Katharina T. Huber's list of publications.

Katharina Huber's list of publications (some publications are available for download at the UEA Digital Repository, otherwise please do not hesitate to contact Katharina Huber if you would like a copy of a publication)

In press

[63] ape 3.0: new tools for distance based phylogenetics and evolutionary analysis in R. A.-A. Popescu, K.T. Huber, E. Paradis Bioinformatics.

[62] Orthology Relations, Symbolic Ultrametrics, and Cographs. M. Hellmuth, M. Hernandez-Rosales, K. T. Huber, V. Moulton, P. F. Stadler, N. Wieseke. Journal of Mathematical Biology.

[61] Computing a consensus of multilabeled trees, K. T. Huber, V. Moulton, A. Spillner, S. Storandt, R. Suchecki. Meeting on Algorithm Engineering & Experiments (ALENEX12).

[60] Blocks and cut vertices of the Buneman Graph. A. Dress, K.T. Huber, J. Koolen, V. Moulton. SIAM Journal on Discrete Mathematics.

Submitted

Recognizing Treelike $k$-Dissimilarities. S. Herrmann, K. T. Huber, V. Moulton, A. Spillner.

Encoding and constructing 1-nested phylogenetic networks with trinets. K.T. Huber, V. Moulton.

Publications in international journals

2012

[59] On encodings of phylogenetic networks of bounded level. P. Gambette, K.T. Huber. Journal of Mathematical Biology. 65(1) 157-180.

[58] 'Lassoing' a phylogentic tree I: Basic properties, shellings and covers. A.W.M. Dress, K.T. Huber, M. Steel. Journal of Mathematical Biology. 65(1) 77-105.

2011

[57] Metrics on multi-labelled trees: interrelationships and diameter bounds. K.T. Huber, A. Spillner, R. Suchecki, V. Moulton. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(4) 1029-1040.

[56] A practical algorithm for reconstructing level-1 phylogenetic networks, K. T. Huber, L. van Iersel, S. Kelk, R. Suchecki. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(3) 635-649.

2010

[55] Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. J. Byrka, P. Gawrychowski, K.T. Huber, S. Kelk. Journal of Discrete Algorithms. 8(1) (2010) 65-75.

[54] Functional significance may underlie the taxonomic utility of single amino acid substituions in conserved proteins K.M. Tyler, G. Wagner, Q. Wu, K.T. Huber. Journal of Molecular Evolution. 70(4) (2010) 495-402.

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

2009

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

[51] PADRE: A package for analyzing and displaying reticulate evolution. M. Lott, A. Spillner, K.T. Huber, A. Petri, B. Oxelman, V.Moulton. Bioinformatics. 25(9) (2009) 1199-1200.

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

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

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

2008

[47] Two new closure rules for constructing phylogenetic super-networks. S. Gruenewald, K.T. Huber, Q. Wu. Bulletin of Mathematical Biology. 70(7) (2008) 1906-1924.

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

[45] Using supernetworks to distinghish hybridization from lineage-sorting. B.R. Holland, S. Benthin, P.J. Lockhart, V. Moulton, K.T. Huber. BMC Evolutionary Biology. 8 (2008) 202pp.

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

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

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

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

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

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

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

2007

[37] An algorithm for computing virtual cut points in finite metric spaces A.W.M. Dress, K.T.Huber, J.Koolen, V.Moulton. Lecture Notes in.Computer Science 4616 (2007) 4-10.

[36] Untangling complex histories of genome mergings in high polyploids A.K.Brysting, B.Oxelman, K.T.Huber, V.Moulton, C. Brochmann. Systematic Biology. 56(1) (2007) 467-476.

[35] Imputing supertrees and supernetworks from quartets, B.R.Holland, G. Conner, K.T. Huber, V. Moulton. Systematic Biology. 56(1) (2007) 57-67.

[34] Some uses of the Farris transform in mathematics and phylogenetics - a review, A. Dress, K. T. Huber, and V. Moulton, Annals of Combinatorics 11(1) (2007).

2006

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

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

[31] On the structure of the tight-span of a totally split-decomposable metric, K.T. Huber, J. Koolen, and V. Moulton. European Journal of Combinatorics. 27(3) (2006) 461-479.

[30] A novel insight into the perfect phylogeny problem, S. Gruenewald and K.T. Huber. Annals of Combinatorics. 10(1) (2006) 97-109.

[29] Hereditarily optimal realizations of consistent metrics, A. Dress, K.T. Huber, A. Lesser, and V. Moulton. Annals of Combinatorics. 10(1) (2006) 63-76.

2005

[28] Identifying phylogenetic trees, M. Bordewich, K.T. Huber, and C. Semple. Discrete Mathematics. 300(1-3) (2005) 30 - 43.

[27] The tight span of an antipodal metric space: Part I -- Combinatorial properties, K.T. Huber, J. Koolen, and V. Moulton. Discrete Mathematics18(303) (2005) 65 - 79.

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

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

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

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

2004

[22] Recovering trees from well-separated multi-state characters, K.T. Huber. Discrete Mathematics, 278 (2004) 151-164.

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

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

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

2003

[18] Connectivity calculus, D. Cieslik, A. Dress, K.T. Huber and V. Moulton Applied Mathematics Letters, 16(3) (2003) 395-399

2002

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

[16] Spectronet: A package for computing spectra and median networks, K. T. Huber, M. Langton, D. Penny, V. Moulton and M. Hendy Applied Bioinformatics 1(3), (2002) 159-161.

[15] $\delta$ -Plots: A tool for the analysis of phylogenetic distance data, B. R Holland, K.T. Huber, A. Dress and V. Moulton Journal of Molecular Biology and Evolution, 19(12), (2002) 2041-2059.

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

[13] Antipodal metrics and split systems, A. Dress, K.T. Huber and V. Moulton European Journal of Combinatorics, 23(2), (2002) 187-200.

[12] The relation graph K.T. Huber and V. Moulton Discrete Mathematics, 244(1-3), (2002) 153-166.

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

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

2001

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

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

[7] Totally split-decomposable metrics of combinatorial dimension two, A. Dress, K.T. Huber and V. Moulton Annals of Combinatorics, 5 (2001) 97-112.

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

2000

[5] Affine maps that induce polyhedral complex isomorphisms, A. Dress, K.T. Huber and V. Moulton Discrete Computational Geometry 24 (2000) 49-65.

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

1998

[3] A comparison between two distinct models in projective cluster theory: The median and the tight-span construction, A. Dress, K.T. Huber and V. Moulton Annals of Combinatorics 2 (1998) 299-311.

1997

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

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

Publicatons in refereed conference proceedings

[6] A GRASP-based approach for the Pure Parsimony Haplotype Inference Problem, R. Suchecki, P. Chardaire, and K.T. Huber, Proceedings of 2nd Computer Science and Electronic Engineering Conference (CEEC'10), (2010).

[5] Imputing supertrees and supernetworks from quartets, (1 page abstract) B.R.Holland, G. Conner, K.T. Huber, and V. Moulton. In: 6th Workshop on Algorithms in Bioinformatics (WABI 2006) Eds B. Moret and P. Buchner, Lecture Notes in Bioinformatics. 4175 (2006) 162.

[4] Four characters suffice, K.T. Huber, V. Moulton, and M. Steel, In: Proceedings of Formal Power Series and Algebraic Combinatorics (FPSAC 2003), Eds. K. Eriksson and S. Linusson, Linköpings universitet (2003) 133-139.

[3] Metric spaces in pure and applied mathematics, A. Dress, K.T. Huber and V. Moulton Documenta Mathematica, Special Volume Proceedings Quadratic Forms LSU (2001) 121-139.

[2] Hereditarily optimal realizations: Why are they relevant in phylogenetric analysis and how does one compute them?, A. Dress, K.T. Huber and V. Moulton, In: Algebraic combinatorics and its applications (ALCOMA99), Ed.s A. Betten, A. Kohnert, R. Laue and A. Wasserman Springer, 110-117.

[1] Some new perspectives regarding sparse continuous models for discrete data structures. A. Dress, K.T. Huber and V. Moulton, Proceedings of OSDA98 Ordinal and Symbolic Data Analysis, Electronic Notes in Discrete Mathematics 2 (1998).

Books

Basic Phylogenetic Combinatorics, A. Dress, K.T. Huber, J.Koolen, V.Moulton, A. Spillner, Cambrige University Press.

Book chapters

[3] Identifying and defining trees, S.Gruenewald and K.T. Huber, In: Reconstructing evolution: New mathematical and computational advances, eds: O. Gascuel and M. Steel, Oxford University Press.

[2] Network analyses for exploring evolutionary relationships, V.Moulton and K.T.Huber, In: The Phylogenetic Handbook , 2nd edition.

[1] Phylogenetic networks, K. T. Huber and V. Moulton, In: Mathematics of Evolution and Phylogeny, Eds: O. Gascuel, Oxford University Press, 2005.

Book reviews

Dissections: Plane & Fancy, by G. F. Frederickson: K.T. Huber. New Zealand Mathematical Society Newsletter 74 (1998).

Preprints
[3] Some new techniques in statistical geometry with applications to virus data, B.R. Holland, K.T. Huber, A. Dress and V. Moulton, Mid Sweden University preprint (2001).

[2] Upper bounds on the order, size and dimension of a Buneman graph, M.D. Hendy, K.T. Huber, F.M. Dong, C.H.C. Little and K.L. Teo, Massey University preprint (2000).

[1] Lite Buneman networks: A technique for studying plant speciation, A. Dress, K.T. Huber, P. Lockhart and V. Moulton, Mid Sweden University preprint (1999).

Involvement in software development