Arndt von Haeseler

Summary

Affiliation: University of Vienna
Country: Austria

Publications

  1. pmc HvrBase++: a phylogenetic database for primate species
    Jochen Kohl
    Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
    Nucleic Acids Res 34:D700-4. 2006
  2. pmc State-of the art methodologies dictate new standards for phylogenetic analysis
    Maria Anisimova
    Department of Computer Science, Swiss Federal Institute of Technology ETH, Zurich 8092, Switzerland
    BMC Evol Biol 13:161. 2013
  3. pmc On the group theoretical background of assigning stepwise mutations onto phylogenies
    Mareike Fischer
    Department of Statistics and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
    Algorithms Mol Biol 7:36. 2012
  4. pmc Do we still need supertrees?
    Arndt von Haeseler
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna and Medical University Vienna, Dr, Bohr Gasse 9, 1030 Vienna, Austria
    BMC Biol 10:13. 2012
  5. pmc Loss of matK RNA editing in seed plant chloroplasts
    Michael Tillich
    Institut fur Biologie, Humboldt Universitat zu Berlin, Molekulare Genetik, Berlin D 10115, Germany
    BMC Evol Biol 9:201. 2009
  6. pmc TonB-dependent transporters and their occurrence in cyanobacteria
    Oliver Mirus
    JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max von Laue Str 9, 60438 Frankfurt, Germany
    BMC Biol 7:68. 2009
  7. ncbi request reprint Maximum-likelihood analysis using TREE-PUZZLE
    Heiko A Schmidt
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Vienna, Austria
    Curr Protoc Bioinformatics . 2007
  8. doi request reprint Taxon Selection under Split Diversity
    Bui Quang Minh
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr Bohr Gasse 9 6, 1030 Vienna, Austria
    Syst Biol 58:586-94. 2009
  9. pmc A consistent phylogenetic backbone for the fungi
    Ingo Ebersberger
    Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Vienna, Austria
    Mol Biol Evol 29:1319-34. 2012
  10. doi request reprint MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment
    Minh Anh Thi Nguyen
    Max F Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, Vienna, Austria
    Mol Biol Evol 28:143-52. 2011

Collaborators

Detail Information

Publications31

  1. pmc HvrBase++: a phylogenetic database for primate species
    Jochen Kohl
    Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
    Nucleic Acids Res 34:D700-4. 2006
    ..HvrBase++ is Oracle based and easily accessible by a web interface (http://www.hvrbase.org). As a new key feature, HvrBase++ provides an interactive graphical tool to easily access data from dynamically created geographical maps...
  2. pmc State-of the art methodologies dictate new standards for phylogenetic analysis
    Maria Anisimova
    Department of Computer Science, Swiss Federal Institute of Technology ETH, Zurich 8092, Switzerland
    BMC Evol Biol 13:161. 2013
    ..The rapid pace at which sequence data accumulate quickly outdates such publications. Although clearly, discoveries stemming from data mining, reports of new tools and databases and review papers are also desirable. ..
  3. pmc On the group theoretical background of assigning stepwise mutations onto phylogenies
    Mareike Fischer
    Department of Statistics and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
    Algorithms Mol Biol 7:36. 2012
    ..We illustrate this approach by looking at Abelian groups over twenty states and critically discuss their biological usefulness when investigating amino acids...
  4. pmc Do we still need supertrees?
    Arndt von Haeseler
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna and Medical University Vienna, Dr, Bohr Gasse 9, 1030 Vienna, Austria
    BMC Biol 10:13. 2012
    ..I discuss the principles of supertree methods and the competitor supermatrix approaches. I argue that both methods are important to infer phylogenetic relationships.See research article http://www.biomedcentral.com/1741-7007/10/12...
  5. pmc Loss of matK RNA editing in seed plant chloroplasts
    Michael Tillich
    Institut fur Biologie, Humboldt Universitat zu Berlin, Molekulare Genetik, Berlin D 10115, Germany
    BMC Evol Biol 9:201. 2009
    ..However, large-scale analyses of the evolution of individual editing sites have not yet been undertaken...
  6. pmc TonB-dependent transporters and their occurrence in cyanobacteria
    Oliver Mirus
    JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max von Laue Str 9, 60438 Frankfurt, Germany
    BMC Biol 7:68. 2009
    ..However, for cyanobacteria almost nothing is known about possible TonB-dependent uptake systems for iron or other substrates...
  7. ncbi request reprint Maximum-likelihood analysis using TREE-PUZZLE
    Heiko A Schmidt
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Vienna, Austria
    Curr Protoc Bioinformatics . 2007
    ..Basic Protocol 2 discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. Basic Protocol 3 explains how to compare tree topologies using different tests...
  8. doi request reprint Taxon Selection under Split Diversity
    Bui Quang Minh
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr Bohr Gasse 9 6, 1030 Vienna, Austria
    Syst Biol 58:586-94. 2009
    ..We illustrate our method using a case study of game birds ("Galliformes") and discuss the different choices of taxa based on our approach and PD...
  9. pmc A consistent phylogenetic backbone for the fungi
    Ingo Ebersberger
    Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Vienna, Austria
    Mol Biol Evol 29:1319-34. 2012
    ..A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses...
  10. doi request reprint MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment
    Minh Anh Thi Nguyen
    Max F Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, Vienna, Austria
    Mol Biol Evol 28:143-52. 2011
    ..We illustrate the method on several examples and then give a survey about the goodness of fit of the selected models to the alignments in the PANDIT database...
  11. pmc The impact of single substitutions on multiple sequence alignments
    Steffen Klaere
    Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University Vienna, Veterinary University Vienna, Max F Perutz Laboratories, Dr Bohrgasse 9, 1030 Wien, Austria
    Philos Trans R Soc Lond B Biol Sci 363:4041-7. 2008
    ..This matrix leads to analytical formulae for the posterior probability distribution of the number of substitutions for an alignment column...
  12. pmc Rooted triple consensus and anomalous gene trees
    Gregory B Ewing
    Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, Dr, Bohr Gasse 9, A 1030 Vienna, Austria
    BMC Evol Biol 8:118. 2008
    ..In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs...
  13. pmc ImOSM: intermittent evolution and robustness of phylogenetic methods
    Minh Anh Thi Nguyen
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Vienna, Austria
    Mol Biol Evol 29:663-73. 2012
    ..The outcome of the tests can help to actually gain confidence in the inferred trees. Therefore, we recommend using these tests in practical phylogenetic analyses...
  14. pmc The evolution of the ribosome biogenesis pathway from a yeast perspective
    Ingo Ebersberger
    Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt 60438, Germany, Center for Integrative Bioinformatics, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna 1030, Austria, Institute for Molecular Biosciences, Goethe University, Frankfurt 60438, Germany, Faculty of Computer Science, University of Vienna, Vienna 1030, Austria, Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt 60438, Germany, Department of Biochemistry I, Universitatsmedizin Gottingen, Gottingen 37073, Germany and Center of Membrane Proteomics, Goethe University, Frankfurt 60438, Germany
    Nucleic Acids Res 42:1509-23. 2014
    ..Within eukaryotes, RBF repertoires vary considerably. A comparison of yeast and human reveals that lineage-specific adaptation via RBF exclusion and addition characterizes the evolution of this ancient pathway. ..
  15. pmc Ultrafast approximation for phylogenetic bootstrap
    Bui Quang Minh
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
    Mol Biol Evol 30:1188-95. 2013
    ..This provides a more direct interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference...
  16. pmc HaMStR: profile hidden markov model based search for orthologs in ESTs
    Ingo Ebersberger
    Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, Vienna, Austria
    BMC Evol Biol 9:157. 2009
    ..Existing methods either depend on a known species tree or cannot cope with redundancy in EST data...
  17. ncbi request reprint Mapping human genetic ancestry
    Ingo Ebersberger
    Center for Integrative Bioinformatics of Vienna, Max F Perutz Laboratories, Vienna, Austria
    Mol Biol Evol 24:2266-76. 2007
    ....
  18. doi request reprint NextGenMap: fast and accurate read mapping in highly polymorphic genomes
    Fritz J Sedlazeck
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr Bohrgasse 9, A 1030 Vienna, Austria and Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria
    Bioinformatics 29:2790-1. 2013
    ..In addition, NextGenMap handles automatically any read data independent of read length and sequencing technology...
  19. ncbi request reprint TreeSnatcher: coding trees from images
    Thomas Laubach
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr Bohr Gasse 9 6, A 1030 Vienna, Austria
    Bioinformatics 23:3384-5. 2007
    ..AVAILABILITY: TreeSnatcher was developed in JAVA under Mac OS X and is executable on UNIX/Linux, Windows and Mac OS X systems. The application and its documentation can be freely downloaded from http://www.cibiv.at/software/treesnatcher...
  20. pmc Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets
    Fritz Joachim Sedlazeck
    Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, Dr Bohr Gasse 9, A 1030 Vienna, Austria
    Genomics 101:204-9. 2013
    ..The method can easily be applied to complete genome sequence data of sufficient coverage...
  21. pmc INVHOGEN: a database of homologous invertebrate genes
    Ingo Paulsen
    Department of Bioinformatics, Institute for Computer Sciences, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
    Nucleic Acids Res 34:D349-53. 2006
    ..Thus, INVHOGEN complements the well-known HOVERGEN database. The databank is available at http://www.bi.uni-duesseldorf.de/~invhogen/invhogen.html...
  22. pmc TreeSnatcher plus: capturing phylogenetic trees from images
    Thomas Laubach
    Department of Bioinformatics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf 40225, Germany
    BMC Bioinformatics 13:110. 2012
    ..However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research...
  23. ncbi request reprint The tetratricopeptide repeats of receptors involved in protein translocation across membranes
    Thomas Schlegel
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Veterinary University of Vienna, Austria
    Mol Biol Evol 24:2763-74. 2007
    ..Our findings are discussed in the context of the evolutionary development of translocation systems with focus on the occurrence of Hsp70/Hsp90-recognizing TPR domains in these machineries...
  24. doi request reprint An exact algorithm for the geodesic distance between phylogenetic trees
    Anne Kupczok
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Veterinary University of Vienna, Austria
    J Comput Biol 15:577-91. 2008
    ..The program GeoMeTree is a python implementation of the geodesic distance, and it is approximations and is available from www.cibiv.at/software/geometree...
  25. pmc FACT: functional annotation transfer between proteins with similar feature architectures
    Tina Koestler
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr Bohrgasse 9, A 1030 Vienna, Austria
    BMC Bioinformatics 11:417. 2010
    ..Finally, due to convergent evolution, functional equivalence is not necessarily linked to common ancestry. Therefore complementary approaches are required to identify functional equivalents...
  26. pmc Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
    Anne Kupczok
    Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Dr, Bohr Gasse 9, A 1030 Vienna, Austria
    Algorithms Mol Biol 5:37. 2010
    ..abstract:..
  27. doi request reprint Exploring the sampling universe of RNA-seq
    Stefanie Tauber
    Center for Integrative Bioinformatics, Max F Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
    Stat Appl Genet Mol Biol 12:175-88. 2013
    ....
  28. pmc NGC: lossless and lossy compression of aligned high-throughput sequencing data
    Niko Popitsch
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr Bohr Gasse 9, Vienna A 1030, Austria
    Nucleic Acids Res 41:e27. 2013
    ..By applying two popular variant and genotype prediction tools to the decompressed data, we could show that the lossy compression modes preserve >99% of all called variants while outperforming comparable methods in some configurations...
  29. pmc Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis
    Huy Q Dinh
    Max F Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna, Vienna, Austria
    PLoS ONE 7:e41528. 2012
    ..Thus, BiSS explores BS-Seq data more extensively and provides more information for downstream analysis...
  30. pmc Gene expression profiling for molecular distinction and characterization of laser captured primary lung cancers
    Astrid Rohrbeck
    Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
    J Transl Med 6:69. 2008
    ....
  31. ncbi request reprint Phylogenetic diversity within seconds
    Bui Quang Minh
    Center for Integrative Bioinformatics, Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Veterinary University of Vienna, Dr Bohr Gasse 9 6, A 1030, Vienna, Austria
    Syst Biol 55:769-73. 2006
    ..Both algorithms compute within seconds a subtree with maximal phylogenetic diversity for trees with 100,000 taxa or more...