The research I’m doing is in bioinformatics. These days I primarily work on evolutionary genomics. Previously I did work on phylogenetics and association mapping.
Evolutionary genomics involves full genome analysis for phylogenetics, comparative genomics or population genetics at the full genome level (population genomics). Of these, population genomics is my main interest.
I have worked extensively on ape genomics and was part of the International Orang-Utan Genome Analysis Consortium, the International Gorilla Genome Analysis Consortium and the International Bonobo Genome Analysis Consortium. Combining phylogenetic inference with population genetics, I was part of the Great Ape Genome Diversity Project where we sequenced full genomes of 79 individuals from all great ape species and most sub-species to characterise the genetic variation in great apes and to understand the evolution of this variation over the history of the great apes.
My main work in this field involves so-called Coalescent Hidden Markov Models.
Phylogenetics is concerned with inferring and comparing evolutionary trees. In this area I’m mainly working on algorithmical problems, funded by the SNF project Faster programs for reconstructing evolution.
I’ve also developed some software for inferring trees:
- QuickJoin: Fast neighbour-joining tree construction.
- RapidNJ: Even faster neighbour-joining tree construction. Here I only
helped out a little while the real work was done by Martin Simonsen.
- CoAnnealing: A tool for inferring local phylogenies.
and for comparing trees
- SplitDist: Computation of the split distance between trees.
- QDist: Computation of the quartet distance between trees.
Association mapping is concerned with locating disease genes (or in general genes affecting a given phenotype) from genotype data. In my research I now mainly focus on genome-wide association studies, where the entire genome is scanned for disease association. My research is funded by the FNU and FTP project Tools for genome-wide and fine-scale association mapping and the EU funded project PolyGene.
My group and I have developed the following software packages for fine-scale mapping:
- GeneRecon: MCMC based fine-scale association mapping.
- HapCluster++: A C++ implementation of the HapCluster method.
and genome-wide mapping:
- SNPFile: File format for SNP marker data.
- SMA: Single marker association tests.
- Blossoc: Block-association mapping.
plus the simulation tool: