Vincent Moulton's Publications

(some publications are available for download at the UEA Digital Repository, otherwise please contact Vincent Moulton if you would like a copy of a publication)


Papers in Refereed Journals


In press

[152] Encoding and constructing 1-nested phylogenetic networks with trinets, K.Huber, V.Moulton. Algorithmica.

[151] PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing, L.Folkes, S.Moxon, H.Woolfenden, M.Stocks, G.Szittya, T.Dalmay, V.Moulton, Nucleic Acids Research.

[150] Reducing ligation bias of small RNAs in libraries for next generation sequencing, K.Sorefan, H.Pais, A.Hall, A.Kozomara, S.Griffith-Jones, V.Moulton, T.Dalmay, Silence.

[149] Trees, tight-spans and point configurations, S.Herrmann, V.Moulton, Discrete Mathematics.

[148] Orthology relations, symbolic ultrametrics, and cographs, M.Hellmuth, M.Hernandez-Rosales, K.Huber, V.Moulton, P.Stadler, N.Wieseke, Journal of Mathematical Biology.

[147] Recognizing treelike k-dissimilarities, S.Herrmann, K.Huber, V.Moulton, A.Spillner, Journal of Classification.

[146] The split decomposition of a k-dissimilarity map, S.Herrmann, V.Moulton, Advances in Applied Mathematics.

[145] The size of 3-compatible, weakly compatible split systems, S.Gruenewald, J.Koolen, V.Moulton, T.Wu, Journal of Applied Mathematics and Computing.

[144] Injective optimal realizations of finite metric spaces, J.Koolen, A.Lesser, V.Moulton, T.Wu, Discrete Mathematics.

[143] FiRePat - Finding Regulatory Patterns between sRNAs and putative target genes, I.Mohorianu, S.Lopez-Gomollon, F.Schwach, T.Dalmay, V.Moulton. WIREs Data Mining and Knowledge Discovery.

[142] The 'Butterfly effect' in Cayley graphs with applications to genomics, V.Moulton, M.Steel, Journal of Mathematical Biology.

[141] Optimal algorithms for computing edge weights in planar split-networks, A.Spillner, V.Moulton, Journal of Applied Mathematics and Computing.



2012

[140] Activation of the innate immune response and interferon signalling in myotonic dystrophy type 1 and type 2 cataracts, J.Rhodes, M.Lott, S.Russell, V.Moulton, J.Sanderson, M.Wormstone, D.Broadway, Human Molecular Genetics, 21(4), 2012, 852-862.

[139] Constructing and drawing planar split networks, A.Spillner, B.Nguyen, V.Moulton, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(2), 2012, 395-407.

[138] Computing evolutionary distinctiveness indices in large scale analysis, I.Martyn, T.Kuhn, A.Mooers, V.Moulton, A.Spillner, Algorithms for Molecular Biology 2012, 7:6.



2011

[137] Blocks and cut vertices of the Buneman Graph, A.Dress, K.Huber, J.Koolen, V.Moulton, SIAM Journal on Discrete Mathematics, 25, 2011, 1902-1919.

[136] Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns, I.Mohorianu, R.Jing, F.Schwach, S.Lopez-Gomollon, G.Szittya, S.Moxon, K.Sorefan, V.Moulton, T.Dalmay, Plant Journal, 67(2), 232-246, 2011.

[135] mRNA expression profiling reveals conserved and non-conserved miR-140 targets, F.Nicolas, H.Pais, F.Schwach, M.Lindow, S.Kauppinen, V.Moulton, T.Dalmay, RNA Biology, 8(4), 607-615, 2011.

[134] Metrics on multi-labeled trees: Interrelationships and diameter bounds, K.Huber, A.Spillner, R.Suchecki, V.Moulton, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(4), 1029-40, 2011.

[133] A 'non-additive' characterization of p-adic norms, A.Dress, J.Kahrstrom, V.Moulton, Annals of Combinatorics, 15, 37–50, 2011.

[132] Identifying and reconstructing lateral transfers from evolutinary distances by applying the Minimum Contradiction Method to Neighbor-Net, M.Thuillard, V.Moulton, Journal of Bioinformatics and Computational Biology, 9(4), 453-470, 2011.



2010

[131] Species, Clusters and the 'Tree of Life': A graph-theoretic perspective, A.Dress, V.Moulton, M.Steel, T.Wu, Journal of Theoretical Biology, 265(4), 535-42, 2010.

[130] RDP3: A flexible and fast computer program for analysing recombination, D.Martin, P.Lemey, M.Lott, V.Moulton, D.Posada, P.Lefeuvre, Bioinformatics, 26(19), 2462-2463, 2010.

[129] Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis, V.Pantaleo, G.Szittya, S.Moxon, L.Miozzi, V.Moulton, T.Dalmay, J.Burgyan, Plant Journal, 62(6), 960-976, 2010.

[128] Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides, F.Nicolas, S.Moxon, J.Haro, S.Calo, I.Grigoriev, S.Torres-Martinez, V.Moulton, R.Ruiz-Vazquez, T.Dalmay, Nucleic Acids Research, 38(16), 5535-5541, 2010.

[127] An algorithm for computing cutpoints in finite metric spaces, A.Dress, K.Huber, J.Koolen, V.Moulton, A.Spillner, Journal of Classification, 27(2), 158-172, 2010.

[126] Analysing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level, H.Pais, F.Nicolas, S.Soond, T.Swingler, I.Clark, A.Chantry, V.Moulton, T.Dalmay, RNA, 16, 489-494, 2010.

[125] Finding sRNA generative locales from high-throughput sequencing data with NiBLS, D.MacLean, V.Moulton, D.Studholme, BMC Bioinformatics, 2010, 11:93.

[124] Distinguishing between hot-Spots and melting-pots of genetic diversity, B.Nguyen, A.Spillner, B.Emerson, V.Moulton, Algorithms in Molecular Biology, 2010, 5:19.

[123] Structural and functional analysis of viral siRNAs, G.Szittya, S.Moxon, V.Pantaleo, G.Toth, R.Pilcher, V.Moulton, J.Burgyan, T.Dalmay, PLoS Pathogens, 2010, 6(4): e1000838.



2009

[122] Detecting recombination and identifying hybrids in viral sequence alignments using a quartet scanning approach, P.Lemey, M.Lott, D.Martin, V.Moulton, BMC Bioinformatics, 2009, 10:126.

[121] There are finitely many regular near polygons and geodetic distance-regular graphs with fixed valency, S.Bang, J.Koolen, V.Moulton, Journal fur die reine und angewandte Mathematik, 635, 2009, 213-235.

[120] The maximum coverage problem and strongly greedy hypergraphs, V.Moulton, A.Spillner, Applied Mathematics Letters, 22(10), 2009, 1496-1499.

[119] Barriers in metric spaces, A.Dress, V.Moulton, A.Spillner, T.Wu, Applied Mathematics Letters, 22(8), 2009, 1150-1153.

[118] PADRE: A Package for Analyzing and Displaying Reticulate Evolution, M.Lott, A.Spillner, K.Huber, V.Moulton, Bioinformatics, 25, 2009, 1199-1200.

[117] Optimal realizations of generic 5-point metrics, J.Koolen, A.Lesser, V.Moulton, European Journal of Combinatorics, 30(5), 2009, 1164-1171.

[116] Consistency of the QNet algorithm for generating planar split graphs from weighted quartets, S.Gruenewald, V.Moulton, A.Spillner, Discrete Applied Mathematics, 157(10), 2009, 2325-2334.

[115] Characterizing weak compatibility in terms of weighted quartets, S.Gruenewald, K.Huber, V.Moulton, C. Semple, A. Spillner, Advances in Applied Mathematics, 42, 2009, 329-341.

[114] Inferring polyploid phylogenies from multiply-labeled gene trees, M.Lott, A.Spillner, K.Huber, A.Petri, B.Oxelman, V.Moulton, BMC Evolutionary Biology, 2009, 9:216.

[113] High throughput sequencing of microRNAs in chicken somites, T.Rathjen, H.Pais, D.Sweetman, V.Moulton, A.Munsterberg, T.Dalmay, FEBS Letters, 583(9), 2009, 1422-1426.

[112] Consistency of phylogenetic tree search algorithms based on the Balanced Minimum Evolution principle, M.Bordewich, O.Gascuel, K.Huber, V.Moulton, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(1), 2009, 110-117.

[111] Maximum parsimony for tree mixtures, S.Gruenewald, V.Moulton, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(1), 2009, 97-102.

[110] Refining phylogenetic trees given additional data: Algorithms based on parsimony, T.Wu, V.Moulton, M.Steel, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(1), 2009, 118-125.

[109] A graph-theoretical invariant of topological spaces, A.Dress, K.Huber, J.Koolen, V.Moulton, Applied Mathematics Letters 22(2), 2009, 159-162.



2008

[108] Experimental identification of microRNA-140 targets by suppressing and over-expressing microRNA-140, F.Molina, H.Pais, F.Schwach, M.Lindow, S.Kauppinen, V.Moulton, T.Dalmay, RNA, 14, 2008, 2513-2520.

[107] Using supernetworks to distinguish hybridization from lineage-sorting, B.Holland, S.Benthin, P.Lockhart, V.Moulton, K.Huber, BMC Evolutionary Biology, 2008, 8:202.

[106] Block realizations of finite metrics and the tight-span construction I: The embedding theorem, A.Dress, K.Huber, J.Koolen, V.Moulton, Applied Mathematics Letters, 21(12), 2008, 1306-1309.

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

[104] High-throughput sequencing of Medicago truncatula short RNAs, G.Szittya, S.Moxon, D.Santos, R.Jing, M.Fevereiro, V.Moulton, T.Dalmay, BMC Genomics, 2008, 9:593.

[103] A toolkit for analysing large-scale plant small RNA datasets, S.Moxon, F.Schwach, D.MacLean, T.Dalmay, D.Studholme, V.Moulton, Bioinformatics, 24, 2008, 2252 - 2253.

[102] Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening, S.Moxon, R.Jing, G.Szittya, F.Schwach, R.Pilcher, V.Moulton, T.Dalmay, Genome Research, 18, 2008, 1602-1609.

[101] Cut points in metric spaces, A.Dress, K.Huber, J.Koolen, V.Moulton, Applied Mathematics Letters, 21(6), 2008, 545-548.

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

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

[98] A scoring matrix approach to detecting miRNA target sites, S.Moxon, V.Moulton, J.Kim, Algorithms in Molecular Biology, 2008, 3:3.

[97] Exploring contradictory phylogenetic relationships in yeast, Q.Wu, S.James, I.Roberts, V.Moulton, K.Huber, FEMS Yeast Research, 8(4), 2008, 641-650.

[96] A regular decomposition of the edge-product space of phylogenetic trees, J.Gill, S.Linusson, V.Moulton, M.Steel, Advances in Applied Mathematics, 41, 2008, 158-176.

[95] Computing phylogenetic diversity for split systems, A.Spillner, B.Nguyen, V.Moulton, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5, 2008, 235-244.

[94] Counting vertices and cubes in median graphs associated to circular split systems, Y.Choe, J.Koolen, K.Huber, V.Moulton, Y.Won, European Journal of Combinatorics, 29(2), 2008, 443-456.

[93] Encoding phylogenetic trees in terms of weighted quartets, S.Gruenewald, K.Huber, V.Moulton, C.Semple, Journal of Mathematical Biology, 56(4), 2008, 465-477.



2007

[92] Boltzmann probability of RNA structural neighbors and riboswitch detection, E.Freyhult, V.Moulton, P.Clote, Bioinformatics, 23, 2007, 2054-2062.

[91] Concerning the relationship between realizations and tight spans of finite metrics, A.Lesser, J.Koolen, V.Moulton, Discrete and Computational Geometry, 38, 2007, 605-614.

[90] Two theorems concerning the Bannai Ito Conjecture, S.Bang, J.Koolen, V.Moulton, European Journal of Combinatorics, 28(7), 2007, 2026-2052.

[89] RNAbor: A web server for RNA structural neighbors, E.Freyhult, V.Moulton, P.Clote, Nucleic Acids Research, 35, 2007, W305 - W309.

[88] Estimating parameters for generalized mass action models using constraint propagation, W.Tucker, Z.Kutalik, V.Moulton, Mathematical Biosciences, 208(2), 2007, 607-620.

[87] Identification of novel short RNAs in tomato (Solanum lycopersicum), R.Rusholme, S.Moxon, N.Pakseresht, V.Moulton, K.Mannington, G.Seymour, T.Dalmay, Planta, 3, 2007, 709-717.

[86] Consistency of the Neighbor-Net algorithm, D.Bryant, V.Moulton, A.Spillner, Algorithms in Molecular Biology, 2007, 2:8.

[85] S-system parameter estimation for noisy metabolic profiles using Newton-flow analysis, Z.Kutalik, W.Tucker, V.Moulton, IET Systems Biology, 1, 2007, 174-180.

[84] Some uses of the Farris Transform in mathematics and phylogenetics - A review, A.Dress, K.Huber, V.Moulton, Annals of Combinatorics, 11, 2007, 1-37.

[83] Untangling complex histories of genome mergings in high polyploids, A.Brysting, B.Oxelman, K.Huber, V.Moulton, C.Brochmann, Systematic Biology, 56, 2007, 467-476.

[82] Optimizing phylogenetic diversity under constraints, V.Moulton, C.Semple, M.Steel, Journal of Theoretical Biology, 246, 2007, 186-194.

[81] Imputing supertrees and supernetworks from quartets, B.Holland, G.Conner, K.Huber, V.Moulton, Systematic Biology, 56, 2007, 57-67.

[80] QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets, S.Gruenewald, K.Forslund, A.Dress, V.Moulton, Molecular Biology and Evolution, 24, 2007, 532-538.

2006

[79] Reconstructing the evolutionary history of polyploids from multi-labelled trees, K.Huber, B.Oxelman, M.Lott, V.Moulton, Molecular Biology and Evolution, 23, 2006, 1784-1791.

[78] Hereditarily optimal realizations of consistent metrics, A.Dress, K.Huber, A.Lesser, V.Moulton, Annals of Combinatorics, 10, 2006, 63-67.

[77] Parameter reconstruction for biochemical networks using interval analysis, W.Tucker, V.Moulton, Reliable Computing, 12(5), 2006, 1-14.

[76] Improved consensus network techniques for genome-scale phylogeny, B.Holland, L.Jermiin, V.Moulton, Molecular Biology and Evolution, 23, 2006, 848-855.

[75] Phylogenetic networks from multi-labeled trees, K.Huber, V.Moulton, Journal of Mathematical Biology, 52(5), 2006, 613-632.

[74] Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos, E.Freyhult, V.Moulton, D.Ardell, Nucleic Acids Research, 34(3), 2006, 905-916.

[73] On the structure of the tight-span of a totally split-decomposable metric, K.Huber, J.Koolen, V.Moulton, European Journal of Combinatorics, 27, 2006, 461-479.

2005

[72] The tight span of an antipodal metric space: Part I - Combinatorial properties, K.T.Huber, J.H.Koolen, V.Moulton, Discrete Mathematics, 303, 2005, 65-79.

[71] A comparison of RNA folding measures, E.Freyhult, P.Gardner, V.Moulton, BMC Bioinformatics, 2005, 6:241.

[70] Bounding the number of hybridisation events for a consistent evolutionary history, M.Baroni, S.Grunewald, V.Moulton, Charles Semple, Journal of Mathematical Biology, 51, 2005, 171-182.

[69] Four characters suffice to convexly define a phylogenetic tree, K.Huber, V.Moulton, M.Steel, SIAM Journal on Discrete Mathematics, 18(4), 2005, 835-843.

[68] Predicting RNA structure using mutual information, E.Freyhult, V.Moulton, P.Gardner, Applied Bioinformatics, 4, 2005, 53-59.

[67] Visualizing conflicting evolutionary hypotheses in large collections of trees using consensus networks, B.Holland, F.Delsuc, V.Moulton, Systematic Biology, 54, 2005, 66-76.

[66] Biogeographic interpretation of split graphs: Least squares optimization of edge lengths, R.Winkworth, D.Bryant, P.Lockhart, D.Havell, V.Moulton, Systematic Biology, 54, 2005, 56-65.

[65] Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling, E.Freyhult, P.Prusis, M.Lapinsh, J.Wikberg, V.Moulton, M.Gustafsson, BMC Bioinformatics, 2005, 6:50.

[64] Tracking down noncoding RNAs, V.Moulton, PNAS, 7, 2005, 2269-2270.

[63] Recovering a phylogenetic tree using pairwise closure operations, K.Huber, V.Moulton, C.Semple, M.Steel, Applied Mathematics Letters, 18, 2005, 361-366.

[62] The MinMax Squeeze: Guaranteeing a minimal tree for population data, B.Holland, K.Huber, D.Penny, V.Moulton, Molecular Biology and Evolution, 22, 2005, 235-242.

[61] 4n-10, A.Dress, J.Koolen, V.Moulton, Annals of Combinatorics, 8, 2005, 463-471.

[60] Delta-additive and Delta-ultra-additive maps, Gromov's trees, and the Farris transform, A.Dress, B.Holland, K.T.Huber, J.H.Koolen, V.Moulton, J.Weyer-Menkhoff, Discrete Applied Mathematics, 146, 2005, 51-73.

2004

[59] VisRD - Visual Recombination Detection, K.Forslund, D.Huson, V.Moulton, Bioinformatics, 20, 2004, 3654-3655.

[58] Peeling phylogenetic 'oranges', V.Moulton, M.Steel, Advances in Applied Mathematics, 33(4), 2004, 710-727.

[57] Using consensus networks to visualize contradictory evidence for species phylogeny, B.Holland, K.Huber, V.Moulton, P.Lockhart, Molecular Biology and Evolution, 21, 2004, 1459-1461.

[56] Replacing cliques by stars in quasi-median graphs, K.Huber, V.Moulton, C.Semple, Discrete Applied Mathematics, 143, 2004, 194-203.

[55] Phylogenetic analysis of the full-length SARS-CoV sequences: Evidence for phylogenetic discordance in three genomic regions, G.Magiorkinis, E.Magiorkinis, D.Paraskevis, A.M. Vandamme, M. Van Ranst, V. Moulton, A.Hatzakiu, Journal of Medical Virology, 74(3), 2004, 369-372.

[54] There are finitely many triangle-free distance-regular graphs with degree 8, 9 or 10, J.Koolen, V.Moulton, Journal of Algebraic Combinatorics, 19, 2004, 205-217.

[53] The tight span of an antipodal metric space: Part II - Geometrical properties, K.T.Huber, J.H.Koolen, V.Moulton, Discrete and Computational Geometry, 31, 2004, 567-586.

[52] NeighborNet: An agglomerative method for the construction of phylogenetic networks, D.Bryant, V.Moulton, Molecular Biology and Evolution, 21, 2004, 255-265.

[51] The structure of spherical graphs, J.Koolen, V.Moulton, D.Stevanovic, European Journal of Combinatorics, 25, 2004, 213-227

2003

[50] Mosaic genomes of the six major Primate lentivirus lineages revealed by phylogenetic and split-decomposition analyses, M.Salemi, T. De Oliveira, V. Courgnaud, V.Moulton, B.Holland, S.Cassol, M.Peeters, A.-M. Vandamme, Journal of Virology, 77, 2003, 7202-7213.

[49] A bound for the number of columns l(c,a,b) in the intersection array of a distance-regular graph, S.Bang, J.Koolen, V.Moulton, European Journal of Combinatorics, 24, 2003, 785-795.

[48] New exploratory methods for visual recombination detection, K.Strimmer, K.Forslund, B.Holland, V.Moulton, Genome Biology, 4, 2003, R33.

[47] Optimal alphabets for an RNA world, P. Gardner, B.Holland, V.Moulton, M.Hendy, D.Penny, The Royal Society Proceedings: Biological Sciences, 270, 2003, 1177-1182.

[46] A search for noncoding RNAs using predicted MFE secondary structures, S.Edvardsson, P.P. Gardner, A.M.Poole, M.D.Hendy, D.Penny, V.Moulton, Bioinformatics, 19, 2003, 865-873.

[45] Maximal energy bipartite graphs, J.Koolen, V.Moulton, Graphs and Combinatorics, 19(1), 2003, 131-135.

[44] Connectivity calculus, D.Cieslik, A.Dress, K.T.Huber, V.Moulton, Applied Mathematics Letters, 16, 2003, 395-399.


2002

[43] Embedding complexity and discrete optimization I: A new divide & conquer approach to discrete optimization, D.Cieslik, A.Dress, K.T.Huber, V.Moulton, Annals of Combinatorics, 6, 2002, 257-273.

[42] Embedding complexity and discrete optimization II: A dynamical programming approach to the Steiner-Tree Problem, D.Cieslik, A.Dress, K.T.Huber, V.Moulton, Annals of Combinatorics, 6, 2002, 275-283.

[41] The relation graph, K.Huber, V.Moulton, Discrete Mathematics, 244, 2002, 153-166.

[40] Antipodal metrics and split systems, A.Dress, K.Huber, V.Moulton, European Journal of Combinatorics, 23, 2002, 187-200.

[39] Quasi-median graphs from sets of partitions, H.-J. Bandelt, K.T.Huber, V.Moulton, Discrete Applied Mathematics, 122, 2002, 23-35.

[38] An explicit computation of the injective hull of certain finite metric spaces in terms of their associated Buneman complex, A.Dress, K.Huber, V.Moulton, Advances in Mathematics, 168, 2002, 1-28.

[37] Hyperbolic bridged graphs, J.Koolen, V.Moulton, European Journal of Combinatorics, 23, 2002, 683-699.

[36] Delta-plots: A tool for the analysis of phylogenetic distance data, B.Holland, K.Huber, A.Dress, V.Moulton, Molecular Biology and Evolution, 19, 2002, 2051-2059.

[35] On a conjecture of Bannai and Ito: There are finitely many distance-regular graphs with degree 5, 6 or 7, J.Koolen, V.Moulton, European Journal of Combinatorics, 23, 2002, 987-1006.

[34] Spectronet: A package for computing spectra and median networks, K.T.Huber, M.Langton, D.Penny, V.Moulton, M.Hendy, Applied Bioinformatics, 1, 2002, 159-161.

[33] On line arrangements in the hyperbolic plane, A.Dress, J.Koolen, V.Moulton, European Journal of Combinatorics, 23, 2002, 549-557. (see also Addendum, European Journal of Combinatorics, 24, 2003, 347).


2001

[32] Maximal energy graphs, J.Koolen, V.Moulton, Advances in Applied Mathematics, 26, 2001, 47-52.

[31] Recombination analysis using directed graphical models, K.Strimmer, C.Wiuf, V.Moulton, Molecular Biology and Evolution, 18, 2001, 97-99.

[30] Totally decomposable metrics of combinatorial dimension two, A.Dress, K.Huber, V.Moulton, Annals of Combinatorics, 5, 2001, 99-112.

[29] Pruned median networks: a technique for reducing the complexity of median networks, K.Huber, V.Moulton, P.Lockhart, A.Dress, Molecular Phylogenetics and Evolution, 19 (2), 2001, 302-310.

[28] On the hyperbolicity of chordal graphs, G.Brinkmann, J.Koolen, V.Moulton, Annals of Combinatorics, 5, 2001, 61-69.

[27] Six points suffice: How to check for metric consistency, A.Dress, K.Huber, J.Koolen, V.Moulton, European Journal of Combinatorics, 22, 2001, 465-474.

[26] 2nk-{(2k+1) choose 2}: A Note on Extremal Combinatorics of Cyclic Split Systems, A.Dress, M.Klucznik, J.Koolen, V.Moulton, Seminaire Lotharingien de Combinatoire, 47, 2001 (http://www.mat.univie.ac.at/~slc).


2000

[25] Evolutionary rate and genetic drift of hepatitis C virus are poorly correlated with the host immune response: studies of infected donor-recipient clusters, J.-P. Allain, Y.Dong, A.-M. Vandamme, V.Moulton, M.Salemi, Journal of Virology, 74(6), Mar. 2000, 2541-25.

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

[23] Estimating and approximating the total pi-electron energy of benzenoid hydrocarbons, I. Gutman, J.Koolen, V.Moulton, M.Parac, T.Soldatovic, D.Vidovic, Zeitschrift fur Naturforschung, 55a, 2000, 507-512.

[22] On the tight span of an antipodal graph, O.Goodmann, V.Moulton, Discrete Mathematics, 218, 2000, 73-96.

[21] More hyperenergetic molecular graphs, J.Koolen, V.Moulton, I.Gutman, D.Vidovic, Journal of the Serbian Chemical Society, 65(8), 2000, 571-575.

[20] Affine maps that induce polytopal complex isomorphisms, A.Dress, K.Huber, V.Moulton, Discrete and Computational Geometry, 24, 2000, 49-60.

[19] A classification of the six-point prime metrics, J.Koolen, V.Moulton, U.Toenges, European Journal of Combinatorics, 21, 2000, 815-829.

[18] Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP, L.Collins, V.Moulton, D.Penny, Journal of Molecular Evolution, 51, 2000, 194-204.

[17] RNA folding argues against a hot-start origin of life, V.Moulton, G.Jameson, P.Gardner, L.Creamer, R.Pointon, D.Penny, Journal of Molecular Evolution, 51, 2000, 416-421. Mathematics, Editor's Choice, 1999 Edition.

[16] Improving the McClelland inequality for total pi-electron energy, J.Koolen, V.Moulton, I.Gutman, Chemical Physics Letters, 320/3-4, 2000, 213-216.

[15] Metrics on RNA secondary structures, V.Moulton, M.Zuker, M.Steel, R.Pointon, D.Penny, Journal of Computational Biology, 7, 2000, 277-292.

[14] An exceptional split geometry, A.Dress, K.Huber, V.Moulton, Annals of Combinatorics, 4, 2000, 1-11.


1999

[13] A polynomial time algorithm for constructing the refined Buneman tree, D.Bryant, V.Moulton, Applied Mathematics Letters, 12, 1999, 51-56.

[12] Retractions of finite distance functions onto tree metrics, V.Moulton, M.Steel, Discrete Applied Mathematics, 91, 1999, 215-233. Also appearing in Discrete Applied Mathematics, Editor's Choice, 1999 Edition.


1998

[11] Hopf-Braid groups, V.Moulton, Journal of Knot Theory and its Ramifications, 7, No. 8, 1998, 1107-1117.

[10] A comparison between the median and the tight-span completion of finite split systems, A.Dress, K.Huber, V.Moulton, Annals of Combinatorics, 2, 1998, 299-311.

[9] The coherency index, J.Koolen, V.Moulton, U.Toenges, Discrete Mathematics, 192, 1998, 205-222.

[8] Vector braids, Journal of Pure and Applied Algebra, V.Moulton, 131, 1998, 245-296.


1997

[7] A note on the uniqueness of coherent decompositions, J.Koolen, V.Moulton, Advances in Applied Mathematics, 19, 1997, 444-449.

[6] DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment, J.Stoye, V.Moulton, A.Dress, Computer Applications in the Biosciences, 13, 1997, 625-626.

[5] On the number of vertices and edges of the Buneman graph, A.Dress, M.Hendy, K.Huber, V.Moulton, Annals of Combinatorics, 1, 1997, 329-337.

[4] Some variations on a theme by Buneman, A.Dress, K.Huber, V.Moulton, Annals of Combinatorics, 1, 1997, 339-352.

[3] Trees, taxonomy and strongly compatible multi-state characters, A.Dress, V.Moulton, M.Steel, Advances in Applied Mathematics, 19, 1997, 1-30.


1996

[2] T-Theory, A.Dress, V.Moulton, W.Terhalle, The European Journal of Combinatorics, 17, 1996, 161-175.

[1] Analyzing and visualizing sequence and distance data using SplitsTree, A.Dress, D.Huson, V.Moulton, Discrete Applied Mathematics, 71, 1996, 95-110.


Papers in Refereed Conference Proceedings


[13] Computing a consensus of multilabeled trees, K.T.Huber, V.Moulton, A.Spillner, S.Storandt, R.Suchecki, Algorithm Engineering and Experiments (ALENEX12), SIAM, 84-92, 2012.

[12] Constructing phylogenetic supernetworks from quartets, S.Gruenewald, A.Spillner, K.Forslund, V.Moulton, WABI 2008, Lecture Notes in Computer Science 5251, Springer Berlin/Heidelberg, 2008, 284-295.

[11] Time series data mining algorithms for identifying short RNA in Arabidopsis thaliana, A.Bagnall, S.Moxon, D.Studholme, V.Moulton, BIOCOMP'08.

[10] An algorithm for computing virtual cut points in finite metric spaces, A.Dress, K.Huber, J.Koolen, V.Moulton, COCOA 2007, Lecture Notes in Computer Science 4616, Springer Berlin/Heidelberg, 2007, 4-10.

[9] Reconstructing metabolic networks using interval analysis, W.Tucker, V.Moulton, WABI 2005, Lecture Notes in Computer Science 3692, Springer Berlin/Heidelberg, 2005, 192-203.

[8] Exploration of germplasm resources: progress and results from the application of molecular markers to the whole JIC Pisum collection, M. Ambrose, M. Knox, A.Vershinin, A. Flavell, V. Moulton, T.N. Ellis, Proceedings of the 5th European Conference on Grain Legumes & 2nd International Conference on Legume Genomics and Genetics, Dijon, 7-11 June 2004, 157-160.

[7] Consensus networks: A method for visualising incompatibilities in collections of trees, B.Holland, V.Moulton, WABI 2003, Lecture Notes in Computer Science 2812, Springer Berlin/Heidelberg, 2003, 165-176.

[6] Four characters suffice, K.Huber, V.Moulton, M.Steel, proceedings of Formal Power Series and Algebraic Combinatorics 2003 (FPSAC'03), in press.

[5] NeighborNet: an agglomerative method for the construction of planar phylogenetic networks, D.Bryant, V.Moulton, WABI 2002, Lecture Notes in Computer Science 2452, Springer Berlin/Heidelberg, 2002, 375-391.

[4] Metric spaces in pure and applied mathematics, A.Dress, K.T.Huber, V.Moulton, Documenta Mathematica, Quadratic Forms LSU, 2001, 121-139.

[3] Hereditarily optimal realizations: Why are they relevant in phylogenetic analysis, and how does one compute them? A.Dress, K.Huber, V.Moulton, In; Algebraic Combinatorics and its Applications, Eds A.betten, A,Kohnert, R.Laue, A.Wasserman, Springer, 2001, pp 110-117.

[2] Some new perspectives regarding sparse continuous models for discrete data structures, A.Dress, K.Huber, V.Moulton, OSDA98 Ordinal and Symbolic Data Analysis, University of Massachusetts (Amherst, MA 01003, USA) September 28-30, 1998 Guest Editor: Melvin F. Janowitz, Electronic Notes in Discrete Mathematics, , 2, 1998.

[1] Dissimilarity maps and substitution models, V.Moulton, M.Steel, C.Tuffley, In; Mathematical Hierarchies and Biology: Dimacs Workshop, November 13-15, 1996 (Dimacs Series in Discrete Mathematics and Theoretical Computer Science), Eds B.Mirkin, F.McMorris, F.Roberts, 37, 1997, pp 111-131.


Books

[1] Basic Phylogenetic Combinatorics, A.Dress, K.Huber, J.Koolen, V.Moulton, A.Spillner, Cambridge University Press, 2012.

[2] Algorithms in Bioinformatics, 10th International Workshop, WABI 2010, Liverpool, UK, September 6-8, 2010, Proceedings, V.Moulton, M.Singh (Eds), Springer, 2010.


Book Chapters/Reviews


[6] Small RNA discovery and characterization in eukaryotes using high throughput approaches, H.Pais, S.Moxon, T.Dalmay, V.Moulton, in "RNA Infrastructure and Networks", ed. L.Collins, Landes Bioscience, 2011.

[5] A topological approach to tree (re-)construction, A.Dress, V.Moulton, T.Wu. In: The Math of Flu, Shaker Verlag, Aachen 2010.

[4] Deciphering the diversity of small RNAs in plants: the long and short of it, F.Schwach, S.Moxon, V.Moulton, T.Dalmay, Briefings in Functional Genomics and Proteomics, 8(6), 2009, 472-481.

[3] Split Networks. A tool for exploring complex evolutionary relationships in molecular data, V.Moulton, K.Huber, In: The Phylogenetic Handbook, 2nd edition, Ed.s P.Lemey, M.Salemi, A.-M. Vandamme, Cambridge University Press, 2009.

[2] Phylogenetic networks, K.Huber, V.Moulton. In: Mathematics of Evolution, Ed. O.Gascuel, Oxford University Press, 2005, pp.178-200.

[1] SplitsTree: A network based tool for exploring evolutionary relationships in molecular data, V.Moulton. In: The Phylogenetic Handbook, Ed.s M.Salemi, A.-M. Vandamme, Cambridge University Press, 2003, pp. 312-328


Communications


[11] I.Mohorianu, V.Moulton, Revealing biological information using data structuring and automated learning, Recent Pat DNA Gene Seq, 4(3), 181-91, 2010.

[10] Statistical analysis of the growth and morphology of the filamentous microbe Streptomyces coelicolor, R.Leggett, S.Grandison, R.Morris, G.Kelemen, V.Moulton, In A.Gusnanto, K.Mardia, C.Fallaize (eds), Statistical Tools for Challenges in Bioinformatics, pp.107-110. Leeds, Leeds University Press, 2009.

[9] Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update, E.Freyhult, S.Edvardsson, I.Tamas, V.Moulton, A.Poole BMC Research Notes, 1:49, 2008.

[8] Reconstructing the tree of life, D.Huson, V.Moulton, M.Steel, Plus Magazine, Issue 46, 2008.

[7] Final report for the Phylogenetics programme, D.Huson, V.Moulton, M.Steel, Isaac Newton Institute for Mathematical Sciences, Programme Reports, 2008.

[6] Imputing supertrees and supernetworks from quartets, B.R.Holland, G. Conner, K.T. Huber, V. Moulton. In: 6th Workshop on Algorithms in Bioinformatics (WABI 2006) Eds B. Moret and P. Buchner, Lecture Notes in Bioinformatics 4175, 2006, 162.

[5] Preface to Special Issue on Phylogenetic Combinatorics, V.Moulton, Annals of Combinatorics, 10, 2006.

[4] Representing all finite metrics, J.Koolen, V.Moulton, Problems on discrete metric spaces (pp. 833-834), Ed. P.Cameron, European Journal of Combinatorics, 21, 2001, 831-838.

[3] Splits Tree: A tool for analyzing viral evolution, V.Moulton, Abstracts from the fourth european workshop on virus evolution and molecular epidemiology Rega Institute for Medical Research, Leuven, Belgium, The Infectious Disease Review, 1(1), 1999.

[2] The T-construction and the Buneman complex, V.Moulton, communication to 2nd Combinatorial Methods conference, Porto, Portugal 1998.

[1] On coherent decompositions of metric spaces, J.Koolen, V.Moulton, communication to Algebraic Combinatorics conference, Yamagata, Japan 1998.


Submitted


[1] There are only finitely many distance-regular graphs of fixed valency greater than two, S.Bang, A.Dubickas, J.Koolen, V.Moulton.

[2] Obtaining splits from cut sets of tight spans, A.Dress, V.Moulton, A.Spillner, T.Wu.

[3] Generating functions for multi-labeled trees, E.Czabarka, P.L.Erdos V.Johnson, V.Moulton.

[4] Optimal realisations of two-dimensional, totally decomposable metrics, S.Herrmann, J.Koolen, A.Lesser, V.Moulton, T.Wu.

[5] Mutual exclusion and temporal regulation are both prevalent modes of action by plant, S.Lopez-Gomollon, I.Mohorianu, G.Szittya, V.Moulton, T.Dalmay.

[6] Computational modelling of the regulatory network organising the wound response in Arabidopsis thaliana, J.Kim, A.Camargo, A.Devoto, V.Moulton, J.Turner.

[7] Evolution of trans-acting siRNA producing genes in plants, G.Szittya, S.Moxon, I.Mohorianu, T.Csorba, L.Cano, S.Kamoun, V.Moulton, Y.Eshed, T.Dalmay.

[8] On patchworks and hierarchies, A.Dress, V.Moulton, M.Steel, T.Wu.

[9] Novel distances for Dollo data, M.Woodhams, D.Steane, R.Jones, D.Nicolle, V.Moulton. B.Holland.

[10] Searching for realizations of finite metric spaces in tight spans, S.Herrmann, V.Moulton, A.Spillner.

[11] The UEA sRNA Workbench: A suite of tools for analysing and visualising next generation sequencing microRNA and small RNA datasets, M.Stocks, S.Moxon, D.Mapleson, H.Woolfenden, I.Mohorianu, L.Folkes, F.Schwach, T.Dalmay, V.Moulton


Preprints

(only those preprints that are significantly different from the publications above are listed)


[1] Fast and accurate approximation to sums-of-pairs score simultaneous alignment, J.Stoye, V.Moulton, S.Perrey, Technical Report, FSPM, Bielefeld University, Germany, 1997.

[2] On simultaneous versus iterative sequence alignment, A.Dress, S.Perrey, V.Moulton, J.Stoye, Technical Report, FSPM, Bielefeld University, Germany, 1997.

[3] Crinkled zonotopes, V.Moulton, I.Da Silva, Report 3, Mathematics Department, Mid Sweden University, 1998.

[4] RNA secondary structure as an identification tool in the identification of putative pRNA sequences in the chloroplasts of four green plant species, L.Collins, V.Moulton, D.Penny, Report 3, Mathematics Department, Mid Sweden University, 1999.

[5] Plant Dispersal N.E.W.S. from the South Pacific, R.Winkworth, S.Wagstaff, D.Glenny, J.Grau, V.Moulton, P.Lockhart, Report 11, Mathematics Department, Mid Sweden University, 2000.


Vincent Moulton
Computational Biology Laboratory,
School of Computing Sciences,
University of East Anglia,
Norwich, NR4 7TJ, UK.

Updated 040512