Article

Lopez-Gomollon, S, Mohorianu, I, Szittya, G, Moulton, V and Dalmay, T (2012) Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta. ISSN 0032-0935 (In Press)

Folkes, L, Moxon, S, Woolfenden, HC, Stocks, MB, Szittya, G, Dalmay, T and Moulton, V (2012) PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Research, 40 (13). e103-e103. ISSN 0305-1048

Gruenewald, S, Koolen, J, Moulton, V and Wu, T (2012) The size of 3-compatible, weakly compatible split systems. Journal of Applied Mathematics and Computing, 40 (1-2). pp. 249-259.

Hellmuth, M, Hernandez-Rosales, M, Huber, KT, Moulton, V, Stadler, PF and Wieseke, N (2012) Orthology relations, symbolic ultrametrics and cographs. Journal of Mathematical Biology. (In Press)

Herrmann, S, Huber, KT, Moulton, V and Spillner, A (2012) Recognizing treelike dissimilarities. Journal of Classification, 29 (3). pp. 321-340.

Herrmann, S and Moulton, V (2012) The split decomposition of a k-dissimilarity map. Advances in Applied Mathematics, 49 (1). pp. 39-56. ISSN 01968858

Herrmann, S and Moulton, V (2012) Trees, tight-spans and point configurations. Discrete Mathematics, 312 (16). pp. 2506-2521. ISSN 0012365X

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

Koolen, JH, Lesser, A, Moulton, V and Wu, T (2012) Injective optimal realizations of finite metric spaces. Discrete Mathematics, 312 (10). pp. 1602-1610. ISSN 0012365X

Martyn, I, Kuhn, TS, Mooers, AO, Moulton, V and Spillner, A (2012) Computing evolutionary distinctiveness indices in large scale analysis. Algorithms for Molecular Biology, 7 (1). p. 6. ISSN 1748-7188

Mohorianu, I, Lopez-Gomollon, S, Schwach, F, Dalmay, T and Moulton, V (2012) FiRePat-Finding Regulatory Patterns between sRNAs and Genes. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 2 (3). pp. 273-284. ISSN 19424787

Moulton, V and Spillner, A (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

Rhodes, JD, Lott, MC, Russell, SL, Moulton, V, Sanderson, J, Wormstone, IM and Broadway, DC (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.

Sorefan, K, Pais, H, Hall, AE, Kozomara, A, Griffiths-Jones, S, Moulton, V and Dalmay, T (2012) Reducing sequencing bias of small RNAs. Silence, 3 (1). p. 4.

Spillner, A, Nguyen, B and Moulton, V (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, MB, Moxon, S, Mapleson, D, Woolfenden, HC, Mohorianu, I, Folkes, L, Schwach, F, Dalmay, T and Moulton, V (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, AWM, Huber, KT, Koolen, J and Moulton, V (2011) Blocks and Cut Vertices of the Buneman Graph. SIAM Journal on Discrete Mathematics, 25 (4). pp. 1902-1919. ISSN 08954801

Huber, KT, Spillner, A, Suchecki, R and Moulton, V (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 09607412

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

Huber, KT, Moulton, V, Spillner, A, Storandt, R and Suchecki, R (2011) Computing a consensus of multilabeled trees. Meeting on Algorithm Engineering & Experiments (ALENEX12). (In Press)

Nicolas Molina, F, Pais, H, Schwah, F, Lindow, M, Kauppinen, S, Moulton, V and Dalmay, T (2011) mRNA expression profiling reveals conserved and non-conserved miR-140. RNA Biology, 8 (4). pp. 607-615. ISSN 1547-6286

Pais, H, Moxon, S, Dalmay, T and Moulton, V (2011) Small RNA Discovery and Characterisation in Eukaryotes Using High-Throughput Approaches. Advances in Experimental Medicine and Biology, 722. pp. 239-254. ISSN 0065-2598

Thuillard, M and Moulton, V (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, A, Moulton, V, Steel, M and Wu, T (2010) Species, clusters and the ‘Tree of life’: A graph-theoretic perspective. Journal of Theoretical Biology, 265 (4). pp. 535-542. ISSN 00225193

Pais, H, Nicolas, FE, Soond, S, Swingler, T, Clark, I, Chantry, A, Moulton, V and Dalmay, T (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, AWM, Huber, KT, Koolen, J, Moulton, V and Spillner, A (2010) An algorithm for computing cutpoints in finite metric spaces. Journal of Classification, 27 (2). pp. 158-172.

MacLean, D., Moulton, V. and Studholme, D. (2010) Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics, 11. p. 93.

Martin, DP, Lemey, P, Lott, M, Moulton, V, Posada, D and Lefeuvre, P (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26 (19). pp. 2462-2463. ISSN 1367-4803

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. p. 19. ISSN 1748-7188

Nicolas, F. E., Moxon, Simon, de Haro, J. P., Calo, S., Grigoriev, I. V., Torres-Martinez, S., Moulton, Vincent, Ruiz-Vazquez, R. 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, V, Szittya, G, Moxon, S, Miozzi, L, Moulton, V, Dalmay, T and Burgyan, J (2010) Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis. The Plant Journal, 62 (6). pp. 960-976.

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). e1000838. ISSN 1553-7374

Lott, M., Spillner, A., Huber, K. T., Petri, A., Oxelman, B. and Moulton, V. (2009) Inferring polyploid phylogenies from multiply-labeled gene trees. BMC Evolutionary Biology, 9 (216).

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.

Grünewald, S., Huber, K. T., Moulton, V., Semple, C. and Spillner, A. (2009) Characterizing weak compatibility in terms of weighted quartets. Advances in Applied Mathematics., 42 (3). pp. 329-341.

Bang, S., Koolen, J. and Moulton, V. (2009) There are finitely many regular near polygons and geodetic distance-regular graphs with fixed valency. Journal fur die reine und angewandte Mathematik. pp. 213-235.

Bordewich, M., Gascuel, O., Huber, K. T. and Moulton, V. (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

Dres, A, Moulton, V, Spillner, A and Wu, T (2009) Barriers in metric spaces. Applied Mathematics Letters,, 22 (8). pp. 1150-1153. ISSN 08939659

Dress, A., Huber, K. T., Koolen, J. and Moulton, V. (2009) A graph-theoretical invariant of topological spaces. Applied Mathematics Letters (2). pp. 159-162.

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, J., Lesser, A. and Moulton, V. (2009) Optimal realizations of generic 5-point metrics. European Journal of Combinatorics, 30 (5). pp. 1164-1171. ISSN 0195-6698

Lemey, P., Lott, M., Martin, D. and Moulton, V. (2009) Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics, 10. p. 126.

Lott, M., Spillner, A., Huber, K.T. and Moulton, V. (2009) PADRE: A Package for Analyzing and Displaying Reticulate Evolution. Bioinformatics, 25 (9). pp. 1199-1200. ISSN 1367-4803

Moulton, Vincent and Spillner, Andreas (2009) The maximum coverage problem and strongly greedy hypergraphs. Applied Mathematics Letters, 22 (10). pp. 1496-1499.

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.

Schwach, F., Moxon, S., 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, M. (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, G, Moxon, S, Santos, DM, Jing, R, Fevereiro, MP, Moulton, V and Dalmay, T (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics, 9 (1). p. 593.

Moxon, S, Jing, R, Szittya, G, Schwach, F, Rusholme Pilcher, RL, Moulton, V and Dalmay, T (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, FE, Pais, H, Schwach, F, Lindow, M, Kauppinen, S, Moulton, V and Dalmay, T (2008) Experimental identification of microRNA-140 targets by silencing and over-expressing miR-140. RNA, 14. pp. 2513-2520.

Gill, J, Linusson, S, Moulton, V and Steel, M (2008) A regular decomposition of the edge-product space of phylogenetic trees. Advances in Applied Mathematics, 41 (2). pp. 158-176.

Moxon, Simon, Moulton, Vincent and Kim, Jan T. (2008) A scoring matrix approach to detecting miRNA target sites. Algorithms in Molecular Biology, 3 (3).

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, A., Huber, K. T., Koolem, J. and Moulton, V. (2008) Cut points in metric spaces. Applied Mathematics Letters, 21 (6). pp. 545-548.

Dress, A. W. M., Huber, K. T., Koolen, J. and Moulton, V. (2008) Block realizations of finite metrics and the tight-span construction I: The embedding theorem. Applied Mathematics Letters (2). pp. 1306-1309.

Dress, A.W.M., Huber, K.T., Koolen, J. and Moulton, V. (2008) Compatible decompositions and block realizations of finite metrics. European Journal of Combinatorics, 29 (7). pp. 1617-1633.

Grünewald, S., Huber, K. T., Moulton, V. and Semple, C. (2008) Encoding phylogenetic trees in terms of weighted quartets. Journal of Mathematical Biology, 56 (4). pp. 465-477. ISSN 0303-6812

Holland, B. R., Benthin, S., Lockhart, P. J., Moulton, V. and Huber, K. T. (2008) Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evolutionary Biology, 8. p. 202. ISSN 1471-2148

Huber, K. T., Koolen, J., Moulton, V. and Spillner, A. (2008) Characterizing cell-decomposable metrics. The Electronic Journal of Combinatorics, 15 (1). N7.

Huber, K. T., Lott, M., Moulton, V. and Spillner, A. (2008) The complexity of deriving multi-labeled trees from bipartitions. Journal of Computational Biology, 15 (6). pp. 639-651.

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, A., Nguyen, B. T. and Moulton, V. (2008) Computing Phylogenetic Diversity for Split Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5 (2). pp. 235-244. ISSN 1545-5963

Wu, Q., James, S. A., Roberts, I. N., Moulton, V. and Huber, K. T (2008) Exploring contradictory phylogenetic relationships in yeasts. FEMS Yeast Research, 8 (4). pp. 641-650.

Bryant, David, Moulton, Vincent and Spillner, Andreas (2007) Consistency of the Neighbor-Net algorithm. Algorithms for Molecular Biology, 2 (8). 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, A., Oxelman, B., Huber, K. T., Moulton, V. and Brochmann, C. (2007) Untangling complex histories of genome mergings in high polyploids. Systemic 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, E., Moulton, V. and Clote, P. (2007) Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics, 23 (16). pp. 2054-2062. ISSN 1367-4803

Freyhult, E., Moulton, V. and Clote, P. (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, G., Huber, K.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, B., Jermiin, L. and Moulton, V. (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, A., Huber, K. T., Lesser, A. and Moulton, V. (2006) Hereditarily optimal realizations of consistent metrics. Annals of Combinatorics, 10 (1). pp. 63-67. ISSN 0218-0006

Freyhult, E., Moulton, V. and Ardell, D. (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, K. T., Oxelman, B., Lott, M. and Moulton, V. (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 (241). 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, V. (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, A., Koolen, J. and Moulton, V. (2005) 4n-10. Annals of Combinatorics, 8 (4). pp. 463-471. ISSN 0218-0006

Freyhult, E., Moulton, V. and Gardner, P. (2005) Predicting RNA structure using mutual information. Applied Bioinformatics, 4 (1). pp. 53-59. ISSN 1175-5636

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. p. 50.

Holland, B., Delsuc, F. and Moulton, V. (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

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

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, K. T., Moulton, V. and Steel, M. (2005) Four characters suffice to convexly define a phylogenetic tree. SIAM Journal on Discrete Mathematics, 18 (4). pp. 835-843. ISSN 0895-4801

Winkworth, R., Bryant, D., Lockhart, P., Havell, D. and Moulton, V. (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, K. T., Moulton, V. and Semple, C. (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, D. and Moulton, V. (2004) NeighborNet: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution, 21 (2). pp. 255-265. ISSN 0737-4038

Forslund, K., Huson, D. and Moulton, V. (2004) VisRD - Visual Recombination Detection. Bioinformatics, 20 (18). pp. 3654-3655. ISSN 1367-4803

Holland, B., Huber, K. T., Moulton, V. and Lockhart, P. (2004) Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution, 21 (7). pp. 1459-1461. ISSN 0737-4038

Huber, K. T., Koolen, J. and Moulton, V. (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. The Royal Society Proceedings: Biological Sciences, 270 (1520). pp. 1177-1182. ISSN 1471-2954

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, S., Gardner, P., Poole, A. M., Hendy, M., Penny, D. and Moulton, V. (2003) A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics, 19 (7). pp. 865-873. ISSN 1367-4803

Koolen, J. and Moulton, V. (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, K., Forslund, K., Holland, B. and Moulton, V. (2003) A novel exploratory method for visual recombination detection. Genome Biology, 4. R33.

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, J. and Moulton, V. (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, K. T., Langton, M., Penny, D., Moulton, V. and Hendy, M. (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, K. T., Moulton, V., Lockhart, P. and Dress, A. (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, J. and Moulton, V. (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, G., Koolen, J. 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, O. 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 Moleculary Evolution, 51 (3). pp. 194-204. ISSN 0022-2844

Dress, A., Huber, K. T. and Moulton, V. (2000) An exceptional split geometry. Annals of Combinatorics, 4 (1). pp. 1-11. ISSN 0218-0006

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

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, V., Zuker, M., Steel, M., Pointon, R. and Penny, D. (2000) Metrics on RNA secondary structures. Journal of Computational Biology, 7. pp. 277-292.

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

Strimmer, K. and Moulton, V. (2000) Likelihood analysis of phylogenetic networks using directed graphical models. Molecular Biology and Evolution, 17 (6). pp. 875-881.

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

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, A. W. M., Huber, K. T., Koolen, J. and Moulton, V. (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, W. and Moulton, V. (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, B. and Moulton, V. (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, D. and Moulton, V. (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, pp. 375-391. ISBN 978-3-540-44211-0

Monograph

Moulton, V and Da Silva, I (1998) Crinkled zonotopes. Research Report. Mathematics Dept, Mid Sweden University.

Conference or Workshop Item

Leggett, RM, Grandison, S, Morris, RM, Kelemen, G and Moulton, V (2009) Statistical analysis of the growth and morphology of the filamentous microbe Streptomyces coelicolor. In: Statistical Tools for Challenges in Bioinformatics, 7th-9th July 2009, Leeds, UK.

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: Proceedings of the 5th European Conference on Grain Legumes & 2nd International Conference on Legume Genomics and Genetics, 7-11 June, 2004, Palais de Congres, Dijon.

Huber, K. T., Moulton, V. and Steel, M. (2003) Four characters suffice. In: Proceedings of Formal Power Series and Algebraic Combinatorics FPSAC 2003, June 23 - 27, 2003, Linköping University, Sweden.

Dress, A., Huber, K. T. and Moulton, V. (2001) Metric spaces in pure and applied mathematics. In: Proceedings of the Conference on Quadratic Forms and Related Topics, 26-30 March 2001, Baton Rouge, Louisiana, USA.

Moulton, V. L., Steel, M. A. and Tuffley, C. (1997) Dissimilarity maps and substitution models. In: Mathematical Hierarchies and Biology: Dimacs Workshop.