- State-of the art methodologies dictate new standards for phylogenetic analysis
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. ..
- TreeSnatcher plus: capturing phylogenetic trees from images
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...
- On the group theoretical background of assigning stepwise mutations onto phylogenies
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...
- 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...
- Gene expression profiling for molecular distinction and characterization of laser captured primary lung cancers
Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
J Transl Med 6:69. 2008
- Loss of matK RNA editing in seed plant chloroplasts
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...
- 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...
- HaMStR: profile hidden markov model based search for orthologs in ESTs
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...
- TonB-dependent transporters and their occurrence in cyanobacteria
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...
- FACT: functional annotation transfer between proteins with similar feature architectures
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...
- Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
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