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Publications

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

2008

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.

2007

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.

2006

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.
Science.

2005

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.

2004

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.

Huson, D and Steel, M (2004).
Distances that perfectly mislead
Syst. Biol(53):327–332.