Our view on organismal evolution is intimately connected to our understanding of how genomes and the encoded information change over time, and how this translates to the phenotypic and functional characteristics of contemporary species. The sequencing of entire genomes and transcriptomes from species covering all major groups in the tree of life has lifted the data basis for evolutionary research with a functional perspective to an unprecedented level. In its combination, this data facilitates access to the full repertoire of information stored in a species’ genome and allows unraveling individual cellular programs translating genetic information into a diverse set of functions. However, the effort connected to the experimental functional characterization of even considerably few proteins in the lab is still enormous. It is for this reason that exhaustive functional studies are limited to few and well established model organisms, many of which are of economical or medical relevance. More often only individual pathways are studied in niche model organisms featuring a particular trait of interest. However, for the vast majority of species only a draft genome assembly or transcript data is available without further experimental support. In these instances the in silico prediction of genes together with a subsequent tentative transfer of functional annotation from corresponding sequences in experimentally characterized model organisms provides the only source of functional information. Integrating all available information into a comprehensive picture of organismal and functional evolution is the common denominator of the individual projects in our group.
More specifically, we concentrate on the following main topics: Expand all...
1) Deep phylogenies and phylogenetic profiling
2) Functional annotation transfer
3) Phylostratigraphy and evolution of gene interaction networks
4) Source of genetic and functional innovation
5) Development of software and workflows for biological sequence analysis
Complementary to our evolutionary research activities we are developing, improving and benchmarking software and workflows for biological sequence analysis in a functional and evolutionary context. Main ongoing projects include (i) the targeted search for orthologs in large species sets (HaMStR; sourceforge.net/projects/hamstr), (ii) the use of feature architectures for similarity-based searches independent from amino acid sequence similarity (FACT http://www.biomedcentral.com/1471-2105/11/417), and (iii) the integration of the two concepts to develop a tool for a function-aware phylogenetic profiling of individual proteins. In addition we are currently investigating how to interpret phylogenetic profiles in an imperfect world where non-detection of a protein cannot be equated with its absence in a given species. To this end we build a simulation framework around the tool REvolver (www.ncbi.nlm.nih.gov/pubmed/22383532) to delineate the evolutionary distances beyond which homologous sequences are likely to have diverged to an extent that they no longer display a significant sequence similarity. If for two species and the corresponding proteins this distance is not exceeded non-detection can indeed be equated with absence.
Department for Applied Bioinformatics
Institute for Cell Biology and Neuroscience
Prof. Dr. Ingo Ebersberger
Max-von-Laue Str. 13
Phone +49 69 798 - 42112
Biologicum; Room 3.205
Phone +49 69 798-42110