Phylogenomics and phylotranscriptomics of eukaryotes
We are using PhyloFisher, a phylogenomic package for analyses of hundreds of protein-coding genes, to resolve phylogenetic relationships of selected eukaryotic lineages. Phylofisher is software that was developed in Matthew Brown laboratory at Mississippi State University during the postdoctoral stay of Tomáš Pánek. To download Phylofisher, go to its github page. Video presentation of this software from Matthew Brown is here. If you are using Phylofisher during your research, please cite Phylofisher paper.
Novel lineages of anaerobic protists
We combine classical culture-based approaches with Electron Microscopy, transcriptomics and genomics to discover and characterize novel deep-branching lineages of microbial eukaryotes living in anoxic or microoxic environments. We were involved in studies that discovered and characterized many novel species and genera, but also families or even classes. You can read here, here or here for the most recent examples.
Evolution of organelles and metabolic pathways
We use our expertise in eukaryotic diversity, phylogenetics, genomics, and transcriptomics to reveal evolution of organelles and metabolic pathways of eukaryotic cell. You can read one very interesting example here.