Items where School is "University of East Anglia > Faculty of Science > Research Groups > Computational Biology (subgroups are shown below) > Phylogenetics

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Number of items at this level: 152.

A

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.

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

B

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

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

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

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

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

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

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

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

Bordewich, M., Huber, K. T. and Semple, C. (2005) Identifying phylogenetic trees. Discrete Mathematics, 300 (1-3). pp. 30-43. ISSN 0012-365X

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

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

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

Brysting, A., Oxelman, B., Huber, K. T., Moulton, V. and Brochmann, C. (2007) Untangling complex histories of genome mergings in high polyploids. Systematic Biology, 56 (3). pp. 467-476. ISSN 1063-5157

Buchheim, C, Cameron, PJ and Wu, T (2009) On the subgroup distance problem. Discrete Mathematics, 309 (4). pp. 962-968. ISSN 1872-681X

Byrka, Jaroslaw, Gawrychowski, Pawel, Huber, Katharina T. and Kelk, Steven (2010) Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. Journal of Discrete Algorithms, 8 (1). pp. 65-75. ISSN 1570-8667

C

Cameron, PJ and Wu, T (2010) The complexity of the weight problem for permutation and matrix groups. Discrete Mathematics, 310 (3). pp. 408-416. ISSN 1872-681X

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.

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

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

E

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

F

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

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

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

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

Freyhult, E., Gardner, P. and Moulton, V. (2005) A comparison of RNA folding measures. BMC Bioinformatics, 6. ISSN 1471-2105

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

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

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. ISSN 1471-2105

G

Gambette, Philippe, Huber, K. T. and Kelk, S. (2017) On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters. Journal of Mathematical Biology, 74 (7). 1729–1751. ISSN 0303-6812

Gambette, Philippe and Huber, KT (2012) On encodings of phylogenetic networks of bounded level. Journal of Mathematical Biology, 65 (1). pp. 157-180. ISSN 0303-6812

Gambette, Philippe, Huber, Katharina T. and Scholz, Guillaume E. (2017) Uprooted Phylogenetic Networks. Bulletin of Mathematical Biology, 79 (9). 2022–2048. ISSN 0092-8240

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. ISSN 0196-8858

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

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.

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.

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

Grünewald, S. and Huber, K. T. (2006) A novel insight into the perfect phylogeny problem. Annals of Combinatorics, 10 (1). pp. 97-109. ISSN 0218-0006

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

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. ISSN 0196-8858

Grünewald, S., Huber, Katharina T. and Wu, Qiong (2008) Two novel closure rules for constructing phylogenetic super-networks. Bulletin of Mathematical Biology, 70 (7). pp. 1906-1924. ISSN 0092-8240

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

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

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

H

Hellmuth, M, Hernandez-Rosales, M, Huber, KT, Moulton, V, Stadler, PF and Wieseke, N (2013) Orthology relations, symbolic ultrametrics and cographs. Journal of Mathematical Biology, 66 (1-2). pp. 399-420.

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.

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) Trees, tight-spans and point configurations. Discrete Mathematics, 312 (16). pp. 2506-2521. ISSN 1872-681X

Herrmann, S and Moulton, V (2012) The split decomposition of a k-dissimilarity map. Advances in Applied Mathematics, 49 (1). pp. 39-56. ISSN 0196-8858

Herrmann, Sven, Koolen, J, 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

Herrmann, Sven and Moulton, Vincent (2014) Computing the blocks of a quasi-median graph. Discrete Applied Mathematics, 179. pp. 129-138. ISSN 0166-218X

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

Huber, K. T. (2004) Recovering trees from well-separated multi-state characters. Discrete Mathematics, 278 (1-3). pp. 151-164. ISSN 0012-365X

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

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

Huber, K. T., Koolen, J., Moulton, V. and Spillner, A. (2008) Characterizing cell-decomposable metrics. Electronic Journal of Combinatorics, 15 (1). N7. ISSN 1077-8926

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

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. ISSN 1557-8666

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

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. and Moulton, V. (2002) The relation graph. Discrete Mathematics, 244 (1-3). pp. 153-166. ISSN 0012-365X

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

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

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., Van Iersel, L., Moulton, V. and Wu, T. (2015) How much information is needed to infer reticulate evolutionary histories? Systematic Biology, 64 (1). pp. 102-111. ISSN 1063-5157

Huber, K. T., Watson, E. E. and Hendy, M. D. (2001) An algorithm for constructing local regions in a phylogenetic network. Molecular Phylogenetics and Evolution, 19 (1). pp. 1-8. ISSN 1055-7903

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

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

Huber, Katharina and Scholz, Guillaume (2018) Beyond representing orthology relations by trees. Algorithmica, 80 (1). 73–103. ISSN 0178-4617

Huber, Katharina, van Iersel, L., 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 T. and Kettleborough, George (2015) Distinguished minimal topological lassos. SIAM Journal on Discrete Mathematics, 29 (2). 940–961. ISSN 0895-4801

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

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, 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.

Huber, Katharina T. and Steel, Mike (2014) Reconstructing fully-resolved trees from triplet cover distances. Electronic Journal of Combinatorics, 21 (2). ISSN 1077-8926

Humphries, Peter J. and Wu, Taoyang (2013) On the Neighborhoods of Trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (3). pp. 721-728. ISSN 1545-5963

K

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

Kettleborough, George, Dicks, Jo L., Roberts, Ian N. and Huber, Katharina T. (2015) Reconstructing (super)trees from data sets with missing distances: Not all is lost. Molecular Biology and Evolution, 32 (6). pp. 1628-1642. ISSN 0737-4038

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

Koolen, J. and Moulton, V. (2002) Hyperbolic bridged graphs. European Journal of Combinatorics, 23 (6). pp. 683-699. ISSN 0195-6698

Koolen, J. and Moulton, V. (2003) Maximal energy bipartite graphs. Graphs and Combinatorics, 19 (1). pp. 131-135. ISSN 0911-0119

Koolen, J. and Moulton, V. (2001) Maximal energy graphs. Advances in Applied Mathematics, 26 (1). pp. 47-52. ISSN 0196-8858

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

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

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

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 1872-681X

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

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

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

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

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

L

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. ISSN 1471-2105

Li, Si, Choi, Kwok Pui, Wu, Taoyang and Zhang, Louxin (2013) Maximum Likelihood Inference of the Evolutionary History of a PPI Network from the Duplication History of Its Proteins. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (6). pp. 1412-1421. ISSN 1545-5963

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, 236 (6). pp. 1875-1887. ISSN 0032-0935

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. ISSN 1471-2148

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

M

MacLean, D., Moulton, V. and Studholme, D. (2010) Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics, 11. ISSN 1471-2105

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

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

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

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

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

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

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

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. ISSN 1557-8666

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, 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

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

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

Moulton, Vincent and Steel, Mike (2004) Peeling phylogenetic 'oranges'. Advances in Applied Mathematics, 33 (4). pp. 710-727. ISSN 0196-8858

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

Moulton, Vincent and Wu, Taoyang (2015) A parsimony-based metric for phylogenetic trees. Advances in Applied Mathematics, 66. 22–45. ISSN 0196-8858

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

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

N

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

P

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

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. ISSN 1365-313X

Penso-Dolfin, L, Wu, Taoyang and Greenman, C (2015) The Combinatorics of Tandem Duplication. Discrete Applied Mathematics, 194. 1–22. ISSN 0166-218X

Popescu, Andrei-Alin and Huber, Katharina (2015) PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS. Bioinformatics, 31 (21). pp. 3552-3554. ISSN 1367-4803

Popescu, Andrei-Alin and Huber, Katharina T. (2013) Lassoing and corralling rooted phylogenetic trees. Bulletin of Mathematical Biology, 75 (3). pp. 444-465. ISSN 0092-8240

R

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

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. ISSN 1460-2083

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

S

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

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). ISSN 1758-907X

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

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

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

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. ISSN 1471-2164

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

Székely, LA, Wang, H and Wu, T (2011) The sum of the distances between the leaves of a tree and the ‘semi-regular’ property. Discrete Mathematics, 311 (13). pp. 1197-1203. ISSN 1872-681X

T

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

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

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

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

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

Tyler, KM, Wagner, GK, Wu, Q and Huber, KT (2010) Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins. Journal of Molecular Evolution, 70 (4). pp. 395-402. ISSN 1432-1432

V

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

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

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

W

Wade, Amy S. I., Barov, Boris, Burfield, Ian J., Gregory, Richard D., Norris, Ken, Vorisek, Petr, Wu, Taoyang and Butler, Simon (2014) A Niche-Based Framework to Assess Current Monitoring of European Forest Birds and Guide Indicator Species' Selection. PLoS ONE, 9 (5). ISSN 1932-6203

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

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

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. ISSN 1567-1364

Wu, T, Cameron, P and Riis, S (2009) On the guessing number of shift graphs. Journal of Discrete Algorithms, 7 (2). pp. 220-226.

Wu, T and Zhang, L (2011) Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree. BMC Bioinformatics, 12 (Suppl 9). ISSN 1471-2105

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

Z

Zhu, Sha, Than, Cuong and Wu, Taoyang (2014) Clades and clans: a comparison study of two evolutionary models. Journal of Mathematical Biology, 71 (1). pp. 99-124. ISSN 0303-6812

This list was generated on Sat Dec 15 07:17:57 2018 GMT.