What do we do?
At the Computational Evolutionary Genomics Group we are active in the fields of comparative genomics and shotgun metagenomics. We study molecular evolution, develop approaches to genomics data analyses, and implement computational pipelines. We apply evolutionary models to digest sequencing data, and revise these models using the novel data. We study functional genomic elements on the basis of sequence variability among different species and within populations. Our interests range from arthropod genomics, including invertebrate vectors of human pathogens, to the evolution of viruses and clinical microbiology.
In 2016, we completed the v9.1 update of our database of orthologs, OrthoDB, that provides evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial, and viral genes. Beyond further increase in the coverage of organisms and the depth of collected annotations, the hierarchical catalogue of orthologs now features a comparative chart generator, as well as online BUSCO analysis and OrthoDB mapping for user uploaded sequences.
The remarkable rate of adoption of our BUSCO tool for quantitative assessment of completeness of genome assemblies, gene sets, or transcriptomes (cited 162 times in one and a half years!) prompted us to release version 2 in 2016. The update includes significant expansion of the underlying data sets, now providing 44 clade-specific BUSCOs, and a major revision of the software implementing the procedure. The software is now distributed through GitLab. It is also available as an Ubuntu virtual machine, as well as integrated as an online service for the OrthoDB logged-in users.
In 2016 we have also finished the sequencing of several insects in our lab. The first manuscript, in print, is on the genomic features of the damselfly Calopteryx splendens, which represents a sister clade to most insect orders.
Main publications 2016
- Zdobnov EM et al. OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. Nucleic Acids Res. 2016 Nov 28; doi:10.1093/nar/gkw1119.
- Cordey S et al. Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection. Emerg Infect Dis. 2016 May;22(5):846-53. doi: 10.3201/eid2205.151807.
- Dousse A, Junier T, Zdobnov EM. CEGA--a catalog of conserved elements from genomic alignments. Nucleic Acids Res. 2016 Jan 4;44(D1):D96-100. doi: 10.1093/nar/gkv1163.