Algorithms in Bioinformatics


A   A   A
Sections
Home > Publications

Skip to content. | Skip to navigation

Publications

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

2014

Flade, I, Holst, O, Ruscheweyh, HJ, Wittmann, A, and et al (2014).
Endotoxicity of Lipopolysaccharide as a Determinant of T-Cell-Mediated Colitis Induction in Mice
Gastroenterology, 146(3):765-775.

2013

Huson, DH and Chao Xie, D (2013).
A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA
Bioinformatics:doi: 10.1093/bioinformatics/btt254.

Lange, A, Beier, S, Huson, D, Henz, S, Hantke, K, Autenrieth, I, and Frick, J (2013).
Different survival strategies of gut commensal bacteria in IBD
International Journal for Medical Microbiology, 303:99.

Mitra, S and others (2013).
Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing
BMC Genomics, 14(Suppl 5):S16.

Steel, M, Linz, S, Huson, DH, and Michael J. Sanderson, D (2013).
Identifying a species tree subject to random lateral gene transfer
Journal of Theoretical Biology, 322:81-93.

2012

Huson, DH and Mitra, S (2012).
Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
In: Evolutionary Genomics: Statistical and Computational Methods, ed. by Maria Anisimova. Springer, chap. 17, pp. 415-429.

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.