Items where Author is "Moulton, Vincent"
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Lafond, Manuel and Moulton, Vincent (2025) Path partitions of phylogenetic networks. Theoretical Computer Science, 1024. ISSN 0304-3975
Huber, Katharina T., van Iersel, Leo, Moulton, Vincent and Scholz, Guillaume E. (2025) Is this network proper forest-based? Information Processing Letters, 187. ISSN 0020-0190
Moulton, Vincent and Scholz, Guillaume E. (2024) Compatible split systems on a multiset. Electronic Journal of Combinatorics, 31 (4). ISSN 1077-8926
Huber, Katharina T., Moulton, Vincent 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
Huber, Katharina T., Linz, Simone, Moulton, Vincent and Semple, Charles (2024) Phylogenetic trees defined by at most three characters. Electronic Journal of Combinatorics, 31 (4). ISSN 1077-8926
Moulton, Vincent, 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, 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, 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 (2024) A distance-based model for convergent evolution. Journal of Mathematical Biology, 88. ISSN 0303-6812
Bryant, David, Huber, Katharina T., Moulton, Vincent 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 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 and Murakami, Yukihiro (2023) Polynomial invariants for cactuses. Information Processing Letters, 182. ISSN 0020-0190
Hellmuth, Marc, Huber, Katharina T., Moulton, Vincent, Scholz, Guillaume E. and Stadler, Peter F. (2023) Injective split systems. Graphs and Combinatorics, 39 (4). ISSN 0911-0119
Seemann, Carsten R., Moulton, Vincent, 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 and Mock, Thomas (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 and Wu, Taoyang (2023) Planar rooted phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20 (2). pp. 1289-1297. ISSN 1545-5963
Winder, Johanna C., Boulton, William, Salamov, Asaf, Eggers, Sarah Lena, Metfies, Katja, Moulton, Vincent and Mock, Thomas (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 and Wu, Taoyang (2023) Encoding and ordering X-cactuses. Advances in Applied Mathematics, 142. ISSN 0196-8858
Alzahrani, Salma, Applegate, Christopher, Swarbreck, David, Dalmay, Tamas, Folkes, Leighton and Moulton, Vincent (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 and Nipius, Leonie (2022) An algorithm for reconstructing level-2 phylogenetic networks from trinets. Information Processing Letters, 178. ISSN 0020-0190
Mock, Thomas, 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 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. and Scholz, G. E. (2022) Forest-based networks. Bulletin of Mathematical Biology, 84. ISSN 0092-8240
Moulton, Vincent and Wu, Taoyang (2022) Posets and spaces of k-noncrossing RNA structures. SIAM Journal on Discrete Mathematics, 36 (3). pp. 1586-1611. ISSN 0895-4801
Moulton, Vincent 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 and Mock, Thomas (2022) Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. Microbiome, 10. ISSN 2049-2618
Huber, Katharina, Moulton, Vincent 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 and Murakami, Yuki (2022) Level-2 networks from shortest and longest distances. Discrete Applied Mathematics, 306. pp. 138-165. ISSN 0166-218X
Huber, Katharina, Moulton, Vincent 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 and Mock, Thomas (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 (2021) The rigid hybrid number for two phylogenetic trees. Journal of Mathematical Biology, 82 (5). ISSN 0303-6812
van Iersel, Leo, Moulton, Vincent 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, Ellis, Christopher, Connell, Shea P., Brewer, Daniel and Cooper, Colin (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 (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, 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, Ellis, Christopher, Edwards, Dylan R., Campbell, Colin, Cooper, Rosalin A., Clark, Jeremy, Brewer, Daniel S. and Cooper, Colin S. (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 and Murakami, Yukihiro (2020) Recognizing and realizing cactus metrics. Information Processing Letters, 157. ISSN 0020-0190
Thody, Joshua, Moulton, Vincent 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 (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 (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 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 (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., Moulton, Vincent 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 and Wu, Taoyang (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, 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 (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 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 (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., Edwards, Dylan R., 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 and Cooper, Colin S. 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, Thody, Joshua, Dalmay, Tamas and Moulton, Vincent (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 and Moulton, Vincent (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
Bordewich, Magnus, Huber, Katharina T., Moulton, Vincent 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 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, 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, Semple, Charles and Wu, Taoyang (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 (2018) Leaf-reconstructibility of phylogenetic networks. SIAM Journal on Discrete Mathematics, 32 (3). 2047–2066. ISSN 0895-4801
Francis, Andrew and Moulton, Vincent (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, Spillner, Andreas and Wu, Taoyang (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 and Wu, Taoyang (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, Balvočiūtė, Monika and Moulton, Vincent (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 (2018) Tree-based unrooted phylogenetic networks. Bulletin of Mathematical Biology, 80 (2). 404–416. ISSN 0092-8240
Huber, Katharina T., Moulton, Vincent 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, Moulton, Vincent and Moxon, Simon (2017) miRCat2: Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. Bioinformatics, 33 (16). 2446–2454. ISSN 1367-4803
Moulton, Vincent, Oldman, James and Wu, Taoyang (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 and Moulton, Vincent (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, de Swart, Eveline and Wu, Taoyang (2017) Binets: fundamental building blocks for phylogenetic networks. Bulletin of Mathematical Biology, 79 (5). 1135–1154. ISSN 0092-8240
Collins, David H., Mohorianu, Irina, Beckers, Matthew, Moulton, Vincent, Dalmay, Tamas and Bourke, Andrew F. G. (2017) MicroRNAs associated with caste determination and differentiation in a primitively eusocial insect. Scientific Reports, 7. ISSN 2045-2322
Mock, Thomas, 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, 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, van Oosterhout, Cock 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, Scornavacca, Celine and Wu, Taoyang (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, Steel, Mike and Wu, Taoyang (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 and Wu, Taoyang (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 and Wu, Taoyang (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 (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 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, van Iersel, Leo and Moulton, Vincent (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, Spillner, Andreas and Wu, Taoyang (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 and Wu, Taoyang (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, Daines, Stuart, Geider, Richard, Collins, Sinead, Metoviev, Metovi, Millar, Andrew J, Moulton, Vincent 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 and Wu, Taoyang (2015) Optimal realisations of two-dimensional, totally split-decomposable metrics. Discrete Mathematics, 338 (8). 1289–1299. ISSN 0012-365X
Moulton, Vincent and Wu, Taoyang (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 (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, Spillner, Andreas and Wu, Taoyang (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 and Wu, Taoyang (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 (2014) Computing the blocks of a quasi-median graph. Discrete Applied Mathematics, 179. pp. 129-138. ISSN 0166-218X
Toseland, Andrew, Moxon, Simon, Mock, Thomas and Moulton, Vincent (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, Maumus, Florian, Mohorianu, Irina, Moulton, Vincent, Dalmay, Tamas and Mock, Thomas (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., Semple, C. and Wu, T. (2014) Representing partitions on trees. SIAM Journal on Discrete Mathematics, 28 (3). pp. 1152-1172. ISSN 0895-4801
Van Iersel, Leo and Moulton, Vincent (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, 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 (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 (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 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., Bocking, C., Blyth, M.G., Richardson, D.J. and Moulton, V. (2013) Modeling the effect of copper availability on bacterial denitrification. MicrobiologyOpen, 2 (5). pp. 756-765. ISSN 2045-8827
Dress, A., Moulton, Vincent, Wu, Taoyang 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. (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 and Moulton, Vincent (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 (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. 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, 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, Dalmay, Tamas and Moulton, Vincent (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 (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. and Mock, T. (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 and Dalmay, Tamas (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 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., Moulton, Vincent, Sanderson, Julie, Wormstone, I. Michael 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
Folkes, Leighton, Moxon, Simon, Woolfenden, Hugh C., Stocks, Matthew B., Szittya, Gyorgy, Dalmay, Tamas and Moulton, Vincent (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 and Wu, Taoyang (2012) The size of 3-compatible, weakly compatible split systems. Journal of Applied Mathematics and Computing, 40 (1-2). pp. 249-259.
Herrmann, Sven, Huber, Katharina T., Moulton, Vincent and Spillner, Andreas (2012) Recognizing treelike k-dissimilarities. Journal of Classification, 29 (3). pp. 321-340.
Herrmann, Sven and Moulton, Vincent (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 (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 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 and Wu, Taoyang (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 and Moulton, Vincent (2012) FiRePat-finding regulatory patterns between sRNAs and genes. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 2 (3). pp. 273-284.
Moulton, Vincent 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 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 and Dalmay, Tamas (2012) Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence, 3 (1).
Spillner, Andreas, Nguyen, Binh and Moulton, Vincent (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, Mapleson, Daniel, Woolfenden, Hugh C., Mohorianu, Irina, Folkes, Leighton, Schwach, Frank, Dalmay, Tamas and Moulton, Vincent (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. (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 and Dalmay, Tamas (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 (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, Szittya, G, Sorefan, K, Moulton, V and Dalmay, T (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. (2011) A ‘non-additive’ characterization of $${\wp}$$ -adic norms. Annals of Combinatorics, 15 (1). pp. 37-50. ISSN 0218-0006
Thuillard, Marc and Moulton, Vincent (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, Steel, Mike and Wu, Taoyang (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, Pantaleo, Vitantonio, Toth, Gabor, Rusholme Pilcher, Rachel L., Moulton, Vincent, Burgyan, Jozsef and Dalmay, Tamas (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 (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 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 and Dalmay, Tamas (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 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, 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, de Haro, Juan P., Calo, Silvia, Grigoriev, Igor V., Torres-Martinez, Santiago, Moulton, Vincent, Ruiz-Vazquez, Rosa M. and Dalmay, Tamas (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
Pantaleo, Vitantonio, Szittya, György, Moxon, Simon, Miozzi, Laura, Moulton, Vincent, Dalmay, Tamas 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 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 (2009) Inferring polyploid phylogenies from multiply-labeled gene trees. BMC Evolutionary Biology, 9. ISSN 1471-2148
Dress, Andreas W. M., Moulton, Vincent, Spillner, Andreas and Wu, Taoyang (2009) Barriers in metric spaces. Applied Mathematics Letters, 22 (8). pp. 1150-1153.
Gruenewald, S, Moulton, V 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, Munsterberg, Andrea and Dalmay, Tamas (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 (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, 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 (2009) A graph-theoretical invariant of topological spaces. Applied Mathematics Letters, 22 (2). pp. 159-162.
Bang, S., Koolen, J. and Moulton, V. (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 (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 (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 (2009) Optimal realizations of generic 5-point metrics. European Journal of Combinatorics, 30 (5). pp. 1164-1171. ISSN 0195-6698
Lott, Martin, Spillner, Andreas, Huber, Katharina T. and Moulton, Vincent (2009) PADRE: A Package for Analyzing and Displaying Reticulate Evolution. Bioinformatics, 25 (9). pp. 1199-1200. ISSN 1367-4803
Schwach, Frank, Moxon, Simon, Moulton, Vincent and Dalmay, Tamas (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, Moulton, Vincent 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, Santos, Dulce M., Jing, Runchan, Fevereiro, Manuel P. S., Moulton, Vincent and Dalmay, Tamas (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics, 9. ISSN 1471-2164
Moxon, Simon, Jing, Runchan, Szittya, Gyorgy, Schwach, Frank, Rusholme Pilcher, Rachel L., Moulton, Vincent and Dalmay, Tamas (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 and Dalmay, Tamas (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 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 and Huber, Katharina T. (2008) Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evolutionary Biology, 8. ISSN 1471-2148
Moxon, Simon, Moulton, Vincent 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. 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 (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 (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 (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 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 and Spillner, Andreas (2008) Characterizing cell-decomposable metrics. Electronic Journal of Combinatorics, 15 (1). ISSN 1077-8926
Huber, Katharina T., Lott, Martin, Moulton, Vincent 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, Schwach, Frank, Dalmay, Tamas, MacLean, Dan, Studholme, David J. and Moulton, Vincent (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 (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 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 and Spillner, Andreas (2007) Consistency of the Neighbor-Net algorithm. Algorithms for Molecular Biology, 2. ISSN 1748-7188
Moulton, Vincent, 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. (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 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. (2007) Some uses of the Farris Transform in mathematics and phylogenetics - A review. Annals of Combinatorics, 11 (1). pp. 1-37. ISSN 0218-0006
Freyhult, Eva, Moulton, Vincent 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 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 (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. (2007) Imputing supertrees and supernetworks from quartets. Systematic Biology, 56 (1). pp. 57-67. ISSN 1063-5157
Koolen, Jack, Lesser, Alice and Moulton, Vincent (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. (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, Pakseresht, Nima, Moulton, Vincent, Manning, Kenneth, Seymour, Graham and Dalmay, Tamas (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 (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 (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. (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 (2006) Hereditarily optimal realizations of consistent metrics. Annals of Combinatorics, 10 (1). pp. 63-67. ISSN 0218-0006
Freyhult, Eva, Moulton, Vincent 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. (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 (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. (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. (2005) A comparison of RNA folding measures. BMC Bioinformatics, 6. ISSN 1471-2105
Freyhult, Eva, Prusis, Peteris, Lapinsh, Maris, Wikberg, Jarl E. S., Moulton, Vincent 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. 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 (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 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 (2005) 4n-10. Annals of Combinatorics, 8 (4). pp. 463-471. ISSN 0218-0006
Freyhult, Eva, Moulton, Vincent 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. (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 (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., 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 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
Winkworth, Richard C., Bryant, David, Lockhart, Peter J., Havell, David and Moulton, Vincent (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. 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 and Steel, Mike (2004) Peeling phylogenetic 'oranges'. Advances in Applied Mathematics, 33 (4). pp. 710-727. ISSN 0196-8858
Huber, Katharina T., Moulton, Vincent and Semple, Charles (2004) Replacing cliques by stars in quasi-median graphs. Discrete Applied Mathematics, 143 (1-3). pp. 194-203. ISSN 0166-218X
Koolen, J., Moulton, V. 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 (2004) NeighborNet: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution, 21 (2). pp. 255-265. ISSN 0737-4038
Forslund, Kristoffer, Huson, Daniel H. and Moulton, V. (2004) VisRD - Visual Recombination Detection. Bioinformatics, 20 (18). pp. 3654-3655. ISSN 1367-4803
Holland, Barbara R., Huber, Katharina T., Moulton, Vincent 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 (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. (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. (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., 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
Cieslik, D., Dress, A., Huber, K. T. and Moulton, V. (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 (2003) A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics, 19 (7). pp. 865-873. ISSN 1367-4803
Koolen, Jack H. and Moulton, Vincent (2003) Maximal energy bipartite graphs. Graphs and Combinatorics, 19 (1). pp. 131-135. ISSN 0911-0119
Salemi, Marco, De Oliveira, Tulio, Courgnaud, Valerie, Moulton, Vincent, 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 (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. (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. (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. (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. (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 (2002) Hyperbolic bridged graphs. European Journal of Combinatorics, 23 (6). pp. 683-699. ISSN 0195-6698
Dress, A., Koolen, J. H. and Moulton, V. (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. (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. (2002) The relation graph. Discrete Mathematics, 244 (1-3). pp. 153-166. ISSN 0012-365X
Dress, A., Huber, K. T. and Moulton, V. (2002) Antipodal metrics and split systems. European Journal of Combinatorics, 23 (2). pp. 187-200. ISSN 0195-6698
Cieslik, D., Dress, A., Huber, K. T. and Moulton, V. (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 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. (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, 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
Koolen, Jack H. and Moulton, Vincent (2001) Maximal energy graphs. Advances in Applied Mathematics, 26 (1). pp. 47-52. ISSN 0196-8858
Strimmer, Korbinian, Wiuf, Carsten and Moulton, Vincent (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. (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. (2001) Totally Split-Decomposable Metrics of Combinatorial Dimension Two. Annals of Combinatorics, 5 (1). pp. 99-112. ISSN 0218-0006
Koolen, Jack, Moulton, Vincent 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. (2000) On the tight span of an antipodal graph. Discrete Mathematics, 218 (1-3). pp. 73-96. ISSN 0012-365X
Koolen, Jack, Moulton, Vincent 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 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 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. (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. (2000) An exceptional split geometry. Annals of Combinatorics, 4 (1). pp. 1-11. ISSN 0218-0006
Gutman, I., Koolen, J. H., Moulton, V., 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, 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, 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, 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 (2000) Likelihood analysis of phylogenetic networks using directed graphical models. Molecular Biology and Evolution, 17 (6). pp. 875-881. ISSN 1537-1719
Moulton, Vincent and Steel, Mike (1999) Retractions of finite distance functions onto tree metrics. Discrete Applied Mathematics, 91 (1-3). pp. 215-233. ISSN 0166-218X
Book Section
Mock, Thomas, Hodgkinson, Kat, Wu, Taoyang, Moulton, Vincent, Duncan, Anthony, Oosterhout, Cock van 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
Delabre, Matteo, El-Mabrouk, Nadia, Huber, Katharina, Lafond, Manuel, Moulton, Vincent, 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
Mohorianu, Irina, Stocks, Matthew Benedict, Applegate, Christopher Steven, Folkes, Leighton and Moulton, Vincent (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
Moulton, Vincent and Huber, Katharina T. (2012) Network analyses for exploring evolutionary relationships. In: The Phylogenetic Handbook 2nd edition. UNSPECIFIED.
Pais, Helio, Moxon, Simon, Dalmay, Tamas and Moulton, Vincent (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
Pais, H, Moxon, S, Dalmay, T and Moulton, V (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
Dress, Andreas W. M., Huber, Katharina T., Koolen, Jack H. and Moulton, Vincent (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 (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.
Huber, K. T. and Moulton, V. (2005) Phylogenetic networks. In: Mathematics of Evolution and Phylogeny. Oxford University Press, pp. 178-200. ISBN 978-0-19-856610-6
Tucker, Warwick and Moulton, Vincent (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
Holland, Barbara and Moulton, Vincent (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.
Moulton, Vincent (2003) SplitsTree: A network based tool for exploring evolutionary relationships in molecular data. In: The Phylogenetic Handbook. Cambridge University Press, pp. 312-328.
Bryant, David and Moulton, Vincent (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
Monograph
Moulton, V and Da Silva, I (1998) Crinkled zonotopes. Working Paper. Mathematics Dept, Mid Sweden University.
Conference or Workshop Item
Huber, Katharina T., Moulton, Vincent, 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.
Hernandez-Rosales, M, Hellmuth, M, Wieseke, N, Huber, Katharina T., Moulton, Vincent and Stadler, PF (2012) From event-labeled gene trees to species trees. In: UNSPECIFIED.
Leggett, Richard M., Grandison, Scott, Morris, Richard J., Kelemen, Gabriella and Moulton, Vincent (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.
Ambrose, M. J., Knox, M., Vershinin, A., Flavell, A. J., Moulton, V. 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.
Huber, Katharina T., Moulton, Vincent and Steel, Mike (2003) Four characters suffice. In: Formal Power Series and Algebraic Combinatorics, 2003-06-23 - 2003-06-27, Linköping University.
Dress, A., Huber, K. T. and Moulton, V. (2001) Metric spaces in pure and applied mathematics. In: Conference on Quadratic Forms and Related Topics, 2001-03-26 - 2001-03-30.
Moulton, V. L., Steel, M. A. and Tuffley, C. (1997) Dissimilarity maps and substitution models. In: Mathematical Hierarchies and Biology: Dimacs Workshop, 1997-01-01.
Book
Dress, A, Huber, Katharina, Koolen, J, Moulton, Vincent and Spillner, A (2004) Basic Phylogenetic Combinatorics. Cambridge University Press.