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


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

Richter, DC, Ott, F, Auch, AF, Schmid, R, and Huson, DH (2008).
MetaSimA Sequencing Simulator for Genomics and Metagenomics
PLoS ONE, 3(10):e3373+.

Urich, T, Lanzén, A, Qi, J, Huson, DH, Schleper, C, and Schuster, SC (2008).
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome.
PloS one, 3(6):e2527+.

Whitfield, J, Cameron, S, Huson, D, and Steel, M (2008).
Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees
Systematic Biology, 57(6):939–947.


Clark, RM, Schweikert, G, Toomajian, C, Ossowski, S, Zeller, G, Shinn, P, Warthmann, N, Hu, TT, Fu, G, Hinds, DA, Chen, H, Frazer, KA, Huson, DH, Scholkopf, B, Nordborg, M, Ratsch, G, Ecker, JR, and Weigel, D (2007).
Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana
Science, 317(5836):338–342.

Huson, DH (2007).
Split Networks and Reticulate Networks
In: Reconstructing Evolution: new mathematical and computational advances, ed. by Gascuel, O. and Steel, M. A., pp. 247-276, Oxford University Press.

Huson, DH and Klöpper, TH (2007).
Beyond Galled Trees - Decomposition and Computation of Galled Networks.
In: Proceedings of the 11th International Conference on Research in Computational Molecular Biology (RECOMB), vol. 4453, pp. 211-225, Springer. Lecture Notes in Computer Science.

Huson, DH, Auch, A, Qi, J, and Schuster, SC (2007).
Metagenome analysis using MEGAN
In: Proceedings of the 5th Asia-Pacific Bioinformatics Conference, ed. by D. Sankoff, L. Wang and Chin, F., vol. 5, pp. 7-16, Imperial College Press.

Huson, DH, Auch, A, Qi, J, and Schuster, SC (2007).
MEGAN Analysis of Metagenomic Data
Genome Research, 17(3):377-386.

Huson, DH, Richter, DC, Rausch, C, Dezulian, T, Franz, M, and Rupp, R (2007).
Dendroscope: An interactive viewer for large phylogenetic trees
BMC Bioinformatics, 8(1):460.

Palatnik, JF, Wollmann, H, Schommer, C, Schwab, R, Boisbouvier, J, Rodriguez, R, Warthmann, N, Allen, E, Dezulian, T, Huson, D, Carrington, JC, and Weigel, D (2007).
Sequence and Expression Differences Underlie Functional Specialization of Arabidopsis MicroRNAs miR159 and miR319.
Dev Cell, 13(1):115–125.

Rausch, C, Hoof, I, Weber, T, Wohlleben, W, and Huson, DH (2007).
Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution
BMC Evolutionary Biology, 7:78+.

Reinert, K and Huson, D (2007).
Bioinformatics Support for Genome-Sequencing Projects
In: Bioinformatics- From Genomes to Therapies,, ed. by T. Lengauer, vol. 1, chap. 2, pp. 25–56, Wiley-VCH Verlag, Weinheim.

Richter, DC, Schuster, SC, and Huson, DH (2007).
OSLay: optimal syntenic layout of unfinished assemblies
Bioinformatics, 23(13):1573–1579.


Dezulian, T, Remmert, M, Palatnik, JF, Weigel, D, and Huson, DH (2006).
Identification of plant microRNA homologs
Bioinformatics, 22(3):359–360.

Dezulian, T, Schaefer, M, Wiese, R, Weigel, D, and Huson, DH (2006).
CrossLink: visualization and exploration of sequence relationships between (micro) RNAs.
Nucleic Acids Res, 34(Web Server issue).

Huson, DH and Bryant, D (2006).
Application of phylogenetic networks in evolutionary studies
Molecular Biology and Evolution, 23:254-267.

Huson, DH, Steel, MA, and Whitfield, J (2006).
Reducing Distortion in Phylogenetic Networks
In: Algorithms in Bioinformatics, ed. by Bücher, P. and Moret, B. M. E., vol. 4175, pp. 150-161, Springer. LNBI.

Poinar, HN, Schwarz, C, Qi, J, Shapiro, B, Macphee, RD, Buigues, B, Tikhonov, A, Huson, D, Tomsho, LP, Auch, A, Rampp, M, Miller, W, and Schuster, SC (2006).
Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA.


Henz, SR, Huson, DH, Auch, AF, Nieselt-Struwe, K, and Schuster, SC (2005).
Whole-genome prokaryotic phylogeny
Bioinformatics, 21(10):2329–2335.

Huson, DH and Klöpper, TH (2005).
Computing Recombination Networks from Binary Sequences
Bioinformatics, 21(suppl. 2):ii159-ii165.

Huson, DH, Kloepper, T, Lockhart, PJ, and Steel, MA (2005).
Reconstruction of Reticulate Networks from Gene Trees
In: Proceedings of the Ninth International Conference on Research in Computational Molecular Biology (RECOMB), vol. 3500, pp. 233-249, Springer. LNCS.

Rausch, C, Weber, T, Kohlbacher, O, Wohlleben, W, and Huson, DH (2005).
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs).
Nucleic Acids Res, 33(18):5799–5808.


Dress, AW and Huson, DH (2004).
Constructing Splits Graphs
IEEE/ACM Transactions in Computational Biology and Bioinformatics, 1(3):109-115.

Friedrichs, OD, Halpern, AL, Lippert, R, Rausch, C, Schuster, SC, and Huson, D (2004).
Syntenic Layout of Two Assemblies of Related Genomes
In: Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, Germany, October 4-6, 2004, ed. by Robert Giegerich and Jens Stoye, vol. 53, pp. 3–12, GI. LNI.