Article

Dress, AWM, Huber, KT and Steel, M (2012) ‘Lassoing’ a phylogenetic tree I: basic properties, shellings, and covers. Journal of Mathematical Biology, 65 (1). pp. 77-105. 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

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.

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

Popescu, A-A, Huber, KT and Paradis, E (2012) ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics, 28 (11). pp. 1536-1537. 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

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)

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

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.

Huber, K. T., van Iersel, L., Kelk, S. and Suchecki, R. (2010) A practical algorithm for reconstructing level-1 phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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.

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).

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.

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

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.

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

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

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

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.

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.

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

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

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

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

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

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

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

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

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

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

Cieslik, D., Dress, A., Huber, K. T. and Moulton, V. (2003) Connectivity calculus. Applied Mathematics Letters, 16 (3). pp. 395-399. ISSN 0893-9659

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

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

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

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

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

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

Book Section

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

Conference or Workshop Item

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.