Daniel H Huson

Summary

Country: Germany

Publications

  1. ncbi request reprint A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome
    Richard J Mural
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 296:1661-71. 2002
  2. doi request reprint Introduction to the analysis of environmental sequences: metagenomics with MEGAN
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Tubingen, Germany
    Methods Mol Biol 856:415-29. 2012
  3. pmc MEGAN analysis of metagenomic data
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
    Genome Res 17:377-86. 2007
  4. ncbi request reprint Phylogenetic super-networks from partial trees
    Daniel H Huson
    Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
    IEEE/ACM Trans Comput Biol Bioinform 1:151-8. 2004
  5. doi request reprint Drawing rooted phylogenetic networks
    Daniel H Huson
    Tuebingen University, Tuebingen Sand 14, D 72076 Tuebingen, Germany
    IEEE/ACM Trans Comput Biol Bioinform 6:103-9. 2009
  6. ncbi request reprint Application of phylogenetic networks in evolutionary studies
    Daniel H Huson
    Center for Bioinformatics ZBIT, Tubingen University, Tubingen, Germany
    Mol Biol Evol 23:254-67. 2006
  7. ncbi request reprint Computing recombination networks from binary sequences
    Daniel H Huson
    Center for Bioinformatics, Tübingen University Sand 14, Tubingen, Germany
    Bioinformatics 21:ii159-65. 2005
  8. pmc Methods for comparative metagenomics
    Daniel H Huson
    Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
    BMC Bioinformatics 10:S12. 2009
  9. pmc Dendroscope: An interactive viewer for large phylogenetic trees
    Daniel H Huson
    Center for Bioinformatics Tübingen ZBIT, Eberhard Karls Universitat Tubingen, Sand 14, 72076 Tubingen, Germany
    BMC Bioinformatics 8:460. 2007
  10. ncbi request reprint Distances that perfectly mislead
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Tuebingen, Germany
    Syst Biol 53:327-32. 2004

Detail Information

Publications44

  1. ncbi request reprint A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome
    Richard J Mural
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 296:1661-71. 2002
    ....
  2. doi request reprint Introduction to the analysis of environmental sequences: metagenomics with MEGAN
    Daniel 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...
  3. pmc MEGAN analysis of metagenomic data
    Daniel 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...
  4. ncbi request reprint Phylogenetic super-networks from partial trees
    Daniel 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...
  5. doi request reprint Drawing rooted phylogenetic networks
    Daniel 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...
  6. ncbi request reprint Application of phylogenetic networks in evolutionary studies
    Daniel 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...
  7. ncbi request reprint Computing recombination networks from binary sequences
    Daniel H Huson
    Center for Bioinformatics, Tübingen University Sand 14, Tubingen, Germany
    Bioinformatics 21:ii159-65. 2005
    ....
  8. pmc Methods for comparative metagenomics
    Daniel 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...
  9. pmc Dendroscope: An interactive viewer for large phylogenetic trees
    Daniel 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...
  10. ncbi request reprint Distances that perfectly mislead
    Daniel 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...
  11. ncbi request reprint Phylogenetic trees based on gene content
    Daniel 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...
  12. pmc Computing galled networks from real data
    Daniel H Huson
    Center for Bioinformatics ZBIT, Tubingen University, Tubingen, Germany
    Bioinformatics 25:i85-93. 2009
    ....
  13. pmc Integrative analysis of environmental sequences using MEGAN4
    Daniel 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...
  14. pmc Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution
    Christian 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...
  15. ncbi request reprint Whole-genome prokaryotic phylogeny
    Stefan R Henz
    Center for Bioinformatics Tübingen ZBIT, Sand 14, Tubingen 72076, 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...
  16. pmc CrossLink: visualization and exploration of sequence relationships between (micro) RNAs
    Tobias Dezulian
    Department of Algorithms in Bioinformatics, Center for Bioinformatics Tubingen, Tubingen University, D 72076 Tubingen, 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...
  17. pmc Drawing explicit phylogenetic networks and their integration into SplitsTree
    Tobias 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...
  18. ncbi request reprint What if I don't have a tree? Split decomposition and related models
    Daniel 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...
  19. pmc Short clones or long clones? A simulation study on the use of paired reads in metagenomics
    Suparna 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...
  20. ncbi request reprint OSLay: optimal syntenic layout of unfinished assemblies
    Daniel C Richter
    Center for Bioinformatics ZBIT, Institute for Computer Science, Tubingen University, 72076 Tubingen, Germany
    Bioinformatics 23:1573-9. 2007
    ..The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure...
  21. ncbi request reprint COPYCAT: cophylogenetic analysis tool
    Jan P Meier-Kolthoff
    Center for Bioinformatics ZBIT, Sand 14, Tubingen, Germany
    Bioinformatics 23:898-900. 2007
    ..CopyCat offers various features, such as the creation of customized host-parasite association data and the computation of phylogenetic host/parasite trees based on the NCBI taxonomy...
  22. pmc LOCAS--a low coverage assembly tool for resequencing projects
    Juliane 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...
  23. pmc Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
    Suparna 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...
  24. pmc Evolution of Arabidopsis thaliana microRNAs from random sequences
    Felipe 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...
  25. pmc MetaSim: a sequencing simulator for genomics and metagenomics
    Daniel 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...
  26. ncbi request reprint Identification of plant microRNA homologs
    Tobias 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...
  27. doi request reprint Visual and statistical comparison of metagenomes
    Suparna 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...
  28. ncbi request reprint Comparative analysis of four Campylobacterales
    Mark Eppinger
    Max Planck Institute for Developmental Biology, Genome Centre, Spemannstr 35, 72076 Tubingen, Germany
    Nat Rev Microbiol 2:872-85. 2004
    ....
  29. pmc Tanglegrams for rooted phylogenetic trees and networks
    Celine 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...
  30. pmc Analysis of 16S rRNA environmental sequences using MEGAN
    Suparna 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...
  31. doi request reprint Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks
    Daniel H Huson
    Department of Computer Science, Center for Bioinformatics ZBIT, University of Tubingen, 72076 Tubingen, Germany
    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.]...
  32. doi request reprint Microbial community analysis using MEGAN
    Daniel H Huson
    Center for Bioinformatics, University of Tubingen, Tubingen, Germany Electronic address
    Methods Enzymol 531:465-85. 2013
    ..The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de. ..
  33. doi request reprint Fast computation of minimum hybridization networks
    Benjamin 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...
  34. doi request reprint Comparison of multiple metagenomes using phylogenetic networks based on ecological indices
    Suparna 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...
  35. ncbi request reprint Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
    Richard 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...
  36. pmc A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA
    Daniel H Huson
    Singapore Centre on Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Center for Bioinformatics, University of Tubingen, 72076 Tubingen, Germany and Life Sciences Institute, National University of Singapore, Singapore 117456
    Bioinformatics 30:38-9. 2014
    ....
  37. pmc 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...
  38. pmc A survey of combinatorial methods for phylogenetic networks
    Daniel 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...
  39. pmc Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin 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...
  40. ncbi request reprint VisRD--visual recombination detection
    Kristoffer Forslund
    The Linnaeus Centre for Bioinformatics, BMC, Box 598, Uppsala 751 24, Sweden
    Bioinformatics 20:3654-5. 2004
    ..VisRD, a program for visual recombination detection in a sequence alignment is presented. VisRD is written in Java and is designed to complement the multi-purpose phylogenetic software package SplitsTree4...
  41. ncbi request reprint Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA
    Hendrik 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...
  42. ncbi request reprint Constructing splits graphs
    Andreas 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...
  43. doi request reprint Improved layout of phylogenetic networks
    Philippe 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
    ....
  44. pmc Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome
    Tim 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...