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Publications

Publications from the Huson lab, sorted by year and author.

2012

Huson, DH and Scornavacca, C (2012).
Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks
Systematic Biology.

Lanzen, A, Joergensen, SL, Huson, DH, Gorfer, M, Grindhaug, SH, Jonassen, I, Ovreas, L, and Urich, T (2012).
CREST - A Classification Resources for Environmental Sequence Tags
PLoS ONE, 7(11):e49334.

2011

Albrecht, B, Scornavacca, C, Cenci, A, and Huson, DH (2011).
Fast computation of minimum hybridization networks
Bioinformatics.

Huson, DH and Scornavacca, C (2011).
A survey of combinatorial methods for phylogenetic networks
Genome Biology and Evolution, 3:23-35.

Huson, DH, Mitra, S, Weber, N, Ruscheweyh, H, and Schuster, SC (2011).
Integrative analysis of environmental sequences using MEGAN4
Genome Research, 21:1552-1560.

Klein, JD, Ossowski, S, Schneeberger, K, Weigel, D, and Huson, DH (2011).
LOCAS – A Low Coverage Assembly Tool for Resequencing Projects
PLoS ONE, 6(8):e23455.

Mitra, S, Rupek, P, Richter, DC, Urich, T, Gilbert, JA, Meyer, F, Wilke, A, and Huson, DH (2011).
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
BMC Bioinformatics, 12(Suppl 1):S21+ .

Schneeberger, K, Ossowski, S, Ott, F, Klein, JD, Wang, X, Lanz, C, Smith, LM, Cao, J, Fitz, J, Warthmann, N, Henz, S, Huson, D, and Weigel, D (2011).
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
. Proceedings of the National Academy of Sciences of the United States of America.

Scornavacca, C, Berry, V, and Ranwez, V (2011).
Building species trees from larger parts of phylogenomic databases
Information and Computation, 209(3):590-605.

Scornavacca, C, Zickmann, F, and Huson, D (2011).
Tanglegrams for rooted phylogenetic trees and networks
Bioinformatics, 27(13):i248-i256.

2010

Fischer, J and Huson, DH (2010).
New common ancestor problems in trees and directed acyclic graphs
Information Processing Letters.

Huson, D, Rupp, R, and Scornavacca, C (2010).
Phylogenetic Networks. Concepts, Algorithms and Applications
Cambridge University Press. (ISBN: 9780521755962).

Huson, DH and Mitra, S (2010).
Comparative metagenome analysis using MEGAN
In: Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, ed. by Frans de Bruijn. Wiley Blackwell Publishers, chap. , pp. .

Mitra, S, Gilbert, JA, Field, D, and Huson, DH (2010).
Comparison of multiple metagenomes using phylogenetic networks based on ecological indices
ISME Journal, 4:1236–1242.

Mitra, S, Schubach, M, and Huson, DH (2010).
Short clones or long clones? A simulation study on the use of paired reads in metagenomics
BMC Bioinformatics, 11(Suppl 1):S12+.

2009

Huson, DH (2009).
Drawing Rooted Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(1):103-109.

Huson, DH, Moulton, V, and Steel, MA (2009).
Special Section: Phylogenetics
IEEE/ACM Transactions in computational biology and bioinformatics , 6(1):4-6.

Huson, DH, Richter, D, Mitra, S, Auch, A, and Schuster, SC (2009).
Methods for comparative metagenomics
BMC Bioinformatics, 10(Suppl 1):S12+.

Huson, DH, Rupp, R, Berry, V, Gambette, P, and Paul, C (2009).
Computing galled networks from real data
Bioinformatics, 25(12):i85-93.

Miller, W, Drautz, DI, Janecka, JE, Lesk, AM, Ratan, A, Tomsho, LP, Packard, M, Zhang, Y, McClellan, LR, Qi, J, Zhao, F, Gilbert, MT, Dal\'en, L, Arsuaga, JL, Ericson, PG, Huson, DH, Helgen, KM, Murphy, WJ, Götherström, A, and Schuster, SC (2009).
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
Genome research, 19(2):213-220.

Mitra, S, Klar, B, and Huson, DH (2009).
Visual and statistical comparison of metagenomes
Bioinformatics, 25(15):1849–1855.

2008

Fenselau de Felippes, F, Schneeberger, K, Dezulian, T, Huson, DH, and Weigel, D (2008).
Evolution of Arabidopsis thaliana microRNAs from random sequences.
RNA (New York, N.Y.), 14(12):2455-2459.

Gambette, P and Huson, DH (2008).
Improved Layout of Phylogenetic Networks
IEEE/ACM Trans. Comput. Biology Bioinform., 5(3):472-479.

Huson, D and Rupp, R (2008).
Summarizing Multiple Gene Trees Using Cluster Networks
In: Proceedings of the Eighth International Workshop on Algorithms in Bioinformaticsy (WABI), vol. 5251, pp. 211–225. LNBI.

Klöpper, T and Huson, DH (2008).
Drawing explicit phylogenetic networks and their integration into SplitsTree
BMC Evolutionary Biology, 8:22.