Research Topics
| Daniel H HusonSummaryCountry: Germany Publications
| Collaborators
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Detail Information
Publications
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genomeRichard J Mural
Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
Science 296:1661-71. 2002....
Introduction to the analysis of environmental sequences: metagenomics with MEGANDaniel H Huson
Center for Bioinformatics, Tubingen University, Tubingen, Germany
Methods Mol Biol 856:415-29. 2012..The discussion is conducted using a number of published marine datasets comprising metagenomic, metatranscriptomic, metaproteomic, and 16S rRNA data...
MEGAN analysis of metagenomic dataDaniel H Huson
Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
Genome Res 17:377-86. 2007..Also, simulations that evaluate the performance of the approach for different read lengths are presented...- Phylogenetic super-networks from partial treesDaniel H Huson
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
IEEE/ACM Trans Comput Biol Bioinform 1:151-8. 2004..The method is implemented as a plug-in for the program SplitsTree4... - Dendroscope: An interactive viewer for large phylogenetic treesDaniel H Huson
Center for Bioinformatics Tübingen ZBIT, Eberhard Karls Universitat Tubingen, Sand 14, 72076 Tubingen, Germany
BMC Bioinformatics 8:460. 2007..Moreover, many programs are difficult to install or are not available for all common operating systems... - Drawing rooted phylogenetic networksDaniel H Huson
Tuebingen University, Tuebingen Sand 14, D 72076 Tuebingen, Germany
IEEE/ACM Trans Comput Biol Bioinform 6:103-9. 2009..Implementations of the algorithms are available in new releases of the Dendroscope and SplitsTree programs... - Methods for comparative metagenomicsDaniel H Huson
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
BMC Bioinformatics 10:S12. 2009..Increasingly, there is a need for new ways of comparing multiple metagenomics datasets, and for fast and user-friendly implementations of such approaches... - Application of phylogenetic networks in evolutionary studiesDaniel H Huson
Center for Bioinformatics ZBIT, Tubingen University, Tubingen, Germany
Mol Biol Evol 23:254-67. 2006..Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees... - Computing recombination networks from binary sequencesDaniel H Huson
Center for Bioinformatics, Tübingen University Sand 14, Tubingen, Germany
Bioinformatics 21:ii159-65. 2005.... - Computing galled networks from real dataDaniel H Huson
Center for Bioinformatics ZBIT, Tubingen University, Tubingen, Germany
Bioinformatics 25:i85-93. 2009.... - Integrative analysis of environmental sequences using MEGAN4Daniel H Huson
Center for Bioinformatics, Tubingen University, Tubingen, Germany
Genome Res 21:1552-60. 2011..MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan... - Distances that perfectly misleadDaniel H Huson
Center for Bioinformatics, Tubingen University, Tuebingen, Germany
Syst Biol 53:327-32. 2004..We characterize precisely when uncorrected distances are additive on the true (and on a false) tree for four taxa. We also extend this result to a more general setting that applies to distances corrected according to an incorrect model... - Phylogenetic trees based on gene contentDaniel H Huson
Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
Bioinformatics 20:2044-9. 2004..Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad hoc distance method. AVAILABILITY: http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html.. 
Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolutionChristian Rausch
Center for Bioinformatics Tübingen ZBIT, Eberhard Karls Universitat Tubingen, Sand 14, Tubingen, Germany
BMC Evol Biol 7:78. 2007..The homologous Epimerization (E) domain flips the chirality of the last amino acid in the growing peptide; Dual E/C domains catalyze both epimerization and condensation...- Whole-genome prokaryotic phylogenyStefan R Henz
, Sand 14, , Germany
Bioinformatics 21:2329-35. 2005..In this approach, first Blast is used to compare genomes, then a distance matrix is computed, and finally a tree- or network-reconstruction method such as UPGMA, Neighbor-Joining, BioNJ or Neighbor-Net is applied... - Drawing explicit phylogenetic networks and their integration into SplitsTreeTobias H Kloepper
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
BMC Evol Biol 8:22. 2008..It contains a wide variety of methods for the import/export, calculation and visualization of phylogenetic information. The software is developed in Java and implements a command line tool as well as a graphical user interface... - What if I don't have a tree? Split decomposition and related modelsDaniel H Huson
Center for Bioinformatics Tubingen, Tubingen University, Tubingen, Germany
Curr Protoc Bioinformatics . 2003..It also implements a number of distance transformations, the computation of parsimony splits, spectral analysis and bootstrapping... - Short clones or long clones? A simulation study on the use of paired reads in metagenomicsSuparna Mitra
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
BMC Bioinformatics 11:S12. 2010..However, now that reads of length 75 bp can be sequenced in pairs, Illumina sequencing has become a viable option for metagenome studies... - COPYCAT: cophylogenetic analysis toolJan P Meier Kolthoff
Center for Bioinformatics ZBIT, Sand 14, Tubingen, Germany
Bioinformatics 23:898-900. 2007..informatik.uni-tuebingen.de/software/copycat. SUPPLEMENTARY INFORMATION: Results of the real-world example can be found at http://www-ab.informatik.uni-tuebingen.de/software/copycat or Bioinformatics online... - OSLay: optimal syntenic layout of unfinished assembliesDaniel C Richter
Center for Bioinformatics ZBIT, Institute for Computer Science, Tubingen University, 72076 Tubingen, Germany
Bioinformatics 23:1573-9. 2007..Related genome sequences can be used to layout contigs in an assembly. AVAILABILITY: OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay... - LOCAS--a low coverage assembly tool for resequencing projectsJuliane D Klein
University of Tubingen, Tubingen, Germany
PLoS ONE 6:e23455. 2011..However, computational methods capable of discovering other variations such as novel insertions or highly diverged sequence from low coverage NGS data are still lacking... - Functional analysis of metagenomes and metatranscriptomes using SEED and KEGGSuparna Mitra
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
BMC Bioinformatics 12:S21. 2011..The program has subsequently been extended to support comparative analyses of multiple datasets... - Identification of plant microRNA homologsTobias Dezulian
Center for Bioinformatics Tubingen, Tubingen University, Germany
Bioinformatics 22:359-60. 2006..The approach is based on a sequence similarity search step followed by a set of structural filters... - Visual and statistical comparison of metagenomesSuparna Mitra
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
Bioinformatics 25:1849-55. 2009..One major challenge is how to compare multiple datasets. Furthermore, there is a need for bioinformatics tools that can process many large datasets and are easy to use... - Evolution of Arabidopsis thaliana microRNAs from random sequencesFelipe Fenselau de Felippes
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
RNA 14:2455-9. 2008..Subsequent stabilization through coevolution with initially fortuitous targets may lead to fixation of a small subset of these proto-miRNA genes... - MetaSim: a sequencing simulator for genomics and metagenomicsDaniel C Richter
ZBIT Center for Bioinformatics Tübingen, University of Tubingen, Tubingen, Germany
PLoS ONE 3:e3373. 2008..There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets... - Tanglegrams for rooted phylogenetic trees and networksCeline Scornavacca
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
Bioinformatics 27:i248-56. 2011..Thus, the question arises how to define and compute a tanglegram for such networks... - CrossLink: visualization and exploration of sequence relationships between (micro) RNAsTobias Dezulian
Department of Algorithms in Bioinformatics, , , , Germany
Nucleic Acids Res 34:W400-4. 2006..CrossLink is available both online and as a standalone version at http://www-ab.informatik.uni-tuebingen.de/software... - Analysis of 16S rRNA environmental sequences using MEGANSuparna Mitra
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
BMC Genomics 12:S17. 2011..Several tools or packages have been developed for analyzing communities using 16S rRNA sequences. Similarly, a number of tools exist for analyzing randomly sequenced DNA reads... - Fast computation of minimum hybridization networksBenjamin Albrecht
Department of Computer Science, Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
Bioinformatics 28:191-7. 2012..One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events... - Comparison of multiple metagenomes using phylogenetic networks based on ecological indicesSuparna Mitra
Center for Bioinformatics ZBIT, Tubingen University, Tubingen, Germany
ISME J 4:1236-42. 2010..Importantly, the networks provide the both visual definition and metric quantification for the non-rooted relationship between samples, combining the desirable characteristics of other tools into one... - Common sequence polymorphisms shaping genetic diversity in Arabidopsis thalianaRichard M Clark
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
Science 317:338-42. 2007..Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana... - Comparative analysis of four CampylobacteralesMark Eppinger
Max-Planck-Institute for Developmental Biology, Genome Centre, Spemannstr. 35, , Germany
Nat Rev Microbiol 2:872-85. 2004.... - Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)Christian Rausch
Center for Bioinformatics Tübingen ZBIT, University of Tubingen, Germany
Nucleic Acids Res 33:5799-808. 2005..None of the predictive methods could infer any specificity for 2.4% of the sequences, suggesting completely new types of specificity... - Dendroscope 3: an interactive tool for rooted phylogenetic trees and networksDaniel H Huson
Department of Computer Science, Center for Bioinformatics ZBIT, University of Tubingen, 72076 Tubingen, Germany and Institut des Sciences de l Evolution Montpellier ISEM, CNRS UMR 5554, Universite Montpellier II, 34095 Montpellier, France
Syst Biol 61:1061-7. 2012..The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.]... - A survey of combinatorial methods for phylogenetic networksDaniel H Huson
Department of Computer Science, Center for Bioinformatics, Tubingen University, Tubingen, Germany
Genome Biol Evol 3:23-35. 2011..In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation... - Whole-genome shotgun assembly and comparison of human genome assembliesSorin Istrail
Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 101:1916-21. 2004..The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats... - VisRD--visual recombination detectionKristoffer Forslund
The Linnaeus Centre for Bioinformatics, BMC, Box 598, Uppsala 751 24, Sweden
Bioinformatics 20:3654-5. 2004..VisRD is written in Java and is designed to complement the multi-purpose phylogenetic software package SplitsTree4. AVAILABILITY: The software is freely available from http://www.lcb.uu.se/~vmoulton/software/visrd/.. - Constructing splits graphsAndreas W M Dress
Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
IEEE/ACM Trans Comput Biol Bioinform 1:109-15. 2004..This paper addresses the problem of computing a splits graph for a given set of splits. We have implemented all presented algorithms in a new program called SplitsTree4... - Metagenomics to paleogenomics: large-scale sequencing of mammoth DNAHendrik N Poinar
McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada
Science 311:392-4. 2006..The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics... - Improved layout of phylogenetic networksPhilippe Gambette
Departement Informatique, Ecole Normale Superieure de Cachan, 61 Avenue du President Wilson, 94235 Cachan Cedex, France
IEEE/ACM Trans Comput Biol Bioinform 5:472-9. 2008.... - Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptomeTim Urich
Centre of Geobiology, Department of Biology, University of Bergen, Bergen, Norway
PLoS ONE 3:e2527. 2008..Experimental approaches studying these systems usually focus on either the soil community's taxonomic structure or its functional characteristics. Many methods target DNA as marker molecule and use PCR for amplification...