Alexander Auch

Eberhard-Karls-Universität Tübingen

Biology, Computer Science

  • 38Impact points

  • 16Publications

  • 16Followers

Education

Languages:
German, English

Contact Details

Business:
Institution:
Eberhard-Karls-Universität Tübingen

Publications

  • A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA

    Authors: Markus Göker, Guido W Grimm, Alexander F Auch, Ralf Aurahs, Michal Kučera

    Evolutionary bioinformatics online. 01/2010; 6:97-112.

    Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to
  • Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

    Authors: Alexander F Auch, Mathias von Jan, Hans-Peter Klenk, Markus Göker

    Standards in genomic sciences. 01/2010; 2(1):117-34.

    The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity
  • Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

    Authors: Alexander F Auch, Hans-Peter Klenk, Markus Göker

    Standards in genomic sciences. 01/2010; 2(1):142-8.

    DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes
  • A clustering optimization strategy for molecular taxonomy applied to planktonic foraminifera SSU rDNA

    Authors: Michal, Auch

    Evolutionary Bioinformatics Online. 01/2010;

    Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to
  • Computational phylogenetics: Methods for analysing genome-scale data

    Authors: Alexander Auch

    Computational phylogenetics: Methods for analysing genome-scale data

    01/2010; Südwestdeutscher Verlag für Hochschulschriften.

    ISBN: 978-3838118628

  • Methods for comparative metagenomics

    Authors: Daniel H Huson, Daniel C Richter, Suparna Mitra, Alexander F Auch, Stephan C Schuster

    BMC bioinformatics. 02/2009; 10 Suppl 1:S12.

    BACKGROUND: Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in
  • Large-Scale Co-Phylogenetic Analysis on the Grid

    Authors: Alexandros, Auch

    International Journal of Grid and High Performance Computing. 01/2009; 1:39-54.

    Phylogenetic data analysis represents an extremely compute-intensive area of Bioinformatics and thus requires high-performance technologies. Another compute- and memory-intensive problem is that of
  • MetaSim: a sequencing simulator for genomics and metagenomics

    Authors: Daniel C Richter, Felix Ott, Alexander F Auch, Ramona Schmid, Daniel H Huson

    PLoS ONE. 02/2008; 3(10):e3373.

    BACKGROUND: The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a
  • COPYCAT: cophylogenetic analysis tool

    Authors: Jan P Meier-Kolthoff, Alexander F Auch, Daniel H Huson, Markus Göker

    Bioinformatics (Oxford, England). 05/2007; 23(7):898-900.

    We have developed the software CopyCat which provides an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the
  • MEGAN analysis of metagenomic data

    Authors: Daniel H Huson, Alexander F Auch, Ji Qi, Stephan C Schuster

    Genome research. 04/2007; 17(3):377-86.

    Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of
  • AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa

    Authors: Alexandros Stamatakis, Alexander F Auch, Jan Meier-Kolthoff, Markus Göker

    BMC bioinformatics. 02/2007; 8:405.

    BACKGROUND: Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic
  • Metagenome analysis using MEGAN

    Authors: Stephan C, Auch

    01/2007

  • Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

    Authors: Alexander F Auch, Stefan R Henz, Barbara R Holland, Markus Göker

    BMC bioinformatics. 02/2006; 7:350.

    BACKGROUND: Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently
  • Phylogenies from whole genomes: Methodological update within a distance-based framework

    Authors: Auch, Markus

    published via TOBIAS-lib, http://tobias-lib.uni-tuebingen.de/volltexte/2008/3417/. 01/2006;

    Methods which derive pairwise distances directly from complete sequenced genomes are a potentially important and efficient tool within the growing field of phylogenomics. We have shown in two
  • Whole-genome prokaryotic phylogeny

    Authors: Stefan R Henz, Daniel H Huson, Alexander F Auch, Kay Nieselt-Struwe, Stephan C Schuster

    Bioinformatics (Oxford, England). 06/2005; 21(10):2329-35.

    Current understanding of the phylogeny of prokaryotes is based on the comparison of the highly conserved small ssu-rRNA subunit and similar regions. Although such molecules have proved to be very
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Research Keywords

Computational Biology (Bioinformatics), Scientific Computing (Computational Science)