Anne Kupczok

Research Interests

• Supertrees
• Distances between phylogenetic trees
• Phylogenetic congruence
• ...

Short Vita

Degree:

• 2010: 'Ph.D.' in Molecular Biology (Dr. rer. nat.), University of Vienna
  Thesis: Postprocessing Phylogenies: Tree Distances and Supertrees
• 2006: 'Diplom Bioinformatikerin', Friedrich-Schiller University Jena
  Thesis: Evolutionary genomics of the plant pathogenic bacteria Xanthomonas

Professional Experience:

• June 2010 - July 2010: Marie Curie Fellowship at the Renyi Institute of Mathematics of the Hungarian Academy of Sciences (project "Hungarian Bioinformatics")
• February 2010 - present: PostDoc at the Center for Integrative Bioinformatics Vienna (CIBIV)
• November 2006 - January 2010: PhD student at the Center for Integrative Bioinformatics Vienna (CIBIV)
• July 2006 - September 2006: Scholarship at the Max-Planck Instiute for Chemical Ecology, Jena
• January 2006 - July 2006: Diploma student at the Max-Planck Instiute for Chemical Ecology, Jena
• March 2003 - April 2005: Student assistant in the Biosystems analysis group, Jena

Publications

• A. Kupczok and A. von Haeseler (2009) Comment on: A congruency index for testing topological similarity between trees. Bioinformatics, 25, 147-149. (DOI: 10.1093/bioinformatics/btn539, PMID: 18922807)
• A. Kupczok, A. von Haeseler, and S. Klaere (2008) An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. J. Comput. Biol., 15, 577-591. (DOI: 10.1089/cmb.2008.0068, PMID: 18631022)
• A. Kupczok and P. Dittrich (2006) Determinants of Simulated RNA Evolution. J. Theor. Biol., 238, 726-735 (DOI: 10.1016/j.jtbi.2005.06.019, PMID: 16098538)

Talks

• Consequences of different null models on the tree shape bias of supertree methods.
  PhyloGroup 9, Hinxton, UK, 11.12.2009. (Programme pdf)
• Accuracy of phylogeny reconstruction methods combining overlapping gene data sets.
  Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2009), Iowa City, USA, 3.6.-7.6.2009. (Abstract)
• Comparison of commonly used methods for combining multiple phylogenetic data sets.
  Mathematics and Informatics in Evolution and Phylogeny, Hameau de l'Etoile, France, 10.6.-12.6.2008. (Slides)
• An exact algorithm for computing the geodesic distance between phylogenetic trees.
  Phylogenetics (PLG), Future Directions in Phylogenetic Methods and Models, Isaac Newton Institute for Mathematical Sciences, Cambridge, UK, 17.12-21.12.2007. (Slides and video)

Poster

• Consequences of different null models on the tree shape bias of supertree methods.
  Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2010), Lyon, France, 4.7.-8.7.2010. (Programme)
• Genome-wide identification of positively selected genes in plant-pathogenic bacteria.
  Otto Warburg International Summer School and Workshop 2006 on Evolutionary Genomics, Berlin, Germany, 29.8.-8.9.2006. (Programme)

Software

• GeoMeTree: Geodesic Metric on Trees
• mrc.py: Matrix Representation with Compatibility

Addresses

Postal Address:

Anne Kupczok - Last Change: 13.Jul.2010 .