Items where Research Group is "Phylogenetics (former - to 2018)

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Dress, Andreas W. M., Huber, Katharina T. and Steel, Mike (2012) ‘Lassoing’ a phylogenetic tree I: basic properties, shellings, and covers. Journal of Mathematical Biology, 65 (1). pp. 77-105. ISSN 0303-6812

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

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

Gruenewald, S and Huber, Katharina T. (2012) Identifying and defining trees. In: Reconstructing evolution: New Mathematical and computational advances. UNSPECIFIED.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Popescu, Andrei-Alin, Huber, Katharina T. and Paradis, Emmanuel (2012) ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics, 28 (11). pp. 1536-1537. ISSN 1367-4803

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

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

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

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