Research Topics

Polar Pelagic Organisms

Krill

We are collaborating with the Alfred Wegener Institute and the Carl Von Ossietzky University Oldenburg to create and annotate de novo transcriptome assemblies of krill species.

Transcriptome analysis can be considered a key step for interpreting how organisms respond to environmental changes and understanding the functional products of their genome in different conditions or developmental stages. As RNA‑seq allows detecting novel transcripts without additional genomic information, it represents an important and crucial step whenever we want to assess the funtional genomics of non‑model organisms, i.e. organisms for which there is no prior genetic and molecular information.

We are currently focusing on the comparison of gene expression levels across developmental stages and varying environmental conditions, performing a comparative and physiological study. These results are being collected in order to develop a multi‑krill database, upgrading and extending KrillDB (website, paper).

Visualization of Biological Networks

Biological Network

Understanding complicated networks of biomolecular entities and interactions is essential to solving contemporary problems in biology, especially in computational domains such as Systems Biology. Complexity arises due to the sheer size of networks and to the multitude of entities being represented, that range from individual reactions to entire pathways. It is becoming increasingly difficult to interpret the information encoded in networks and to cross‑link their contents across different data sources.

We are exploring dynamic layout algorithms to reduce the clutter present in contemporary visualization formats. We apply graph compression techniques to condense large graphs into a reduced set of visual symbols. The user is then able to selectively increase the level‑of‑detail of the representation around specific areas, following the needs of his analysis.

A fundamental aspect of this work involves the accessibility of the software we build. We decided to rely on web technologies and standards; our viewer is designed to be embeddable in any webpage. As a showcase of its features, we are extending the GraphiteWeb analysis service (website, paper) with new graphical capabilities.