcid.org/0000-0003-4753-9794, Edwards, Dylan R. ORCID: https://orcid.org/0000-0002-3292-2064, Edward, Sandra, Whitaker, Hayley C., Merson, Sue, Denis, Nening, Cooper, Rosalin A., Hazell, Steven, Warren, Anne Y., Eeles, Rosalind, Lynch, Andy G., Ross-Adams, Helen, Lamb, Alastair D., Neal, David E., Sethia, Krishna, Mills, Robert D, Ball, Richard Y., Curley, Helen, Clark, Jeremy, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Cooper, Colin S. ORCID: https://orcid.org/0000-0003-2013-8042 and The CancerMap Group (2018) DESNT: a poor prognosis category of human prostate cancer. European Urology Focus, 4 (6). pp. 842-850. ISSN 2405-4569

Stocks, Matthew B., Mohorianu, Irina, Beckers, Matthew, Paicu, Claudia, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Thody, Joshua, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2018) The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs. Bioinformatics, 34 (19). 3382–3384. ISSN 1367-4803

Thody, Joshua, Folkes, Leighton, Medina-Calzada, Zahara, Xu, Ping, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2018) PAREsnip2: A tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules. Nucleic Acids Research, 46 (17). 8730–8739. ISSN 0305-1048

Delabre, Matteo, El-Mabrouk, Nadia, Huber, Katharina, Lafond, Manuel, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Noutahi, Emmanuel and Sautie Castellanos, Miguel (2018) Reconstructing the History of Syntenies Through Super-Reconciliation. In: Comparative Genomics. Lecture Notes in Computer Science, 11183 . Springer, pp. 179-195. ISBN 978-3-030-00833-8

Bordewich, Magnus, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Semple, Charles (2018) Recovering normal networks from shortest inter-taxa distance information. Journal of Mathematical Biology, 77 (3). 571–594. ISSN 0303-6812

Grunewald, Stefan, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2018) Combinatorial properties of triplet covers for binary trees. Advances in Applied Mathematics, 99. pp. 59-82. ISSN 0196-8858

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Sagot, Marie-France and Sinaimeri, Blerina (2018) Geometric medians in reconciliation spaces of phylogenetic trees. Information Processing Letters, 136. pp. 96-101. ISSN 0020-0190

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Semple, Charles and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2018) Quarnet inference rules for level-1 networks. Bulletin of Mathematical Biology, 80 (8). 2137–2153. ISSN 0092-8240

van Iersel, Leo and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2018) Leaf-reconstructibility of phylogenetic networks. SIAM Journal on Discrete Mathematics, 32 (3). 2047–2066. ISSN 0895-4801

Francis, Andrew and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2018) Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution. Journal of Theoretical Biology, 446. pp. 160-167. ISSN 0022-5193

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2018) UPGMA and the normalized equidistant minimum evolution problem. Theoretical Computer Science, 721. pp. 1-15. ISSN 0304-3975

Francis, Andrew, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2018) Bounds for phylogenetic network space metrics. Journal of Mathematical Biology, 76 (5). 1229–1248. ISSN 0303-6812

Bastkowski, Sarah, Mapleson, Daniel, Spillner, Andreas, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Balvočiūtė, Monika and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2018) SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. Bioinformatics, 34 (6). 1056–1057. ISSN 1367-4803

Francis, Andrew, Huber, Katharina and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2018) Tree-based unrooted phylogenetic networks. Bulletin of Mathematical Biology, 80 (2). 404–416. ISSN 0092-8240

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2017) Minimum triplet covers of binary phylogenetic X-trees. Journal of Mathematical Biology, 75 (6-7). 1827–1840. ISSN 0303-6812

Paicu, Claudia, Mohorianu, Irina-Ioana, Stocks, Matthew, Xu, Ping, Coince, Aurore, Billmeier, Martina, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 (2017) miRCat2: Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. Bioinformatics, 33 (16). 2446–2454. ISSN 1367-4803

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Oldman, James and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2017) A cubic-time algorithm for computing the trinet distance between level-1 networks. Information Processing Letters, 123. 36–41. ISSN 0020-0190

Beckers, Matthew, Mohorianu, Irina-Ioana, Stocks, Matthew, Applegate, Christopher, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2017) Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench. RNA, 23 (6). pp. 823-835. ISSN 1355-8382

Van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, de Swart, Eveline and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2017) Binets: fundamental building blocks for phylogenetic networks. Bulletin of Mathematical Biology, 79 (5). 1135–1154. ISSN 0092-8240

Mohorianu, Irina, Stocks, Matthew Benedict, Applegate, Christopher Steven, Folkes, Leighton and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2017) The UEA small RNA workbench:A suite of computational tools for small RNA analysis. In: MicroRNA Detection and Target Identification. Methods in Molecular Biology . Springer, pp. 193-224. ISBN 978-1-4939-6864-0

Collins, David H., Mohorianu, Irina, Beckers, Matthew, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Bourke, Andrew F. G. ORCID: https://orcid.org/0000-0001-5891-8816 (2017) MicroRNAs associated with caste determination and differentiation in a primitively eusocial insect. Scientific Reports, 7. ISSN 2045-2322

Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, Otillar, Robert P., Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J., Allen, Andrew E., Dupont, Christopher L., Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Barry, Kerrie W., Falciatore, Angela, Ferrante, Maria I., Fortunato, Antonio E., Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G., Kroth, Peter G., Leese, Florian, Lindquist, Erika A., Lyon, Barbara R., Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A., Uhlig, Christiane, Valas, Ruben E., Valentin, Klaus U., Worden, Alexandra Z., Armbrust, E. Virginia, Clark, Matthew D., Bowler, Chris, Green, Beverley R., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X and Grigoriev, Igor V. (2017) Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus. Nature, 541. 536–540. ISSN 0028-0836

Huber, Katharina, van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Scornavacca, Celine and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2017) Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. Algorithmica, 77 (1). pp. 173-200. ISSN 0178-4617

Huber, Katharina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Steel, Mike and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) Folding and unfolding phylogenetic trees and networks. Journal of Mathematical Biology, 73 (6). 1761–1780. ISSN 0303-6812

Kelk, Steven, Fischer, Mareike, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) Reduction rules for the maximum parsimony distance on phylogenetic trees. Theoretical Computer Science, 646. pp. 1-15. ISSN 0304-3975

Huber, Katharina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) Transforming phylogenetic networks: Moving beyond tree space. Journal of Theoretical Biology, 404. pp. 30-39. ISSN 0022-5193

Araujo-Granda, Pablo, Ginovart, Marta, Gras, Anna and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2016) INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium. Journal of Theoretical Biology, 403. 45–58. ISSN 0022-5193

Dress, A, Huber, Katharina, Koolen, Jack, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2016) Characterizing block graphs in terms of their vertex-induced partitions. Australasian Journal of Combinatorics, 66 (1). pp. 1-9. ISSN 1034-4942

Oldman, James, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, van Iersel, Leo and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2016) TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. Molecular Biology and Evolution, 33 (8). pp. 2151-2162. ISSN 0737-4038

Bastkowski, Sarah, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) The minimum evolution problem is hard:A link between tree inference and graph clustering problems. Bioinformatics, 32 (4). pp. 518-522. ISSN 1367-4803

Huber, Katharina T., Linz, Simone, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. Journal of Mathematical Biology, 72 (3). pp. 699-725. ISSN 0303-6812

Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, Daines, Stuart, Geider, Richard, Collins, Sinead, Metoviev, Metovi, Millar, Andrew J, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Lenton, Timothy (2016) Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes. Global Change Biology, 22 (1). pp. 61-75. ISSN 1354-1013

Herrmann, Sven, Koolen, Jack H., Lesser, Alice, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) Optimal realisations of two-dimensional, totally split-decomposable metrics. Discrete Mathematics, 338 (8). 1289–1299. ISSN 0012-365X

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) A parsimony-based metric for phylogenetic trees. Advances in Applied Mathematics, 66. 22–45. ISSN 0196-8858

Bang, Sejeong, Dubickas, Arturas, Koolen, Jack and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2015) There are only finitely many distance-regular graphs of fixed valency greater than two. Advances in Mathematics, 269. pp. 1-55. ISSN 0001-8708

Bastkowski, Sarah, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) Neighborhoods of trees in circular orderings. Bulletin of Mathematical Biology, 77 (1). pp. 46-70. ISSN 0092-8240

Huber, Vincent T., van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) How much information is needed to infer reticulate evolutionary histories? Systematic Biology, 64 (1). pp. 102-111. ISSN 1063-5157

Herrmann, Sven and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2014) Computing the blocks of a quasi-median graph. Discrete Applied Mathematics, 179. pp. 129-138. ISSN 0166-218X

Toseland, Andrew, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2014) Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation. BMC Genomics, 15. ISSN 1471-2164

Lopez-Gomollon, Sara, Beckers, Matthew, Rathjen, Tina, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Maumus, Florian, Mohorianu, Irina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 (2014) Global discovery and characterization of small non-coding RNAs in marine microalgae. BMC Genomics, 15 (1). ISSN 1471-2164

Huber, K. T., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435, Semple, C. and Wu, T. ORCID: https://orcid.org/0000-0002-2663-2001 (2014) Representing partitions on trees. SIAM Journal on Discrete Mathematics, 28 (3). pp. 1152-1172. ISSN 0895-4801

Van Iersel, Leo and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2014) Trinets encode tree-child and level-2 phylogenetic networks. Journal of Mathematical Biology, 68 (7). pp. 1707-1729. ISSN 0303-6812

Volkmann, Logan, Martyn, Iain, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Mooers, Arne O. (2014) Prioritizing populations for conservation using phylogenetic networks. PLoS One, 9 (2). ISSN 1932-6203

Bastkowski, Sarah, Spillner, Andreas and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2014) Fishing for minimum evolution trees with Neighbor-Nets. Information Processing Letters, 114 (1-2). pp. 13-18. ISSN 0020-0190

Balvočiūtė, Monika, Spillner, Andreas and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2014) FlatNJ: A novel network-based approach to visualize evolutionary and biogeographical relationships. Systematic Biology, 63 (3). pp. 383-396. ISSN 1076-836X

Herrmann, Sven, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2013) Searching for realizations of finite metric spaces in tight spans. Discrete Optimization, 10 (4). pp. 310-319. ISSN 1572-5286

Woolfenden, H.C., Gates, A.J. ORCID: https://orcid.org/0000-0002-4594-5038, Bocking, C., Blyth, M.G., Richardson, D.J. ORCID: https://orcid.org/0000-0002-6847-1832 and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2013) Modeling the effect of copper availability on bacterial denitrification. MicrobiologyOpen, 2 (5). pp. 756-765. ISSN 2045-8827

Dress, A., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 and Spillner, A. (2013) Obtaining splits from cut sets of tight spans. Discrete Applied Mathematics, 161 (10-11). pp. 1409-1420. ISSN 0166-218X

Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2013) Encoding and constructing 1-nested phylogenetic networks with trinets. Algorithmica, 66 (3). pp. 714-738. ISSN 0178-4617

Mohorianu, Irina-Ioana, Stocks, Matthew Benedict, Wood, John, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2013) CoLIde: A bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data. RNA Biology, 10 (7). pp. 1221-1230. ISSN 1547-6286

Czabarka, E, Erdős, P L, Johnson, V and Moulton, V ORCID: https://orcid.org/0000-0001-9371-6435 (2013) Generating functions for multi-labeled trees. Discrete Applied Mathematics, 161 (1-2). pp. 107-117. ISSN 0166-218X

Woodhams, Michael, Steane, Dorothy A., Jones, Rebecca C., Nicolle, Dean, Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 and Holland, Barbara R. (2013) Novel distances for Dollo data. Systematic Biology, 62 (1). pp. 62-77. ISSN 1063-5157

Hellmuth, Marc, Hernandez-Rosales, Maribel, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Stadler, Peter F. and Wieseke, Nicolas (2013) Orthology relations, symbolic ultrametrics and cographs. Journal of Mathematical Biology, 66 (1-2). pp. 399-420.

Mapleson, Daniel, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2013) MirPlex:a tool for identifying miRNAs in high-throughput sRNA datasets without a genome. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 320 (1). pp. 47-56. ISSN 1552-5015

Grünewald, Stefan, Spillner, Andreas, Bastkowski, Sarah, Bögershausen, Anja and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2013) SuperQ:computing supernetworks from quartets. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (1). pp. 151-60. ISSN 1557-9964

Toseland, A., Daines, S. J., Clark, J. R., Kirkham, Amy, Strauss, J., Uhlig, C., Lenton, T. M., Valentin, K., Pearson, G. A., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 and Mock, T. ORCID: https://orcid.org/0000-0001-9604-0362 (2013) The impact of temperature on marine phytoplankton resource allocation and metabolism. Nature Climate Change, 3 (11). pp. 979-984. ISSN 1758-678X

Lopez-Gomollon, Sara, Mohorianu, Irina, Szittya, Gyorgy, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2012) Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta, 236 (6). pp. 1875-1887. ISSN 0032-0935

Martyn, Iain, Kuhn, Tyler S., Mooers, Arne O., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2012) Computing evolutionary distinctiveness indices in large scale analysis. Algorithms for Molecular Biology, 7 (1). ISSN 1748-7188

Rhodes, Jeremy D., Lott, Martin C., Russell, Sarah L. ORCID: https://orcid.org/0000-0001-5615-3418, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Sanderson, Julie, Wormstone, I. Michael ORCID: https://orcid.org/0000-0002-6423-7766 and Broadway, David C. (2012) Activation of the innate immune response and interferon signalling in myotonic dystrophy type 1 and type 2 cataracts. Human Molecular Genetics, 21 (4). pp. 852-862. ISSN 1460-2083

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, A, Storandt, S and Suchecki, Radoslaw (2012) Computing a consensus of multilabeled trees. In: Meeting on Algorithm Engineering & Experiments (ALENEX12), 2012-01-16 - 2012-01-16.

Folkes, Leighton, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Woolfenden, Hugh C., Stocks, Matthew B., Szittya, Gyorgy, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Research, 40 (13). ISSN 0305-1048

Gruenewald, Stefan, Koolen, Jack H., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2012) The size of 3-compatible, weakly compatible split systems. Journal of Applied Mathematics and Computing, 40 (1-2). pp. 249-259.

Hernandez-Rosales, M, Hellmuth, M, Wieseke, N, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Stadler, PF (2012) From event-labeled gene trees to species trees. In: UNSPECIFIED.

Herrmann, Sven, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2012) Recognizing treelike k-dissimilarities. Journal of Classification, 29 (3). pp. 321-340.

Herrmann, Sven and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) The split decomposition of a k-dissimilarity map. Advances in Applied Mathematics, 49 (1). pp. 39-56. ISSN 0196-8858

Herrmann, Sven and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) Trees, tight-spans and point configurations. Discrete Mathematics, 312 (16). pp. 2506-2521. ISSN 1872-681X

Huber, KT and Moulton, V (2012) Encoding and constructing 1-nested phylogenetic networks with trinets. Algorithmica. (In Press)

Kim, Jan, Camargo-Rodriguez, Anyela, Devoto, Alessandra, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Turner, John (2012) Computational modeling of the regulatory network organizing the wound response in Arabidopsis thaliana. Artificial Life, 18 (4). pp. 445-460. ISSN 1530-9185

Koolen, Jack H., Lesser, Alice, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2012) Injective optimal realizations of finite metric spaces. Discrete Mathematics, 312 (10). pp. 1602-1610. ISSN 1872-681X

Mohorianu, Irina, Lopez-Gomollon, Sara, Schwach, Frank, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) FiRePat-finding regulatory patterns between sRNAs and genes. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 2 (3). pp. 273-284.

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Huber, Katharina T. (2012) Network analyses for exploring evolutionary relationships. In: The Phylogenetic Handbook 2nd edition. UNSPECIFIED.

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2012) Optimal algorithms for computing edge weights in planar split networks. Journal of Applied Mathematics and Computing, 39 (1-2). pp. 1-13. ISSN 1598-5865

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2012) The 'Butterfly effect' in Cayley graphs with applications to genomics. Journal of Mathematical Biology, 65 (6-7). pp. 1267-1284. ISSN 0303-6812

Sorefan, Karim, Pais, Helio, Hall, Adam E, Kozomara, Ana, Griffiths-Jones, Sam, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2012) Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence, 3 (1).

Spillner, Andreas, Nguyen, Binh and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) Constructing and drawing regular planar split networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9 (2). pp. 395-407. ISSN 1545-5963

Stocks, Matthew B., Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Mapleson, Daniel, Woolfenden, Hugh C., Mohorianu, Irina, Folkes, Leighton, Schwach, Frank, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics, 28 (15). pp. 2059-2061. ISSN 1367-4803

Dress, A. W. M., Huber, K. T., Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2011) Blocks and cut vertices of the Buneman graph. SIAM Journal on Discrete Mathematics, 25 (4). pp. 1902-1919.

Nicolas, Francisco Esteban, Pais, Helio, Schwach, Frank, Lindow, Morten, Kauppinen, Sakari, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2011) mRNA expression profiling reveals conserved and non-conserved miR-140 targets. RNA Biology, 8 (4). pp. 607-615. ISSN 1547-6286

Huber, Katharina T., Spillner, Andreas, Suchecki, Radoslaw and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2011) Metrics on multi-labelled trees: interrelationships and diameter bounds. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (4). pp. 1029-1040. ISSN 1545-5963

Mohorianu, I-I, Schwach, F, Jing, R, Lopez-Gomollon, S, Moxon, S ORCID: https://orcid.org/0000-0003-4644-1816, Szittya, G, Sorefan, K, Moulton, V ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, T ORCID: https://orcid.org/0000-0003-1492-5429 (2011) Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. The Plant Journal, 67 (2). pp. 232-246. ISSN 1365-313X

Dress, A., Kåhrström, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2011) A ‘non-additive’ characterization of $${\wp}$$ -adic norms. Annals of Combinatorics, 15 (1). pp. 37-50. ISSN 0218-0006

Pais, Helio, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2011) Small RNA Discovery and Characterisation in Eukaryotes Using High-Throughput Approaches. In: RNA Infrastructure and Networks. Advances in Experimental Medicine and Biology, 722 . Springer, pp. 239-254. ISBN 978-1-4939-4254-1

Thuillard, Marc and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2011) Identifying and reconstructing lateral transfers from distance matrices by combing the minimum contradiction method and neighbor-net. Journal of Bioinformatics and Computational Biology, 9 (4). pp. 453-470. ISSN 0219-7200

Dress, Andreas, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Steel, Mike and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2010) Species, clusters and the ‘Tree of life’: A graph-theoretic perspective. Journal of Theoretical Biology, 265 (4). pp. 535-542.

Szittya, Gyorgy, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Pantaleo, Vitantonio, Toth, Gabor, Rusholme Pilcher, Rachel L., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Burgyan, Jozsef and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2010) Structural and functional analysis of viral siRNAs. PLoS Pathogens, 6 (4). ISSN 1553-7374

Nguyen, Binh, Spillner, Andreas, Emerson, Brent C. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2010) Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity. Algorithms for Molecular Biology, 5. ISSN 1748-7188

MacLean, Daniel, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Studholme, David J. (2010) Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics, 11. ISSN 1471-2105

Pais, Helio, Nicolas, Francisco Esteban, Soond, Surinder M., Swingler, Tracey E., Clark, Ian M., Chantry, Andrew, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2010) Analyzing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level. RNA, 16 (3). pp. 489-494. ISSN 1355-8382

Dress, Andreas W. M., Huber, Katharina T., Koolen, Jacobus, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2010) An algorithm for computing cutpoints in finite metric spaces. Journal of Classification, 27 (2). pp. 158-172.

Martin, Darren P., Lemey, Philippe, Lott, Martin, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Posada, David and Lefeuvre, Pierre (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26 (19). pp. 2462-2463. ISSN 1367-4803

Nicolas, Francisco Esteban, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, de Haro, Juan P., Calo, Silvia, Grigoriev, Igor V., Torres-Martinez, Santiago, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Ruiz-Vazquez, Rosa M. and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2010) Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Research, 38 (16). pp. 5535-5541. ISSN 0305-1048

Pais, H, Moxon, S ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, T ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, V ORCID: https://orcid.org/0000-0001-9371-6435 (2010) Small RNA Discovery and Characterisation in Eukaryotes Using High-Throughput Approaches. In: Non-coding RNA networks. Landes Bioscience. ISBN 978-1-4614-0331-9

Pantaleo, Vitantonio, Szittya, György, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Miozzi, Laura, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Burgyan, Jozsef (2010) Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis. The Plant Journal, 62 (6). pp. 960-976. ISSN 1365-313X

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2009) Phylogenetic diversity and the maximum coverage problem. Applied Mathematics Letters, 22 (10). pp. 1496-1499.

Lott, Martin, Spillner, Andreas, Huber, Katharina T., Petri, Anna, Oxelman, Bengt and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2009) Inferring polyploid phylogenies from multiply-labeled gene trees. BMC Evolutionary Biology, 9. ISSN 1471-2148

Dress, Andreas W. M., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2009) Barriers in metric spaces. Applied Mathematics Letters, 22 (8). pp. 1150-1153.

Gruenewald, S, Moulton, V ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, A (2009) Consistency of the QNet algorithm for generating planar split graphs from weighted quartets. Discrete Applied Mathematics, 157 (10). pp. 2325-2334.

Rathjen, Tina, Pais, Helio, Sweetman, Dylan, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Munsterberg, Andrea ORCID: https://orcid.org/0000-0002-4577-4240 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2009) High throughput sequencing of microRNAs in chicken somites. FEBS Letters, 583 (9). pp. 1422-1426. ISSN 1873-3468

Lemey, Philippe, Lott, Martin, Martin, Darren P. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2009) Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics, 10. ISSN 1471-2105

Grünewald, Stefan, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Semple, Charles and Spillner, Andreas (2009) Characterizing weak compatibility in terms of weighted quartets. Advances in Applied Mathematics, 42 (3). pp. 329-341. ISSN 0196-8858

Dress, Andreas W. M., Huber, Katharina T., Koolen, Jacobus and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2009) A graph-theoretical invariant of topological spaces. Applied Mathematics Letters, 22 (2). pp. 159-162.

Bang, S., Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2009) There are only finitely many regular near polygons and geodetic distance-regular graphs with fixed valency. Journal fur die reine und angewandte Mathematik, 635. pp. 213-235.

Bordewich, Magnus, Gascuel, Olivier, Huber, Katharina T. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2009) Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6 (1). pp. 110-117. ISSN 1545-5963

Grünewald, Stefan and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2009) Maximum parsimony for tree mixtures. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6 (1). pp. 97-102. ISSN 1545-5963

Koolen, Jack, Lesser, Alice and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2009) Optimal realizations of generic 5-point metrics. European Journal of Combinatorics, 30 (5). pp. 1164-1171. ISSN 0195-6698

Leggett, Richard M., Grandison, Scott, Morris, Richard J., Kelemen, Gabriella and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2009) Statistical analysis of the growth and morphology of the filamentous microbe Streptomyces coelicolor. In: Statistical Tools for Challenges in Bioinformatics, 2009-07-07 - 2009-07-09.

Lott, Martin, Spillner, Andreas, Huber, Katharina T. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2009) PADRE: A Package for Analyzing and Displaying Reticulate Evolution. Bioinformatics, 25 (9). pp. 1199-1200. ISSN 1367-4803

Schwach, Frank, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2009) Deciphering the diversity of small RNAs in plants: the long and short of it. Briefings in Functional Genomics and Proteomics, 8 (6). pp. 472-481. ISSN 1473-9550

Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2009) Refining phylogenetic trees given additional data: An algorithm based on parsimony. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6 (1). pp. 118-125. ISSN 1545-5963

Szittya, György, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Santos, Dulce M., Jing, Runchan, Fevereiro, Manuel P. S., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics, 9. ISSN 1471-2164

Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Jing, Runchan, Szittya, Gyorgy, Schwach, Frank, Rusholme Pilcher, Rachel L., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Research, 18 (10). pp. 1602-1609. ISSN 1088-9051

Nicolas Molina, Francisco Esteban, Pais, Helio, Schwach, Frank, Lindow, Morten, Kauppinen, Sakari, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2008) Experimental identification of microRNA-140 targets by silencing and over-expressing miR-140. RNA, 14. pp. 2513-2520. ISSN 1469-9001

Gill, Jonna, Linusson, Svante, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2008) A regular decomposition of the edge-product space of phylogenetic trees. Advances in Applied Mathematics, 41 (2). pp. 158-176. ISSN 0196-8858

Holland, Barbara R., Benthin, Steffi, Lockhart, Peter J., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Huber, Katharina T. (2008) Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evolutionary Biology, 8. ISSN 1471-2148

Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Kim, Jan T. (2008) A scoring matrix approach to detecting miRNA target sites. Algorithms for Molecular Biology, 3 (3). ISSN 1748-7188

Choe, Y., Koolen, J., Huber, K. T., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 and Won, Y. (2008) Counting vertices and cubes in median graphs associated to circular split systems. European Journal of Combinatorics, 29 (2). pp. 443-456.

Dress, Andreas W. M., Huber, Katharina T., Koolen, Jacobus and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2008) Cut points in metric spaces. Applied Mathematics Letters, 21 (6). pp. 545-548.

Dress, Andreas W. M., Huber, Katharina T., Koolen, Jacobus and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2008) Compatible decompositions and block realizations of finite metrics. European Journal of Combinatorics, 29 (7). pp. 1617-1633.

Dress, Andreas W. M., Huber, Katharina T., Koolen, Jacobus and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2008) Block realizations of finite metrics and the tight-span construction I: The embedding theorem. Applied Mathematics Letters (2). pp. 1306-1309.

Grünewald, Stefan, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Semple, Charles (2008) Encoding phylogenetic trees in terms of weighted quartets. Journal of Mathematical Biology, 56 (4). pp. 465-477. ISSN 0303-6812

Huber, Katharina T., Koolen, Jacobus, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2008) Characterizing cell-decomposable metrics. Electronic Journal of Combinatorics, 15 (1). ISSN 1077-8926

Huber, Katharina T., Lott, Martin, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2008) The complexity of deriving multi-labeled trees from bipartitions. Journal of Computational Biology, 15 (6). pp. 639-651. ISSN 1557-8666

Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Schwach, Frank, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, MacLean, Dan, Studholme, David J. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics, 24 (19). pp. 2252-2253. ISSN 1367-4803

Spillner, Andreas, Nguyen, Binh T. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2008) Computing phylogenetic diversity for split systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5 (2). pp. 235-244. ISSN 1545-5963

Wu, Qiong, James, Steve A., Roberts, Ian N., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Huber, Katharina T (2008) Exploring contradictory phylogenetic relationships in yeasts. FEMS Yeast Research, 8 (4). pp. 641-650. ISSN 1567-1364

Bryant, David, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2007) Consistency of the Neighbor-Net algorithm. Algorithms for Molecular Biology, 2. ISSN 1748-7188

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Semple, Charles and Steel, Mike (2007) Optimizing phylogenetic diversity under constraints. Journal of Theoretical Biology, 246 (1). pp. 186-194. ISSN 0022-5193

Bang, S., Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2007) Two theorems concerning the Bannai-Ito Conjecture. European Journal of Combinatorics, 28 (7). pp. 2026-2052. ISSN 0195-6698

Brysting, Anne K., Oxelman, Bengt, Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Brochmann, Christian (2007) Untangling complex histories of genome mergings in high polyploids. Systematic Biology, 56 (3). pp. 467-476. ISSN 1063-5157

Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2007) Some uses of the Farris Transform in mathematics and phylogenetics - A review. Annals of Combinatorics, 11 (1). pp. 1-37. ISSN 0218-0006

Dress, Andreas W. M., Huber, Katharina T., Koolen, Jack H. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2007) An algorithm for computing virtual cut points in finite metric spaces. In: Combinatorial Optimization and Applications. Lecture Notes in Computer Sciences . Springer. ISBN 978-3-540-73555-7

Dress, Andreas W. M., Huber, Katharina T., Koolen, Jacobus and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2007) An algorithm for computing virtual cut points in finite metric spaces. In: Combinatorial Optimization and Applications. Lecture Notes in Computing Science, 4616 . Springer Berlin / Heidelberg, pp. 4-10.

Freyhult, Eva, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Clote, Peter (2007) Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics, 23 (16). pp. 2054-2062. ISSN 1367-4803

Freyhult, Eva, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Clote, Peter (2007) RNAbor: a web server for RNA structural neighbors. Nucleic Acids Research, 35 (suppl 2). W305-W309. ISSN 0305-1048

Grünewald, Stefan, Forslund, Kristoffer, Dress, Andreas and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2007) QNet: An agglomerative method for the construction of phylogenetic networks from weighted quarters. Molecular Biology and Evolution, 24 (2). pp. 532-538. ISSN 0737-4038

Holland, B., Conner, Glenn, Huber, Katharina T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2007) Imputing supertrees and supernetworks from quartets. Systematic Biology, 56 (1). pp. 57-67. ISSN 1063-5157

Koolen, Jack, Lesser, Alice and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2007) Concerning the relationship between realizations and tight spans of finite metrics. Discrete and Computational Geometry, 38 (3). pp. 605-614. ISSN 0179-5376

Kutalik, Z., Tucker, W. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2007) S-system parameter estimation for noisy metabolic profiles using Newton-flow analysis. IET Systems Biology, 1 (3). pp. 174-180. ISSN 1751-8849

Rusholme Pilcher, Rachel, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Pakseresht, Nima, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Manning, Kenneth, Seymour, Graham and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2007) Identification of novel short RNAs in tomato (Solanum lycopersicum). Planta, 226 (3). pp. 709-717. ISSN 0032-0935

Tucker, Warwick, Kutalik, Zoltán and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2007) Estimating parameters for generalized mass action models using constraint propagation. Mathematical Biosciences, 208 (2). pp. 607-620. ISSN 0025-5564

Holland, Barbara R., Jermiin, Lars S. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2006) Improved consensus network techniques for genome-scale phylogeny. Molecular Biology and Evolution, 23 (5). pp. 848-855. ISSN 0737-4038

Huber, K.T., Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2006) On the structure of the tight-span of a totally split-decomposable metric. European Journal of Combinatorics, 27 (3). pp. 461-479. ISSN 0195-6698

Dress, Andreas, Huber, Katharina T., Lesser, Alice and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2006) Hereditarily optimal realizations of consistent metrics. Annals of Combinatorics, 10 (1). pp. 63-67. ISSN 0218-0006

Freyhult, Eva, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Ardell, David H. (2006) Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos. Nucleic Acids Research, 34 (3). pp. 905-916. ISSN 0305-1048

Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2006) Phylogenetic networks from multi-labelled trees. Journal of Mathematical Biology, 52 (5). pp. 613-632. ISSN 0303-6812

Huber, Katharina T., Oxelman, Bengt, Lott, Martin and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2006) Reconstructing the evolutionary history of polyploids from multilabeled trees. Molecular Biology and Evolution, 23 (9). pp. 1784-1791. ISSN 0737-4038

Huber, K. T., Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2005) The tight span of an antipodal metric space: Part 1 - Combinatorial properties. Discrete Mathematics, 303 (1-3). pp. 65-79. ISSN 0012-365X

Freyhult, E., Gardner, P. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2005) A comparison of RNA folding measures. BMC Bioinformatics, 6. ISSN 1471-2105

Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2005) Phylogenetic networks. In: Mathematics of Evolution and Phylogeny. Oxford University Press, pp. 178-200. ISBN 978-0-19-856610-6

Freyhult, Eva, Prusis, Peteris, Lapinsh, Maris, Wikberg, Jarl E. S., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Gustafsson, Mats G. (2005) Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. BMC Bioinformatics, 6. ISSN 1471-2105

Dress, A., Holland, B., Huber, K. T., Koolen, J., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 and Weyer-Menkoff, J. (2005) Delta- additive and Delta-ultra-additive maps, Gromov's trees and the Farris transform. Discrete Applied Mathematics, 146 (1). pp. 51-73. ISSN 0166-218X

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2005) Tracking down noncoding RNAs. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 102 (7). pp. 2269-2270. ISSN 1091-6490

Baroni, Mihaela, Grünewald, Stefan, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Semple, Charles (2005) Bounding the number of hybridisation events for a consistent evolutionary history. Journal of Mathematical Biology, 51 (2). pp. 171-182. ISSN 0303-6812

Dress, Andreas W. M., Koolen, Jack and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2005) 4n-10. Annals of Combinatorics, 8 (4). pp. 463-471. ISSN 0218-0006

Freyhult, Eva, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Gardner, Paul (2005) Predicting RNA structure using mutual information. Applied Bioinformatics, 4 (1). pp. 53-59. ISSN 1175-5636

Holland, B., Huber, K.T., Penny, D. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2005) The MinMax Squeeze: Guaranteeing a minimal tree for population data. Molecular Biology and Evolution, 22 (2). pp. 235-242. ISSN 0737-4038

Holland, Barbara R., Delsuc, Frédéric and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2005) Visualizing conflicting evolutionary hypotheses in large collections of trees: Using consensus networks to study the origins of placentals and hexapods. Systematic Biology, 54 (1). pp. 66-76. ISSN 1063-5157

Huber, K. T., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435, Semple, C. and Steel, M. (2005) Recovering a phylogenetic tree using pairwise closure operations. Applied Mathematics Letters, 18 (3). pp. 361-366. ISSN 0893-9659

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2005) Four characters suffice to convexly define a phylogenetic tree. SIAM Journal on Discrete Mathematics, 18 (4). pp. 835-843. ISSN 0895-4801

Tucker, Warwick and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2005) Reconstructing metabolic networks using interval analysis. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 3692 . Springer Berlin / Heidelberg, pp. 192-203. ISBN 978-3-540-29008-7

Winkworth, Richard C., Bryant, David, Lockhart, Peter J., Havell, David and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2005) Biogeographic interpretation of split graphs: Least squares optimization of edge lengths. Systematic Biology, 54 (1). pp. 56-65. ISSN 1063-5157

Magiorkinis, G., Magiorkinis, E., Paraskevis, D., Vandamme, A.-M., Van Ranst, M., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 and Hatzakiu, A. (2004) Phylogenetic analysis of the full-length SARS-CoV sequences: Evidence for phylogenetic discordance in three genomic regions. Journal of Medical Virology, 74 (3). pp. 369-372. ISSN 0146-6615

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2004) Peeling phylogenetic 'oranges'. Advances in Applied Mathematics, 33 (4). pp. 710-727. ISSN 0196-8858

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Semple, Charles (2004) Replacing cliques by stars in quasi-median graphs. Discrete Applied Mathematics, 143 (1-3). pp. 194-203. ISSN 0166-218X

Ambrose, M. J., Knox, M., Vershinin, A., Flavell, A. J., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 and Ellis, T. H. N. (2004) Exploration of germplasm resources: progress and results from the application of molecular markers to the whole JIC Pisum collection. In: 5th European Conference on Grain Legumes & 2nd International Conference on Legume Genomics and Genetics, 2004-06-07 - 2004-06-11, Palais de Congres.

Koolen, J., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 and Stevanovic, D. (2004) The structure of spherical graphs. European Journal of Combinatorics, 25 (2). pp. 299-310. ISSN 0195-6698

Bryant, David and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2004) NeighborNet: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution, 21 (2). pp. 255-265. ISSN 0737-4038

Dress, A, Huber, Katharina, Koolen, J, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, A (2004) Basic Phylogenetic Combinatorics. Cambridge University Press.

Forslund, Kristoffer, Huson, Daniel H. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2004) VisRD - Visual Recombination Detection. Bioinformatics, 20 (18). pp. 3654-3655. ISSN 1367-4803

Holland, Barbara R., Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Lockhart, Peter J. (2004) Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution, 21 (7). pp. 1459-1461. ISSN 0737-4038

Huber, Katharina T., Koolen, Jacobus H. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2004) The tight span of an antipodal metric space: Part II - Geometrical properties. Discrete and Computational Geometry, 31 (4). pp. 567-586. ISSN 0179-5376

Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2004) There are finitely many triangle-free distance-regular graphs with degree 8, 9, or 10. Journal of Algebraic Combinatorics, 19 (2). pp. 205-217. ISSN 0925-9899

Bang, S., Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2003) A bound for the number of columns l(c,a,b) in the intersection array of a distance-regular graph. European Journal of Combinatorics, 24 (7). pp. 785-795. ISSN 0195-6698

Gardner, P., Holland, B., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435, Hendy, M. and Penny, D. (2003) Optimal alphabets for an RNA world. Proceedings of the Royal Society B: Biological Sciences, 270 (1520). pp. 1177-1182. ISSN 0962-8452

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2003) Four characters suffice. In: Formal Power Series and Algebraic Combinatorics, 2003-06-23 - 2003-06-27, Linköping University.

Cieslik, D., Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2003) Connectivity calculus. Applied Mathematics Letters, 16 (3). pp. 395-399. ISSN 0893-9659

Edvardsson, Sverker, Gardner, Paul P., Poole, Anthony M., Hendy, Michael D., Penny, David and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2003) A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics, 19 (7). pp. 865-873. ISSN 1367-4803

Holland, Barbara and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2003) Consensus networks: A method for visualising incompatibilities in collections of trees. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 2812 . Springer Berlin / Heidelberg, pp. 165-176.

Koolen, Jack H. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2003) Maximal energy bipartite graphs. Graphs and Combinatorics, 19 (1). pp. 131-135. ISSN 0911-0119

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2003) SplitsTree: A network based tool for exploring evolutionary relationships in molecular data. In: The Phylogenetic Handbook. Cambridge University Press, pp. 312-328.

Salemi, Marco, De Oliveira, Tulio, Courgnaud, Valerie, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Holland, Barbara, Cassol, Sharon, Switzer, William M. and Vandamme, Anne-Mieke (2003) Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses. Journal of Virology, 77 (13). pp. 7202-7213. ISSN 0022-538X

Strimmer, Korbinian, Forslund, Kristoffer, Holland, Barbara and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2003) A novel exploratory method for visual recombination detection. Genome Biology, 4. ISSN 1465-6906

Holland, B. R., Huber, K. T., Dress, A. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) δ Plots: A tool for analyzing phylogenetic distance data. Molecular Biology and Evolution, 19 (12). pp. 2041-2059. ISSN 0737-4038

Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) On a conjecture of Bannai and Ito: There are finitely many distance-regular graphs with degree 5, 6 or 7. European Journal of Combinatorics, 23 (8). pp. 987-1006. ISSN 0195-6698

Bandelt, H.-J., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) Quasi-median graphs from sets of partitions. Discrete Applied Mathematics, 122 (1-3). pp. 23-35. ISSN 0166-218X

Cieslik, D., Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) Embedding complexity and discrete optimization I: A new divide and conquer approach to discrete optimization. Annals of Combinatorics, 6 (3-4). pp. 257-273. ISSN 0218-0006

Koolen, Jack H. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2002) Hyperbolic bridged graphs. European Journal of Combinatorics, 23 (6). pp. 683-699. ISSN 0195-6698

Dress, A., Koolen, J. H. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) On line arrangements in the hyperbolic plane. European Journal of Combinatorics, 23 (5). pp. 549-557. ISSN 0195-6698

Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) An explicit computation of the injective hull of certain finite metric spaces in terms of their associated Buneman complex. Advances in Mathematics, 168 (1). pp. 1-28. ISSN 0001-8708

Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) The relation graph. Discrete Mathematics, 244 (1-3). pp. 153-166. ISSN 0012-365X

Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) Antipodal metrics and split systems. European Journal of Combinatorics, 23 (2). pp. 187-200. ISSN 0195-6698

Bryant, David and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2002) NeighborNet: an agglomerative method for the construction of planar phylogenetic networks. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 2452 . Springer Berlin / Heidelberg, ITA, pp. 375-391. ISBN 978-3-540-44211-0

Cieslik, D., Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2002) Embedding complexity and discrete optimization II: A dynamical programming approach to the Steiner-Tree Problem. Annals of Combinatorics, 6 (3-4). pp. 275-283. ISSN 0218-0006

Huber, Katharina T., Langton, Michael, Penny, David, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Hendy, Michael (2002) Spectronet: A package for computing spectra and median networks. Applied Bioinformatics, 1 (3). pp. 159-161. ISSN 1175-5636

Dress, A., Huber, K. T., Koolen, J. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2001) Six points suffice: How to check for metric consistency. European Journal of Combinatorics, 22 (4). pp. 465-474. ISSN 0195-6698

Huber, Katharina T., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Lockhart, Peter and Dress, Andreas (2001) Pruned median networks: a technique for reducing the complexity of median networks. Molecular Phylogenetics and Evolution, 19 (2). pp. 302-310. ISSN 1055-7903

Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2001) Metric spaces in pure and applied mathematics. In: Conference on Quadratic Forms and Related Topics, 2001-03-26 - 2001-03-30.

Koolen, Jack H. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2001) Maximal energy graphs. Advances in Applied Mathematics, 26 (1). pp. 47-52. ISSN 0196-8858

Strimmer, Korbinian, Wiuf, Carsten and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2001) Recombination analysis using directed graphical models. Molecular Biology and Evolution, 18 (1). pp. 97-99. ISSN 0737-4038

Brinkmann, Gunnar, Koolen, Jack H. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2001) On the hyperbolicity of chordal graphs. Annals of Combinatorics, 5 (1). pp. 61-69. ISSN 0218-0006

Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2001) Totally Split-Decomposable Metrics of Combinatorial Dimension Two. Annals of Combinatorics, 5 (1). pp. 99-112. ISSN 0218-0006

Koolen, Jack, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Tönges, Udo (2000) A classification of the six-point prime metrics. European Journal of Combinatorics, 21 (6). pp. 815-829. ISSN 0195-6698

Goodmann, Oliver and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2000) On the tight span of an antipodal graph. Discrete Mathematics, 218 (1-3). pp. 73-96. ISSN 0012-365X

Koolen, Jack, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Gutman, Ivan (2000) Improving the McClelland inequality for total π-electron energy. Chemical Physics Letters, 320 (3-4). pp. 213-216. ISSN 0009-2614

Allain, Jean-Pierre, Dong, Yan, Vandamme, Anne-Mieke, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Salemi, Marco (2000) Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response: Studies of infected donor-recipient clusters. Journal of Virology, 74 (6). pp. 2541-2549.

Collins, Lesley J., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Penny, David (2000) Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP. Journal of Molecular Evolution, 51 (3). pp. 194-204. ISSN 0022-2844

Dress, A., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2000) Affine maps that induce polyhedral complex isomorphisms. Discrete and Computational Geometry, 24 (1). pp. 49-60. ISSN 0179-5376

Dress, A. W. M., Huber, K. T. and Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435 (2000) An exceptional split geometry. Annals of Combinatorics, 4 (1). pp. 1-11. ISSN 0218-0006

Gutman, I., Koolen, J. H., Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435, Parac, M., Soldatović, T. and Vidović, D. (2000) Estimating and approximating the total pi-electron energy of benzenoid hydrocarbons. Zeitschrift für Naturforschung A, 55a (5). pp. 507-512. ISSN 0932-0784

Koolen, Jack H., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Gutman, Ivan and Vidovic, Dusica (2000) More hyperenergetic molecular graphs. Journal of Serbian Chemical Society, 65 (8). pp. 571-575. ISSN 0352-5139

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Gardner, Paul P., Pointon, Robert F., Creamer, Lawrence K., Jameson, Geoffrey B. and Penny, David (2000) RNA folding argues against a hot-start origin of life. Journal of Molecular Evolution, 51 (4). pp. 416-421. ISSN 0022-2844

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Zuker, Michael, Steel, Michael, Pointon, Robin and Penny, David (2000) Metrics on RNA secondary structures. Journal of Computational Biology, 7. pp. 277-292. ISSN 1557-8666

Strimmer, Korbinian and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2000) Likelihood analysis of phylogenetic networks using directed graphical models. Molecular Biology and Evolution, 17 (6). pp. 875-881. ISSN 1537-1719

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (1999) Retractions of finite distance functions onto tree metrics. Discrete Applied Mathematics, 91 (1-3). pp. 215-233. ISSN 0166-218X

Moulton, V ORCID: https://orcid.org/0000-0001-9371-6435 and Da Silva, I (1998) Crinkled zonotopes. Working Paper. Mathematics Dept, Mid Sweden University.

Moulton, V. L. ORCID: https://orcid.org/0000-0001-9371-6435, Steel, M. A. and Tuffley, C. (1997) Dissimilarity maps and substitution models. In: Mathematical Hierarchies and Biology: Dimacs Workshop, 1997-01-01.